Human Molecular Genetics, 2015, Vol. 24, No. 9
2442–2457
doi: 10.1093/hmg/ddv006
Advance Access Publication Date: 8 January 2015
Original Article
ORIGINAL ARTICLE
Htt CAG repeat expansion confers pleiotropic gains of
mutant huntingtin function in chromatin regulation
1
Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA, 2Department of
Neurology, Harvard Medical School, Boston, MA 02114, USA, 3Center for Biomedical Informatics, Boston, MA
02114, USA, 4University of Alabama in Huntsville, Huntsville, AL 35805, USA, 5RaNA Therapeutics, 790 Memorial
Drive, Cambridge, MA 02139, USA, 6Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 7Department
of Genetics, Harvard Medical School, Boston, MA 02115, USA and 8Division of Genetics, Brigham and Women’s
Hospital, Boston, MA 02115, USA
*To whom correspondence should be addressed. Tel: +1 6176439851; Fax: +1 6176433202; Email: iseong@mgh.harvard.edu
Abstract
The CAG repeat expansion in the Huntington’s disease gene HTT extends a polyglutamine tract in mutant huntingtin that
enhances its ability to facilitate polycomb repressive complex 2 (PRC2). To gain insight into this dominant gain of function, we
mapped histone modifications genome-wide across an isogenic panel of mouse embryonic stem cell (ESC) and neuronal
progenitor cell (NPC) lines, comparing the effects of Htt null and different size Htt CAG mutations. We found that Htt is required
in ESC for the proper deposition of histone H3K27me3 at a subset of ‘bivalent’ loci but in NPC it is needed at ‘bivalent’ loci for both
the proper maintenance and the appropriate removal of this mark. In contrast, Htt CAG size, though changing histone
H3K27me3, is prominently associated with altered histone H3K4me3 at ‘active’ loci. The sets of ESC and NPC genes with altered
histone marks delineated by the lack of huntingtin or the presence of mutant huntingtin, though distinct, are enriched in
similar pathways with apoptosis specifically highlighted for the CAG mutation. Thus, the manner by which huntingtin function
facilitates PRC2 may afford mutant huntingtin with multiple opportunities to impinge upon the broader machinery that
orchestrates developmentally appropriate chromatin status.
Introduction
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder characterized by the prominent loss of
medium size spiny neurons in the caudate and putamen (1,2).
Discovery of the HD mutation revealed an unstable expanded
CAG trinucleotide repeat, of more than ∼35 units, in exon 1 of
HTT ( previously HD) (3). The mutation triggers a truly dominant
disease process that leads to the onset of diagnostic motor
signs in a manner that is inversely correlated with the size of
only the expanded HTT CAG repeat (4), although both the mutant
and normal range repeat HTT alleles are expressed from conception (5–8).
†
The authors wish it to be known that, in their opinion, the first two authors Marta Biagioli and Francesco Ferrari should be regarded as joint First Authors.
Received: November 3, 2014. Revised and Accepted: January 6, 2015
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Marta Biagioli1,2,†, Francesco Ferrari3,†, Eric M. Mendenhall4, Yijing Zhang1,
Serkan Erdin1, Ravi Vijayvargia1,2, Sonia M. Vallabh1, Nicole Solomos1,
Poornima Manavalan1, Ashok Ragavendran1, Fatih Ozsolak5, Jong Min Lee1,2,
Michael E. Talkowski1,6, James F. Gusella1,6,7, Marcy E. Macdonald1,2,7,
Peter J. Park3,8 and Ihn Sik Seong1,2, *
Human Molecular Genetics, 2015, Vol. 24, No. 9
polyglutamine tract, we have mapped histone modifications
genome-wide across all of the members of the isogenic Htt null
and Htt CAG repeat knock-in ESC series and lineage committed
NPC derived from them.
Results
Lack of huntingtin or presence of mutant huntingtin do
not alter PRC2 expression
Our Htt mutation ESC panel is composed of six pluripotent cell
lines (or their derivative cell types) that were created to be analyzed together as a series of isogenic samples that enable the
discovery and direct comparison of the effects of targeted inactivation of both copies of Htt (Htt null cells, dKO) with the more
subtle effects of targeted mutations that progressively expand a
CAG stretch in one allele (Htt CAG knock-in cells) (23). The
panel comprises the parental ESC line with wild-type Htt alleles,
expressing only wild-type huntingtin, the Htt null double knockout Hdh ex4/5/ex4/5 ESC line, which lacks huntingtin, and a set of
four heterozygous Htt CAG repeat knock-in Hdh Q20/7, Hdh Q50/7,
Hdh Q91/7 and Hdh Q111/7 ESC lines, that express both wild-type
huntingtin and mutant huntingtin with expanded polyglutamine
tracts of 20, 50, 91 and 111 residues, respectively (Fig. 2C) (23).
The distinctly altered fates of Htt null and Htt CAG knock-in
neuronal cells do not reflect overt differences at the pluripotent
stem cell or neuronal lineage committed progenitor cell stage.
All six members of the panel exhibit appropriate stage-specific
morphology (Fig. 1A–C) and expression of canonical markers,
such as alkaline phosphatase, Oct-4 and Nanog in ESC (Fig. 1B,
D and F) and Pax6 and Nestin in retinoic acid-induced NPC
(Fig. 1C, E and G). Thus, neither the lack of huntingtin nor the
presence of mutant huntingtin dramatically compromises either
pluripotency or the induced transition to NPC. The specific Htt
genotype also does not obviously alter the expression of Eed,
Ezh2, Suz12 and Rbbp4 or of genes encoding the PRC2-associated
factors (Phf1, Mtf2, Jarid2, Aebp2 and Phf19) and non-canonical
H3K27 methyltransferase (Ezh1). The steady-state mRNA levels
for these genes are not distinguished by Htt genotype at either developmental stage (Fig. 2A, B, E and F) and immunoblot analysis
disclosed similar levels of Ezh2 and Suz12 in wild-type, Htt-null
and Htt CAG knock-in cells (Fig. 2C and D). Since inactivation of
a core member can destabilize and decrease levels of the complex
(30,31), these results imply that the stability of PRC2 is not greatly
altered by the absence of huntingtin or by the presence of mutant
huntingtin.
Genome-wide ChIP-seq and RNA-seq across the
members of the ESC and NPC series
These findings are consistent with the proposed role for huntingtin as a PRC2-facilitator rather than a core member of the
complex (14,32). Therefore, reasoning that the molecular consequences of the absence of huntingtin and the potentially milder
effects of mutant huntingtin on PRC2 function would become
evident from unbiased genome-wide chromatin mapping, we
performed histone H3K27me3, H3K4me3 and H3K36me3 ChIPseq and RNA-seq analyses across the members of the isogenic
Htt ESC and NPC series (Supplementary Material, Table S1). To
gauge the quality of the biological replicates formed by the six
ESC datasets and six NPC datasets, we performed extensive QC
analyses, which demonstrate a high degree of similarity both
across the Htt genotypes for each stage and with previously reported datasets (see Materials and Methods and Supplementary
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The key features of the HD mutation (true dominance and
progressivity with CAG size of the expanded repeat) provide genetic criteria with which to delineate the mutational mechanism
and its earliest consequences. Furthermore, the occurrence of
polyglutamine-encoding CAG-expansion mutations in unrelated
genes that cause eight different inherited neurodegenerative disorders strongly implies a disease mechanism whose specificity
entails an effect of the expanded polyglutamine tract on the
existing function of the protein in which it is embedded (9–11).
Therefore, although other scenarios are possible, the most
parsimonious explanation of the genetic findings is that its
expanded polyglutamine tract endows full-length mutant huntingtin with some novel property that is related to the protein’s
normal function as a HEAT/HEAT-like domain α-helical scaffold
molecule (12–14).
To provide a genetic framework for focused biochemical and
molecular studies, we and others have created precisely targeted
mutations in the mouse HD gene homolog Htt ( previously Hdh).
Phenotypes associated with inactivating Htt mutations disclose
inherent normal huntingtin functions (15–18), whereas phenotypes that worsen with the size of expanded Htt CAG alleles,
which precisely replicate the HD mutation, reveal dominant effects of full-length mutant huntingtin that fulfill the HD genetic
criteria (18–25). Studies with these mutant Htt alleles have revealed that huntingtin function is required for proper embryonic
development and have established that Htt CAG-expansion
alleles can bypass blocks early in embryonic (15–17) and fetal (18)
development imposed by huntingtin deficiency, thereby arguing
against loss of function (simple or dominant-negative) mechanisms for the HD mutation. In support of a simple gain of existing
function, extending its polyglutamine tract enhances huntingtin’s function as a facilitator for the chromatin regulator polycomb repressive complex 2 (PRC2) (14), comprising Eed (Extra sex
combs—Esc) (26), Suz12 (Suppressor of Zeste 12—Su(z)12), Ezh2
(Enhancer of Zeste E(z) (27) and RbAp48/Caf1/Nurf55. Full-length
wild-type huntingtin protein is able to physically interact with
Ezh2 and Suz12 PRC2 core component in the nucleus of embryoid
bodies (EBs) and in vitro, suggesting its function as a PRC2 facilitator is, at least in part, mediated by this interaction (14). EBs developing from embryonic stem cells (ESCs) that lack huntingtin
exhibit inefficient deposition of the histone H3K27me3 mark,
whereas EBs with Htt CAG-expansion display mildly increased
histone H3K27me3 (14). Moreover, purified full-length human
huntingtin stimulates, progressively with its polyglutamine
tract size, the histone H3K27me3 catalytic activity of reconstituted PRC2 (14).
Using an approach that compares the members of an isogenic
Htt knock-out and Htt CAG knock-in mutant ESC panel (23), it has
been shown recently that full-length mutant huntingtin subtly
alters the developmental fate of lineage committed neuronal
progenitor cells (NPC) in a qualitatively different manner than
does lack of huntingtin. One study demonstrates that neurons
derived from CAG-expanded NPC have an increased propensity
to undergo apoptosis, whereas NPC that lack huntingtin tend to
give rise to glial cells in a slightly, but significantly higher proportion than wild-type Htt NPC (28). Another study finds that CAG
knock-in NPC have unaltered multi-lineage potential, but premature neuronal differentiation, whereas Htt null NPC exhibit increased cell death and altered lineage potential (29). Based
upon these observations, we hypothesized distinctly altered
molecular states for huntingtin-null and mutant huntingtin
expressing cells at earlier developmental stages. To delineate
these states, while gaining molecular insights into huntingtin’’s
facilitation of PRC2 activity and the effects of extending its
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Figure 1. Members of the isogenic Htt null and Htt CAG-expansion ESC and NPC panels exhibit similar stage-appropriate morphological and molecular characteristics. (A)
Schematic representation of the protocol by which mouse embryonic stem cells (ESC) develop into neuronal progenitor cells (NPC) through EBs and timed addition of
retinoic acid (RA). (B and C) Phase contrast micrographs of wild-type (WT), Htt null Hdh ex4/5/ex4/5 (dKO) and heterozygous Htt CAG knock-in Hdh Q20/7, Hdh Q50/7 Hdh Q91/7
and Hdh Q111/7 (CAG 18/+, 48/+, 89/+, 109/+) ESC lines showing colonies stained for alkaline phosphatase and the NPC lines derived from them displaying appropriate
morphology with neurite extensions. (D and E) Images of cells, with DAPI stained nuclei to show proper Oct-4 expression in Htt wild-type, Htt null and Htt CAG knockin ESC colonies and appropriate expression of Pax6 and Nestin neuroectodermal markers in the NPC for each genotype. (F and G) Bar graphs plot relative normalized mRNA
expression levels of pluripotency marker genes Pou5f1 and Nanog encoding Oct-4 and Nanog and neuroectodermal marker genes Pax6 and Nes encoding Pax6 and Nestin as
determined by RT-qPCR amplification assays. Error bars represent standard deviations from the mean of two biological and two technical replicates.
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Figure 2. PRC2 core and accessory factors are similar in across the Htt allelic series. (A and B) Bar graphs plotting normalized relative mRNA levels of genes encoding PRC2
core subunits (Ezh2, Suz12, Eed and Rbbp4/RbAp48) determined by RT-qPCR amplification assays for wild-type (WT) and Htt null (dKO) ESC and NPC lines and (B) for the
heterozygous Htt CAG knock-in HdhQ20/7, HdhQ50/7, HdhQ91/7, HdhQ111/7 (CAG 18/+, 48/+, 89/+ 109/+) ESC and NPC lines. (C) Immunoblot analyses of wild-type (WT)
and Htt null (dKO) and HdhQ20/7, HdhQ50/7, HdhQ91/7, HdhQ111/7 (CAG 18/+, 48/+, 89/+ 109/+) ESC and NPC lines. The band of normal mouse huntingtin (7 glutamine
tract) is absent in Htt null cells and across the CAG knock-in series the normal mouse huntingtin band and the more slowly migrating mutant huntingtin bands are
progressively separated with increasing size of the latter’s polyglutamine tract (comprising 20, 50, 91 and 111 glutamines, respectively). The bands of Ezh2 and Suz12
and β-actin (Actb) are detected in all of the lines. (D) Quantification of Esh2 and Suz12 immunoreactive bands relative to β-actin using ImageJ software. The mean
values determined in two independent biological replicates are plotted. Error bars represent the standard deviations from the mean. (E and F) Bar graphs plotting
normalized relative mRNA levels of genes encoding PRC2-associated factors (Phf1, Mtf2, Ezh1, Aebp2, Phf19, Jarid2) determined by RT-qPCR amplification assays for
wild-type (WT) and Htt null (dKO) ESC and NPC lines and (F) for the heterozygous Htt CAG knock-in HdhQ20/7, HdhQ50/7, HdhQ91/7, HdhQ111/7 (CAG 18/+, 48/+, 89/+
109/+) ESC and NPC lines. Error bars represent standard deviations from the mean for two biological replicates and two technical replicates.
Material, Figs S1A, B and S2A, B). As an example, during the transition of ESC to NPC the Hoxb cluster is expected to show loss
of histone H3K27me3 and increases of histone H3K4me3 at
transcriptional start site (TSS) and histone H3K36me3 over the
gene body with increasing RNA expression (33). All six Htt genotypes display comparable, stage-appropriate histone H3K27me3,
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H3K4me3 and H3K36me3 marks and RNA profiles across this
dynamically regulated gene cluster (Fig. 3).
Htt null mutation but not Htt CAG expansion
predominantly affects histone H3K27me3
We then performed comparative quantitative analysis of the
chromatin marks at the TSSs of genes genome-wide to determine
the global consequences of the absence of huntingtin, by
comparing wild-type versus Htt null cells, and of lengthening
mutant huntingtin’s polyglutamine tract by examining the four
Htt CAG knock-in cell lines. The number of TSS enriched over
input control for histone H3K4me3 and the number of genes
with histone H3K36me3 over the gene body is not greatly affected
by the Htt null genotype or by the Htt CAG-expansion alleles at
either the ESC or the NPC developmental stages (Supplementary
Material, Fig. S2C and D). However, using the most stringent
threshold (Threshold 4) (see Materials and Methods), and as
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Figure 3. Hoxb cluster illustrating genome-wide ChIP-seq and RNA-seq analyses. A snapshot of the IGV (http://broadinstitute.org) genome browser view at the location of
the developmentally regulated Hoxb cluster (mouse chromosome 11qD) shows the ChIP-seq library-size normalized reads density (see Materials and Methods) for histone
H3K27me3, histone H3K4me3 and histone H3K36me3 across the Htt wild-type, Htt null and the four Htt CAG knock-in ESC lines and for the NPC derived from them. Also
shown are the RNA-seq reads density with the + strand (P) and – strand (N) indicated. Library-size normalized reads density data range for each histone modification and
RNA-seq datasets are indicated on the right side of the tracks. For all six genotypes, after neural induction, the level of histone H3K27me3 at the gene TSSs is decreased
with increased enrichment of histone H3K4me3 that is concomitant with RNA expression and enrichment of histone H3K36me3 across the gene bodies, thereby indicating
comparable pluripotency and neural differentiation status for the members of the isogenic panel. Additional QC results for the ChIP-seq and RNA-seq datasets are
provided in Supplementary Material, Figures S1, S2A and B.
Human Molecular Genetics, 2015, Vol. 24, No. 9
The absence of huntingtin predominantly affects histone
H3K27me3 at ‘bivalent’ loci
To understand the impact of the Htt null genotype, we utilized an
approach pioneered by Mikkelsen et al. (34) to generate ESC and
NPC chromatin maps. The marked TSSs are classified as transcriptionally ‘repressed’ (histone H3K27me3 only) or ‘active’ (histone H3K4me3 only) or are classified as ‘bivalent’ (histone
H3K27me3 and histone H3K4me3) and poised for transcription.
At the ESC stage, the fraction of TSS in each category for wildtype parental ESC is similar to that reported in the literature
(34) and, as reported, only ∼8% of genes in the ‘bivalent’ category
are expressed, as judged by RNA-seq analysis (>2RPKM) and histone H3K36me3 enrichment across the gene body (34) (Supplementary Material, Table S2).
By comparison, the latter ‘bivalent’ chromatin class is predominantly affected by the absence of huntingtin. In Htt null
ESC, although the proportions of TSS in each category are similar
to wild-type ESC (Fig. 4C), nearly 42% of the TSS classified as ‘bivalent’ in wild-type ESC are instead classified as ‘active’ in HTT
null ESC, such that 1229 TSS display the histone H3K4me3
mark but lack histone H3K27me3 (Fig. 4D and Supplementary
Material, Table S2), consistent with inefficient PRC2 deposition
of H3K27me3 in the absence of huntingtin. About 14% of these
abnormally ‘active’ category genes exhibit an increase (>1.5fold) in RNA expression in Htt null ESC (Supplementary Material,
Table S2), which is consistent with the previous report showing
the increased expression of only a small fraction of the genes
with decreased histone H3K27me3 in Eed-null ESC (35,36).
In contrast, Htt null NPC exhibit a relative excess of TSS in the
‘bivalent’ category, although the fractions of TSS in the other
chromatin categories resemble those of wild-type NPC (Fig. 4E).
In wild-type NPC, the majority of loci with TSS classified as ‘bivalent’ at the ESC stage have lost the histone H3K27me3 mark
and are found in the ‘active’ category (Fig. 4F). However, a small
fraction (7.9%) of TSS that are properly ‘bivalent’ in Htt null ESC
are inappropriately resolved to ‘active’ loci in Htt null NPC
(Fig. 4F and Supplementary Material, Table S2), thereby implying
that lack of huntingtin impairs the efficiency with which histone
H3K27me3 is maintained at 121 poised loci. In addition, a larger
proportion (17.6%) of the TSS that are appropriately ‘bivalent’ in
Htt null ESC inappropriately retain the histone H3K27me3 mark
and remain aberrantly ‘bivalent’ in Htt null NPC (Fig. 4F and
Supplementary Material, Table S2), as confirmed by ChIP-qPCR
analysis of selected loci (Supplementary Material, Fig. S3).
This reveals impaired removal of the PRC2-deposited mark in
the absence of huntingtin at 223 ‘bivalent’ TSS and highlights
an unexpected role for huntingtin in the process by which
histone H3K27me3 is removed from promoters of genes that are
destined to be expressed during the transition to neuronal
lineage fate.
Mutant huntingtin mainly affects histone H3K4me3 and
gene expression at ‘active’ loci
To uncover the mild effects of the CAG-expansion mutation,
which must satisfy the genetic parameters of the HD mechanism
(dominance and progressivity with CAG size), we performed continuous analysis across the Htt CAG knock-in ESC ChIP-seq and
NPC ChIP-seq datasets to disclose marks at TSS whose enrichment is progressively increased or decreased with increasing
size of mutant huntingtin’s polyglutamine tract [see Fig. 5A
and B for visual examples of integrative genomics viewer (IGV)
snapshots of H3K27me3, H3K4me3]. Across the ESC lines,
CAG-progressive enrichment is found at 360 of the histone
H3K27me3 marked TSS (6.05%) and 962 of the histone
H3K4me3 TSS (4.21%), as confirmed by ChIP-qPCR analysis of selected loci (Supplementary Material, Fig. S4A–H). At the NPC
stage, CAG-associated enrichment is detected at 110 histone
H3K27me3 marked TSS (3.91%) and 933 histone H3K4me3 decorated TSS (5.09%), as validated by ChIP-qPCR analysis for selected
genes with decreases in histone H3K4me3 (Supplementary
Material, Fig. S4I and J).
From the HD criteria-conforming histone marks that are located at the TSS of genes for which RNA is reliably detected (>1
RPKM), we generated ESC and NPC chromatin maps displayed
as HEAT maps in Figure 5C–F (Supplementary Material, Table S3),
which reveal apparently pleiotropic effects of mutant huntingtin.
In pluripotent stem cells, most genes with progressively enriched
histone H3K27me3 (increases and decreases) are in the ‘bivalent’
class (Fig. 5C) (Supplementary Material, Table S3). Notably, regardless of their TSS histone H3K27me3 level, the majority of
all of the conforming ‘bivalent’ genes are not reliably expressed
(<1 RPKM), as found for ‘bivalent’ genes in wild-type ESC, and,
therefore, did not meet the criteria of this analysis. In contrast,
most genes with progressive histone H3K4me3 TSS levels (increases and decreases) are in the ‘active’ category and are expressed (>1 RPKM) (Supplementary Material, Table S3) (Fig. 5D).
Interestingly, genes with increasing histone H3K4me3 enrichment exhibit concomitantly increasing RNA levels (Pearson’s R ≥
0.5), indicating an effect of mutant huntingtin on gene regulation
in pluripotent cells.
At the NPC stage, most of the TSS with altered histone
H3K27me3 levels are those that remained ‘bivalent’ in Hdh Q20/7
NPC but with increasing Htt CAG-size tend to exhibit decreasing
enrichment and, thereby, tend to be classified as ‘active’ in the
NPC lines with longer repeats (Hdh Q91/7, Hdh Q111/7) (Fig. 5E and
Supplementary Material, Table S3). However, the predominant
progressive changes are in histone H3K4me3 enrichment where
the bulk of the conforming TSS exhibit decreasing levels of this
mark at ‘active’ chromatin genes, with concomitantly decreased
RNA expression (Pearson’s correlation coefficient R ≤ −0.5) that
discloses an effect of mutant huntingtin on gene regulation in
mutant huntingtin expressing neuronal lineage cells (Fig. 5F).
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confirmed by analysis at more relaxed thresholds (Thresholds
1–3) (data not shown), the numbers of histone H3K27me3
enriched TSS are significantly decreased by one-third (4.47 × 10−79,
χ 2 test) in Htt null ESC and, seemingly incongruously, are nearly
doubled (1.23 × 10−22, χ 2 test) in Htt null NPC (Fig. 4A), compared
with their wild-type counterparts. This mark is not consistently
changed across the CAG knock-in ESC or NPC series (Supplementary
Material, Fig. S2C and D), thereby revealing that mutant huntingtin
does not mimic the loss of huntingtin function. Furthermore,
we analyzed metagene profiles plotting the average ChIP-seq
enrichment signals (input normalized ChIP enrichment) for three
different groups of TSS presenting H3K27me3 enrichment in (a)
both wild-type and Htt null ESC, (b) wild-type ESC only and (c) Htt
null ESC only. The striking decrease in TSS histone H3K27me3 enrichment in Htt null ESC, which is most evident from the metagene
profiles for genes with this mark in wild-type ESC (WT genotypespecific TSS) but is also noticeable at genes with this mark in both
wild-type and Htt null ESC (TSS common to WT and dKO) (Fig. 4B),
is consistent with huntingtin function assisting PRC2 in the deposition of histone H3K27 trimethyl mark. However, the observation
of a significant excess of histone H3K27me3 enriched genes in Htt
null NPC implies a further, distinct role for huntingtin in the proper
resolution of this mark during neuronal cell differentiation.
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Figure 4. Htt null mutation predominantly affects histone H3K27me3 at ‘bivalent’ loci in ESC and NPC. (A) Bar graph of the total number of TSS with histone H3K27me3
enrichment (scaled ChIP read counts over input control using threshold 4 as described in Materials and Methods) in a region of ±2 kb around the TSS, for the Htt wild-type
(WT) and Htt null (dKO) ESC and NPC lines. Supplementary Material, Figure S3C and D presents the TSS data for all of the other assessed histone marks for all of the
members of the isogenic Htt allelic ESC and NPC series. (B) Metagene profiles displaying the average of TSS histone H3K27me3 enrichment (scaled ChIP read counts
over input control exceeding threshold 3—see also Materials and Methods) in a region of ±2 kb around the TSS in Htt wild-type and Htt null ESC. TSS enriched for
H3K27me3 in both genotypes are depicted in red. TSS enriched only in wild-type are given in blue. TSS enriched only in Htt null ES are depicted in green. Y axis shows
Human Molecular Genetics, 2015, Vol. 24, No. 9
Chromatin changes due to mutant huntingtin gain of
function define distinct processes
Similarly, at the NPC stage, the conforming gene sets are enriched
in processes that imply altered signaling (‘transcription’,
‘membrane vesicle and junctions’), with processes that indicate
‘DNA metabolism’ and ‘apoptosis’, thereby denoting anticipated
stress and cell death.
These observations strongly imply that mutant huntingtin or
the lack of huntingtin may differentially alter the status of pluripotent and neuronal progenitor cells. However, the cell states
highlighted by selected subsets of genes may be misleading because unselected TSS changes do not contribute to the pathways
analysis and genes from each genetic paradigm may be differentially enriched in multiple processes within the same general category. Therefore, we broadened the pathways analyses to
compare the cell states forecast by all ESC and NPC loci whose
TSS histone marks conformed to the HD genetic criteria (Supplementary Material, Table S4) and for all ESC and NPC loci whose
TSS chromatin states are altered in the absence of huntingtin
(Supplementary Material, Table S4). Then, we grouped the resulting significant cellular processes, molecular functions, cellular
components and KEGG pathways (Supplementary Material,
Table S4) into general categories, such that the relative proportions of the processes in each category reveal the evident similarities and differences between the genetic paradigms (Fig. 6B).
Overall, at both the pluripotent and lineage restricted developmental stages, the presence of mutant huntingtin and the lack
of huntingtin produce cell states that are to a similar extent enriched for many different processes that are under the general
categories that denote embryonic and neuronal development
(‘adhesion’, ‘membrane’, ‘ion channel’, ‘signal transduction’).
However, the chromatin states of mutant huntingtin pluripotent
stem cells and neuronal progenitor cells uniquely highlight categories with processes that denote cell stress and cell death
(‘chromosome’, ‘cell cycle’, ‘apoptosis’). Therefore, mutant huntingtin does not replicate the loss of huntingtin function but instead forecasts uniquely altered developmental potential of
progenitor cells that predicts reduced fitness and an enhanced
readiness for cell death.
Discussion
The key genetic parameters of the mechanism by which the
expanded HTT CAG repeat triggers the HD disease process (true
dominance, progressivity with CAG size) and a unique specificity
that is provided by the gene product itself, point to a gain of
mutant huntingtin function. Employing a comparative strategy
that utilizes these HD genetic criteria, we evaluated an initial
hypothesis suggested by previous studies: that expanding mutant huntingtin’s polyglutamine tract may simply enhance its
ability to stimulate PRC2, thereby altering the chromatin landscapes of pluripotent and lineage restricted progenitor cells in a
mean of smoothed maximum likelihood enrichment estimates (MLE) for the groups of genes in each category (red, blue and green). (C) Bar plot depicting the fraction (as
percentage) of the total TSS (N = 30 489) analyzed that are classified as ‘repressed’ (histone H3K27me3 only), ‘active’ (histone H3K4me3 only) or ‘bivalent’ (histone
H3K27me3 and histone H3K4me3) for Htt wild-type (WT) and Htt null (dKO) ESC lines. (D) Composite heatmap plotting (in rows) the 2949 loci with TSS classified in Htt
wild-type (WT) ESC as ‘bivalent’ to illustrate their chromatin status in Htt null (dKO) ESC. The adjacent columns show the corresponding histone H3K36me3
enrichment calculated over the gene body and the RNA-seq expression levels as Log2(RPKM+1) values. The major GO terms highlighted by pathways analyses for the
subsets of loci with Htt null sensitive TSS enrichment (Category 1) and Htt null insensitive TSS enrichment (Category 2) are given (further details on the categories are
provided in the Results). (E) Bar plot depicting the fraction (as percentage) of the total TSS (N = 30 489) analyzed that are classified as ‘repressed’ (histone H3K27me3 only),
‘active’ (histone H3K4me3 only) or ‘bivalent’ (histone H3K27me3 and histone H3K4me3) for Htt wild-type (WT) and Htt null (dKO) NPC lines. (F) Composite heatmap plotting
(in rows) the 1525 TSS that are classified as ‘bivalent’ in both Htt wild-type (WT) ESC and Htt null (dKO) ESC with the adjacent column indicating their chromatin status in
their cognate NPC line. The corresponding paired ESC and NPC histone H3K36me3 enrichment and RNA expression levels, as Log2(RPKM+1) values, are in the adjacent
columns. The major GO terms highlighted by pathways analyses for the subsets of loci with Htt null insensitive TSS enrichment (Categories 1 and 4) or Htt null sensitive
TSS enrichment (Categories 2 and 3) are given (further details on the categories are provided in the Results). Supplementary Material, Figure S3 reports ChIP-qPCR
confirmation of selected Htt null TSS changes in ESC and NPC.
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The polyglutamine expansion mutation is expected to endow
mutant huntingtin with a gain of function that is related to its existing normal huntingtin function. Therefore, although the dominant Htt CAG mutation is expected to target different genes than
the recessive Htt null inactivating mutation, the gain of function
should be reflected in the uniquely altered chromatin states of
ESC and NPC that express the mutant protein when compared
with the chromatin states conferred by the lack of huntingtin
normal function. Comparison of the Htt CAG-delineated ESC
and NPC gene sets (TSS marks fulfilling the HD genetic criteria
of showing a trend across CAG repeat length) (Supplementary
Material, Table S4) with the Htt null-defined ESC and NPC gene
sets (TSS marks differing from wild-type) (Supplementary Material, Table S4) reveals that the overwhelming majority of loci
(∼90%) are unique to one genetic paradigm (Fig. 6A), commensurate with the Htt CAG repeat conferring a gain of new function rather than a loss of huntingtin normal function. Pathways
enrichment analyses were then utilized to determine if the
altered chromatin states delineated by sets of Htt CAG expansionand Htt null-targeted loci might highlight cellular processes that
are similar or dissimilar, such that the latter may denote mutant
huntingtin gains of function.
Huntingtin normal function was evaluated by separately analyzing each of the main subsets of ‘bivalent’ loci for the Htt null
ESC (Categories 1–2 in Fig. 4D) and NPC (Categories 1–4 in
Fig. 4F) as listed in Supplementary Material, Table S4 as well. As
expected, those not changed by the absence of huntingtin (ESC
Category 2; NPC Categories 1 and 4 in Fig. 4D and F) are overrepresented in processes that denote ‘embryonic development’
and ‘neuronal cell morphogenesis’. This finding supports the
concept that genes in the ‘bivalent’ chromatin class anticipate
development in the pluripotent state and are involved in the
commitment to the neuronal cell lineage fate in NPC (34), thereby
confirming the normal developmental potential of Htt null cells.
However, this potential is subtly altered. The subsets of ‘bivalent’
genes that are improperly marked in Htt null pluripotent and
neuronal fated cells (ESC Category 1; NPC Categories 2 and 3 in
Fig. 4D and F) indicate deviations from normalcy in ‘ion transport’, ‘cell adhesion’ and ‘regulation of RNA/transcription’ or in
‘forebrain and inner ear morphogenesis’, respectively.
Mutant huntingtin function was assessed by analyzing
each of the main subsets of Htt CAG-conforming ESC and NPC
loci (Supplementary Material, Table S4), as indicated beside the
heatmaps for each histone mark in Figure 5C–F. At the pluripotent stage, the gene sets highlight processes that imply altered
development (‘regulation of neurogenesis’ and ‘embryonic development and metabolism’) or altered cellular homeostasis (‘regulation of transcription’, ‘stress signaling’, ‘cell cycle’, ‘apoptosis’).
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Figure 5. Htt CAG expansion yields pleiotropic chromatin changes in ESC and NPC. Two illustrative IGV snapshots at two genomic locations presenting decreasing
H3K27me3 (A) and decreasing H3K4me3 (B) enrichments show the ChIP-seq library-size normalized reads (RPKM) for histone H3K27me3 or histone H3K4me3 across
the four Htt CAG knock-in ESC lines. Vertical dashed lines indicate the ±2 kb region around the TSS considered for the evaluation of the histone modifications
enrichment. Also shown are the RNA-seq reads (RPKM) with the + strand (P) and – strand (N) indicated. Library-size normalized RPKM data range for each histone
modification and RNA-seq datasets are indicated on the right side of the tracks. The level of histone H3K27me3 and histone H3K4me3 at the specific TSS is decreased
Human Molecular Genetics, 2015, Vol. 24, No. 9
Though huntingtin may separately modulate multiple
discrete chromatin complexes, a more parsimonious hypothesis
is that huntingtin may fine-tune PRC2 in some long-range manner when the complex is embedded within the larger machinery
that coordinates both the balance of ‘activation’ and ‘repressive’
histone marks and the other layers of regulatory factors required
for developmentally appropriate gene silencing and activation.
There is growing precedent for large factories and for longrange regulation. For example, super-complexes containing
histone methyltransferases and demethylases can coordinately
deposit one mark while removing the opposing mark (41).
The ‘repressive complexes’ PRC2 and polycomb-like proteins
(Ring6a/MBLR) coexist with histone H3K4me3 demethylase
(31,42) and ‘activating complexes’ containing MLL2 or MLL4 histone H3K4me3 methyltransferases also contain the histone
H3K27me3 demethylase UTX (39,40). In ESC, Jarid1b histone
H3K4me3 demethylase is found at TSS of genes encoding developmental regulators, together with PRC2 (43). Furthermore, dramatically expanding its chromatin locations, PRC2 polycomb
group proteins detected at ‘active’ chromatin in association
with nascent transcripts suggest a model for PRC2 surveillance
that ‘samples’ TSS, such that PRC2 becomes catalytically active
upon binding of a transcriptional repressor (44,45). Thus, assessing the occupancy of activating and repressing DNA binding proteins may help to characterize the effects of mutant huntingtin
on gene regulation in ESC and NPC. In addition, at a higher
order of structural organization, polycomb group proteins and
trithorax group proteins, with insulator proteins such as CTCF,
orchestrate large scale ‘repressed’ or ‘active’ chromatin loops
that ensure coordinated silencing or expression, respectively, of
genes on the same and different chromosomes, as befits a
given cell state (46–48).
In this view, huntingtin may primarily influence some longrange interaction that fine-tunes the efficiency with which
PRC2 catalyzes histone H3K27me3 to maintain this mark at ‘bivalent’ TSS in ESC. Post neural induction, this long-range function may also serve to fine-tune the catalytic efficiency of the
associated histone H3K27me3 demethylase that removes the trimethyl group at ‘bivalent’ loci that are becoming transcriptionally active, while fine-tuning the efficiency with which PRC2
maintains proper histone H3K27me3 levels at other ‘bivalent’
loci that should remain ‘bivalent’ at the NPC stage. The hypothesized long-range PRC2 fine-tuning role for huntingtin would present multiple opportunities for mutant huntingtin gains of
function: both simple increases in its aforementioned existing
huntingtin activities and the gains of new function at TSS of ‘bivalent’ and transcriptionally ‘active’ genes. For example, the aberrant fine-tuning conferred by mutant huntingtin, which
increases its ‘normal’ huntingtin activities, may also relax the
constraints in ESC that keep some poised ‘bivalent’ loci from becoming excessively ‘active’ or ‘repressed’ and certain ‘active’
genes from being exuberantly transcribed. After neural induction
the aberrant fine-tuning may relax the constraints that keep
with increasing Htt CAG size and this change is concomitant with RNA expression alterations: specifically, increasing RNA levels were observed following histone
H3K27me3 decreased enrichment (A panel, Alg11 gene), while decreasing RNA levels were identified following decreased histone H3K4me3 enrichment (B panel, Aire
gene). Composite heatmaps plotting the loci (rows) with TSS that exhibit continuously (cont.) increasing (brown) or decreasing (blue) levels of histone H3K27me3
enrichment (C and E) or histone H3K4me3 enrichment (D and F) in the CAG knock-in Hdh Q20/7, Hdh Q50/7, Hdh Q91/7, Hdh Q111/7 (CAG 18/+, 48/+, 89/+, 109/+) ESC (C and D)
and NPC lines (E and F), displayed by ranking of their library-size normalized ChIP enrichment relative to that of the CAG 18/+ ESC line (enrichment score). The
respective chromatin status of each TSS by histone code classification as ‘active’, ‘bivalent’ or ‘repressed’ and the respective enrichment of histone H3K36me3 and
RNA-seq expression levels are plotted in the adjacent sets of columns. The loci chosen exhibit at least >1 RPKM in at least one Htt CAG knock-in sample. RNA-seq
data are reported as relative log2(RPKM+1) ratio of over CAG 18/+ ESC line and standardized by dividing these values over standard deviation across the knock-in
samples. The major GO terms highlighted by pathway analyses for the subsets of loci with the TSS histone mark enrichment that increases (Category 1) or decreases
(Category 2) with Htt CAG size are given (further details on the categories are provided in the Results). Supplementary Material, Figure S4 reports ChIP-qPCR
confirmation of progressive TSS enrichment with Htt CAG size.
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predictable manner that provides insights into the distinct fates
of neurons that express mutant huntingtin or lack huntingtin
function. However, while huntingtin’s role as PRC2-facilitator is
evident under some circumstances, the simple hypothesis does
not fully explain all of the chromatin states produced by Htt inactivation. Nor does it readily account for the multiple distinct
chromatin states that are associated with mutant huntingtin in
Htt CAG knock-in cells, which uniquely forecast reduced viability
at the earliest stages of development.
The view of huntingtin as a PRC2-facilitator is supported by
two findings in cells that lack huntingtin: dramatically decreased
H3K27me3 at TSS of developmentally poised ‘bivalent’ loci in Htt
null ESC and the failure of some TSS appropriately marked in Htt
null ESC to remain properly ‘bivalent’ at the NPC stage, which implies that huntingtin is needed to efficiently maintain the trimethyl group deposited by PRC2. The effect of huntingtin on
facilitating the deposition of H3K27me3 could be achieved
through the physical interaction between full-length huntingtin
and the canonical members of PRC2 complex (14) such as Ezh2 or
Suz12, however, an effect on Ezh1, the other H3 methyltransferase with a partially redundant trimethylation activity on lysine
27 (37,38), cannot be excluded and this point warrants additional
investigations. Conversely, huntingtin must also serve to facilitate the removal of this mark, perhaps by a histone H3K27me3
demethylase such as Utx (39,40) because during the transition
of ESC to NPC the histone H3K27me3 mark at ‘bivalent’ loci is
inappropriately retained in the absence of huntingtin. In order to
better understand how huntingtin interplays with PRC2 activity
during neuronal development, additional investigation to reveal
potential variations in PRC2 subunit occupancy in the absence
of huntingtin will be useful. Moreover, a close comparison
between H3K27me3 signature in PRC2 knock-down or conditional
knock-out model systems compared with huntingtin null will
provide additional hints to dissect the PRC2-huntingtin functional
interaction.
Furthermore, since huntingtin normal function provides the
platform for mutant huntingtin’s novel ‘gains’, a refined hypothesis that invokes simple increases in the two aforementioned
functions would readily explain only two of the multiple outcomes of mutant huntingtin that satisfy the HD genetic criteria:
the increases in histone H3K27me3 at a subset of ‘bivalent’ TSS in
Htt CAG knock-in ESC lines and the decreases in histone
H3K27me3 at a subset of ‘bivalent’ loci at the NPC stage. A fundamentally updated hypothesis of huntingtin function that fully
accounts for the pleiotropy conferred by extending its polyglutamine tract in mutant huntingtin should also explain the other
outcomes that we detected: (1) decreases in histone H3K27me3
observed at ‘bivalent’ TSS in the Htt CAG knock-in ESC lines, (2)
increases and decreases in the histone H3K4me3 mark, catalyzed
by Mll methyltransferase and removed by Jarid1/Kdm5 family demethylases (39,40), observed at ‘active’ loci in the Htt CAG knockin ESC lines and (3) decreases in histone H3K4me3 levels that are
found at ‘active’ loci in the Htt CAG knock-in the NPC lines.
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Figure 6. Comparison of the biological states forecast by the chromatin landscapes of Htt CAG knock-in and Htt null ESC and NPC. (A) Venn diagrams showing the modest
intersection of the two genome-wide gene sets that are delineated either by histone H3K27me3 and histone H3K4me3 enrichment that conforms to HD genetic criteria in
Htt CAG knock-in ESC and NPC lines (red) or, alternatively, by enrichment levels that are changed in Htt null ESC and NPC lines compared with their wild-type counterparts
(gray). (B) Bar graph summarizing the results of DAVID pathways analysis for the Htt CAG- and Htt null-delineated ESC gene sets (red and gray, respectively), such that the
proportion of significant Biological Process, Molecular Functions, Cellular Component and KEGG terms in any given general category is plotted as percentage of the total
for each dataset. (C) Bar graph is same as in B, but for NPC samples.
transcribed ‘active’ genes in NPC from becoming excessively
‘repressed’.
The distinctly altered chromatin states of the pluripotent
and neuronal lineage committed progenitor cells that we find
to be associated with either the presence of mutant huntingtin
or the lack of normal huntingtin function in each case consistently
predict distinct subtly altered developmental status’ that
anticipate the different fates for the differentiated mature cell
types that are derived from them, as reported by Conforti et al.
(28). It is now evident that the expression of mutant huntingtin
confers from the earliest stages of development an altered cellular homeostasis that forecasts reduced viability. The specific biological processes and molecular functions that are highlighted by
pathways enrichment analyses of the different chromatin states
Human Molecular Genetics, 2015, Vol. 24, No. 9
produced by the Htt null and Htt CAG-expansion mutations
now provide a framework for investigating the molecular basis
of huntingtin’s role in neuronal development and the dominant
impact of expanding its polyglutamine tract.
Materials and Methods
Cell culture
RNA isolation, reverse transcription and quantitative PCR
RNA was extracted from cell lines by using TRIzol reagent (Invitrogen) and following manufacturer’s instructions. All RNA
samples were subjected to DNAse I treatment (Ambion). One
microgram of RNA was subjected to retro-transcription using
iScript cDNA Synthesis Kit (Bio-Rad) accordingly to the vendor’s
instructions. Quantitative RT-PCR was performed by using
SYBER-Green PCR Master Mix and 480 Light Cycler Detection
System (Roche). TATA-binding protein (Tbp) and glyceraldehyde
3-phosphate dehydrogenase (Gapdh) were used as housekeeping
genes through different samples and conditions. Primers were
chosen by using the Universal ProbeLibrary Assay Design Center
from Roche Applied Science. Primer sequences used in this work
are available upon request. The amplified transcripts were quantified using 2−(▵▵Ct) method and the differences in gene expression were presented as normalized fold expression. All the
results are presented as average ± standard deviation of two biological and two technical duplicates.
Imaging and immunocytofluorescence
For immunofluorescence experiments cells were fixed in 4% paraformaldehyde (Tousimis Research). Cell were then treated with
0.1 glycine in PBS and permeabilized with 0.1% Triton X-100.
After washing and blocking with 0.2% BSA, 1% normal goat
serum, and 0.1% Triton X-100 in PBS (blocking solution),
cells were incubated with the indicated antibodies diluted in
blocking solution. Cells were probed with fluorescent secondary
antibodies (Molecular Probes). For nuclear staining, 1 g/mL
4’,6-diamidino-2-phenylindole (DAPI) staining was used. Cells
were washed and mounted with Vectashield mounting medium
(Vector Laboratories).
All images were collected using an epifluorescence microscope (Zeiss). The following antibodies were used for this study:
anti-Pax6 (1:500) [monoclonal antibody, developed by Dr Atsushi
Kawakami (Yokohama, Japan) was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the
NIH and maintained at The University of Iowa, Department of
Biology, Iowa City, IA 52 242], anti-Oct4 (1:500; Millipore), antiNestin (1:1000; Millipore).
Alkaline phosphatase staining was performed using ‘Alkaline
Phosphatase Detection Kit’ from Millipore Corporation accordingly to the vendor’s instructions.
Protein extraction and immunoblot analysis
Protein extracts were prepared from PBS-washed cell pellets by
RIPA (Boston Bio-Products) lysis buffer and protease inhibitor
mixture (Roche). The lysates were then sonicated with A Bioruptor sonicator (Diagenode), cleared by centrifugation at 14 000g for
30 min and the supernatants collected. The protein concentration was determined using the Bio-Rad (detergent compatible)
protein assay. Fifty micrograms (hundred for Htt) of protein
extract were mixed with SDS-loading buffer, boiled for 5 min
and subjected to 6 or 10% SDS–PAGE. After electrophoresis, the
proteins were transferred to nitrocellulose membranes (Schleicher and Schuell) and incubated for 30 min in a blocking solution
containing 5% non-fat powdered milk in TBS-T (50 m Tris–HCl,
150 m NaCl, pH 7.4, 0.1% Tween-20). The membranes were
probed overnight at 4°C with the primary antibody Htt-mAb2166
(Millipore, 1:500), Ezh2 (Millipore, 1:2000), Suz12 (Abcam, 1:1000)
and β-actin (SIGMA, 1:5000). After TBS-T washes, the blots were
incubated for 1 h at room temperature with horseradish peroxidase-conjugated secondary antibodies. The membranes were
then processed using an ECL chemiluminescence substrate kit
(Pierce) and exposed to autoradiographic film (Hyperfilm ECL;
Amersham Bioscience).
Chromatin immunoprecipitation
Chromatin immunoprecipitation (ChIP) was performed using the
protocol described by (50) with minor modifications. Briefly,
∼40–60 million cells were fixed with 1% formaldehyde, washed
with ice-cold PBS, harvested, pelleted and directly resuspended
in SDS lysis buffer (50 m Tris–HCl [ pH8.1], 1% SDS, 10 m
EDTA) or stored at −80C for future use. Sonication of the samples
was accomplished by using a Bioruptor sonicator (Diagenode),
then, shared-chromatin was centrifuged at 13 000g for 10 min
and diluted 10-fold in ChIP dilution buffer (16.7 m Tris–HCl
[ pH 8.1], 167 m NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 m
EDTA). After removing A control aliquot (INPUT), each sample
was incubated at 4°C overnight with antibodies of interest: histone H3K27me3 (ABE44 or 07-449, Millipore), histone H3K4me3
(07-473, Millipore) and histone H3K36me3 (Ab9050, Abcam).
Chromatin–Antibody complexes were precipitated with Dynabeads Protein A beads (Invitrogen) and washed sequentially
with low-salt (20 m Tris–HCl [ pH 8.1], 150 m NaCl, 0.1% SDS,
1% Triton X-100, 2 m EDTA), high-salt (20 m Tris–HCl [ pH
8.1], 500 m NaCl, 0.1%SDS, 1% Triton X-100, 2 m EDTA), LiCl
(10 m Tris–HCl [ pH 8.1], 0.25 M LiCl, 1% NP40, 1% sodium
deoxycholate,1 m EDTA), and TE wash buffers (10 m Tris–
HCl [ pH 8.0], 1 m EDTA). Immunoprecipitated chromatin was
eluted in elution buffer (TE plus 1% SDS, 150 m NaCl, 5 m
DTT), de-crosslinked at 65°C for 8 h (or overnight), and treated
with proteinase K. The DNA was treated with RNase and purified
with A MinElute Kit (Qiagen). Quantification of ChIP and INPUT
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The isogenic panel of wild-type, Htt null Hdhex4/5/ex4/5 and heterozygous Htt CAG knock-in Hdh Q20/7, Hdh Q50/7 Hdh Q91/7 and Hdh Q111/7
mouse ES cell lines are grown as described previously (15,18,22–
24). Differentiation to neuronal lineage committed progenitor
cells was performed essentially as described in (49). Briefly, ES
cells were maintained on feeder layers of γ-irradiated mouse embryonic fibroblasts (Global Stem Sciences) or on gelatin-coated
plates (1% gelatin solution; Millipore). ES cell media contained
Knock-Out D-MEM (Invitrogen), 15% FBS (Hyclone), 50 I.U/ml of
penicillin, 50 mg/ml of streptomycin (Invitrogen), 0.2 m GlutaMax (Invitrogen), 0.1 m non-essential aminoacids (Invitrogen),
0.1 m 2-mercaptoethanol (Sigma) and 1000 U/ml of leukemia
inhibitory factor (LIF) (Millipore).
For neural progenitors differentiation, ESCs were deprived of
feeder cells for four passages, then 3 × (106) cells were used for
formation of EBs. EBs were grown in non-adherent bacterial
dishes (Greiner, Germany) for 8 days. Retinoic acid (SIGMA,
5 uM) was added from day 4 to day 8 and medium was changed
every other day. Subsequently, EBs were dissociated by trypsin
digestion and plated on Poly-ornithine (SIGMA) and laminin
(SIGMA) coated plates. Two hours after plating, neural committed
cells were collected for different analyses.
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DNA was done using Qubit 2.0 Fluorometer system (Invitrogen).
ChIP enrichments were assessed by quantitative PCR analysis
on 480 Light Cycler Detection System (Roche) with 200–400 pg
of ChIP DNA and an equal amount of un-enriched INPUT DNA.
Enrichments were calculated from 2 biological replicates. A
gene desert region (Chr.6: 120 258 500-120 259 000) (GD) and the
β-actin (Actb) promoter, commercially available from Active
Motif, were used as negative controls. Error bars in the graphs
represent standard error of the mean.
Helicos library preparation and single-molecule
sequencing
ChIP-seq data processing
The sequenced reads were filtered based on quality scores and
aligned to the Mus musculus genome (mm9 assembly) using the
basic processing pipeline available in the Helisphere tools suite
by Helicos (http://sourceforge.net/projects/openhelisphere/).
Default parameters were used, except for ‘globalAmbig = none’
to retain only uniquely aligned reads.
Read density tracks for visual inspection of data were generated using Gaussian smoothing of the 5′-end mapping positions,
normalized by the number of uniquely mapped reads (millions).
A 200 bp bandwidth was used for smoothing to browse data and
5′-end mapping positions were shifted by the average sequencing fragment size estimated from using cross correlation
analysis of histone H3K4me3 samples for each cell type, as implemented in the SPP R package (52).
We detected ChIP-enriched regions by comparing scaled ChIP
and input control read counts to see if their ratio exceeded that
expected from a Poisson process, using get.broad.enrichment.cluster function in the SPP R package with a sliding window of 1 kb
(default). The clusters of significant windows with Z-score > 3
(default) [for Hdh KI ChIP-seq analysis, see Figure 5 and Supplementary Material, Table S3] or >4 (more stringent) [for WT versus
Htt null ChIP-seq comparison, see Figure 4A, C–F and Supplementary Material, Table S2], were determined as enriched regions. Raw
sequencing data are available in the SRA database (http://www.
ncbi.nlm.nih.gov/sra/) with accession number PRJNA252361. A
summary of samples and aligned reads is presented in Supplementary Material, Table S1.
Public ChIP-seq data
Publicly available and previously published ChIP-seq datasets obtained with Helicos sequencing technology were processed as
above described. Public ChIP-seq datasets obtained with Illumina
sequencing instead were aligned using Bowtie (53), to mm9 reference genome. The parameters of alignments were -n 2 -l 28 -E 70
-m 1 for unique mapping. The subsequent analyses steps were
analogous to those used for Helicos ChIP-seq data.
Hdh KI ChIP-seq data analysis
To enable a discovery strategy based on the continuous relationship between CAG size and phenotype, we utilized a correlation
approach to distinguish loci that may specifically be affected by
RNA-seq data processing
RNA-sequence (RNA-seq) data were obtained with strandspecific RNA-seq protocol for Helicos sequencing technology.
Sequencing reads were quality filtered and aligned to reference
RefSeq transcripts sequences for the mm9 genome (RefSeq
build date 29 June 2012) using the DGE analysis pipeline of Helicos
software (Helisphere), which uses the RMC algorithm to assign
read counts to transcripts (54). Default parameters were used,
except for Global.rpkm = True, to obtain read counts normalized
by gene length (RPKM).
Strand-specific read density tracks for visual inspection of
data were generated using Gaussian smoothing of the 5′-end
mapping positions, normalized by the number of uniquely
mapped reads (millions) using the SPP R package. A 200 bp bandwidth was used for smoothing and 5′-end mapping positions
were shifted by half (≈15 bp) of the average read length in each
sample.
Raw sequencing data are available in the SRA database (http://
www.ncbi.nlm.nih.gov/sra/) with accession number PRJNA252362.
A summary of samples and aligned reads is presented in Supplementary Material, Table S1.
Gene annotations
RefSeq annotations tables were retrieved from UCSC Genome
Browser (mm9 genome version—build date 29 June 2012). RefSeq
transcript annotations were downloaded from the UCSC genome
browser. For each RefSeq transcript a window spanning 2 kb upstream and 2 kb downstream the annotated TSS was considered.
This window was truncated downstream of the TSS if the RefSeq
transcript was <2 kb long, and was also truncated upstream of the
TSS if another RefSeq transcript ending on the same genomic
strand was located <2 kb upstream. Each RefSeq TSS was annotated as associated with a chromatin mark (histone H3K27me3
or histone H3K4me3) if any overlap existed between the ChIPseq peak the TSS window. Instead, histone H3K36me3 enrichment regions were compared for overlap with gene body regions
(between annotated 5′ and 3′ ends). Depending on the analysis,
these overlaps were also summarized at the gene level, as indicated in specific results.
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Nanogram quantities of DNA (cDNA) were sequenced on an
Helicoscope single molecule sequencer (Helicos Bioscience,
Cambridge, MA, USA) obtaining an average of 8 million successful reads, consisting of 30–35 bases each (Supplementary Material, Table S1). Poly-A tailing and Helicos sequencing of ChIP
fragments (300–500 bp) was performed as described in (51).
CAG mutation. This approach also did not rely on classification
of loci by combination of histone mark, but evaluated histone
H3K4me3 and histone H3K27me3 separately, as we could not anticipate whether or not a specific category would be affected. We
quantified the enrichment values for ChIP-seq datasets of the
CAG knock-in genotypes in ESC and NPC, evaluating the total
reads number in a region of ±2 kb centered on TSS. The enrichment values for each promoter region in a specific dataset were
then selected to present monotonic increases or decreases with
CAG size thereby assessing quantitative differences in ChIP
enrichment with CAG expansion. In order to discriminate between real ChIP enrichment and fluctuation of the background,
we additionally filtered ChIP enrichment for being higher than
60 normalized reads in the analyzed window (±2 kb) in Q20, the
lowest CAG-expanded allele (for monotonically decreasing
promoters) or Q111, the highest CAG-expanded allele (for monotonically increasing promoters). The ChIP enrichment values obtained using these parameters were further sorted based on the
degree of variance among the different CAG expansions in order
to rank the changes from the top to the least most affected by
CAG size.
Human Molecular Genetics, 2015, Vol. 24, No. 9
In the Venn diagrams (Supplementary Material, Fig. S2A
and B), the lists of chromatin mark-associated genes/TSSs were
compared across different ChIP-seq targets. Venn diagrams
with proportional overlapping areas were plotted using the
Vennerable R package.
Metagene profiles
Accession numbers
The sequencing data were deposited in the Sequence Read Archive under accession numbers PRJNA252361 and PRJNA252362 for
ChIP-seq and RNA-seq data, respectively.
Pathway analysis
To gain insight into the functional roles of genes associated with
a particular chromatin mark in ESC or NPC, we relied on DAVID
(55). In identifying enriched functional terms, we selected those
with nominal P-value < 0.05. DAVID was used with Mus musculus
background. Enriched terms included biological processes (BP),
molecular functions (MF), cellular component (CC) and KEGGS
pathways. A table summarizing pathways analysis (BP only)
results for single categories (related to Figs 4D, F and 5C–F) and
for general analysis (BP, MF, CC and KEGGS) (related to Fig. 6B)
is presented in Supplementary Material, Table S4. To assess commonality between significant pathways in Htt null and CAG
knock-in cells, the top 25 knock-out significant terms (top 25
BP, top 25 MF, top 25 CC and top 25 KEGGS pathways) and the
top 25 terms in the CAG knock-in data were compared. Broad categories of main cellular processes grouping significant terms
from BP, MF, CC and KEGGS pathways were hand-annotated
and. The percentage of significant terms was plotted for Htt
null and Htt CAG knock-in genotypes (23).
Supplementary Material
Supplementary Material is available at HMG online.
Acknowledgements
We are grateful to the MacDonald, Gusella, Seong, Wheeler and
Talkowski laboratory members for helpful discussions. We
thank Eric Vallabh Minikel for helping with statistical analyses,
Jayalakshmi Mysore and Tammy Gillis for technical support.
Pax6 monoclonal antibody, developed by Dr Atsushi Kawakami
(Yokohama, Japan) was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at The University of Iowa, Department of Biology, Iowa
City, IA 52242.
Conflict of Interest statement. F.O. was an employee of Helicos
BioSciences.
Funding
This work was supported by CHDI Foundation Inc.; and the Huntington’s Society of Canada; and National Institutes of Health/
National Institute of Neurological Disorders and Stroke (R01
NS32765 to M.E.M., R01 NS079651 to I.S.S.).
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To obtain an estimation of binding distribution near genes we
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