Abstract
Transcription control plays a key role during development and disease with trans-acting factors (TFs) regulating expression of genes through DNA interaction. ChIP sequencing is widely used to get the genome wide binding profiles of TFs in a cell type of interest. The reduction in cost of sequencing and the technological improvement has resulted in vast amount of ChIP sequencing data accumulating in the public domain. The ENCODE consortium alone provides 690 publicly available ChIP sequencing data sets across 91 human cell types. We performed a multi-facetted bioinformatics analysis of this data to unravel diverse properties of TFs in the cellular context. Specifically, we characterised genomic location as well as sequence motif preference of the factors. We demonstrated that the distal binding of factors is more cell type specific than the promoter proximal. We identified combinations of factors acting in concert at distinct genomic loci. Finally, we highlighted how this data is of value to associate novel regulators to disease by integrating it with disease-associated gene loci obtained from GWAS studies.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bernstein, B.E., Birney, E., Dunham, I., Green, E.D., Gunter, C., Snyder, M.: An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414), 57–74 (2012)
Quinlan, A.R., Hall, I.M.: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6), 841–842 (2010)
Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S., Barnes, I., Bignell, A., Boychenko, V., Hunt, T., Kay, M., Mukherjee, G., Rajan, J., Despacio-Reyes, G., Saunders, G., Steward, C., Harte, R., Lin, M., Howald, C., Tanzer, A., Derrien, T., Chrast, J., Walters, N., Balasubramanian, S., Pei, B., Tress, M., Rodriguez, J.M., Ezkurdia, I., van Baren, J., Brent, M., Haussler, D., Kellis, M., Valencia, A., Reymond, A., Gerstein, M., Guigó, R., Hubbard, T.J.: GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 22(9), 1760–1774 (2012)
Pötzelberger, K., Strasser, H.: Data Compression by Unsupervised Classification. Department of Statistics and Mathematics. WU Vienna University of Economics and Business, Vienna, 11 July 1997
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., Glass, C.K.: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38(4), 576–589 (2010)
Frietze, S., O’Geen, H., Blahnik, K.R., Jin, V.X., Farnham, P.J.: ZNF274 recruits the histone methyltransferase SETDB1 to the 3’ ends of ZNF genes. PLoS ONE 5(12), e15082 (2010)
Teoh, H., Quan, A., Creighton, A.K., Annie Bang, K.W., Singh, K.K., Shukla, P.C., Gupta, N., Pan, Y., Lovren, F., Leong-Poi, H., Al-Omran, M., Verma, S.: BRCA1 gene therapy reduces systemic inflammatory response and multiple organ failure and improves survival in experimental sepsis. Gene Ther. 20(1), 51–61 (2013)
Jackson, K.C., Gidlund, E.-K., Norrbom, J., Valencia, A.P., Thomson, D.M., Schuh, R.A., Neufer, P.D., Spangenburg, E.E.: BRCA1 is a novel regulator of metabolic function in skeletal muscle. J. Lipid Res. 55(4), 668–680 (2014)
Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.-K., Cheng, C., Mu, X.J., Khurana, E., Rozowsky, J., Alexander, R., Min, R., Alves, P., Abyzov, A., Addleman, N., Bhardwaj, N., Boyle, A.P., Cayting, P., Charos, A., Chen, D.Z., Cheng, Y., Clarke, D., Eastman, C., Euskirchen, G., Frietze, S., Fu, Y., Gertz, J., Grubert, F., Harmanci, A., Jain, P., Kasowski, M., Lacroute, P., Leng, J., Lian, J., Monahan, H., O’Geen, H., Ouyang, Z., Partridge, E.C., Patacsil, D., Pauli, F., Raha, D., Ramirez, L., Reddy, T.E., Reed, B., Shi, M., Slifer, T., Wang, J., Wu, L., Yang, X., Yip, K.Y., Zilberman-Schapira, G., Batzoglou, S., Sidow, A., Farnham, P.J., Myers, R.M., Weissman, S.M., Snyder, M.: Architecture of the human regulatory network derived from ENCODE data. Nature 489(7414), 91–100 (2012)
Funding
A.J. is a Chancellors Fellow at the University of Edinburgh. This work was supported by the Roslin Institute Strategic Grant funding from the BBSRC.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Devailly, G., Joshi, A. (2017). Transcription Control in Human Cell Types by Systematic Analysis of ChIP Sequencing Data from the ENCODE. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_29
Download citation
DOI: https://doi.org/10.1007/978-3-319-56154-7_29
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-56153-0
Online ISBN: 978-3-319-56154-7
eBook Packages: Computer ScienceComputer Science (R0)