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Towards a map of cis-regulatory sequences in the human genome
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to co...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009671/ https://www.ncbi.nlm.nih.gov/pubmed/29733395 http://dx.doi.org/10.1093/nar/gky338 |
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author | Niu, Meng Tabari, Ehsan Ni, Pengyu Su, Zhengchang |
author_facet | Niu, Meng Tabari, Ehsan Ni, Pengyu Su, Zhengchang |
author_sort | Niu, Meng |
collection | PubMed |
description | Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs. Here, we integrated 620 TF ChIP-seq datasets produced by the ENCODE project for 168 TFs in 79 different cell/tissue types and predicted an unprecedentedly completely map of CREs in CRMs in the human genome at single nucleotide resolution. The map includes 305 912 CRMs containing a total of 1 178 913 CREs belonging to 736 unique TF binding motifs. The predicted CREs and CRMs tend to be subject to either purifying selection or positive selection, thus are likely to be functional. Based on the results, we also examined the status of available ChIP-seq datasets for predicting the entire regulatory genome of humans. |
format | Online Article Text |
id | pubmed-6009671 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60096712018-06-25 Towards a map of cis-regulatory sequences in the human genome Niu, Meng Tabari, Ehsan Ni, Pengyu Su, Zhengchang Nucleic Acids Res Computational Biology Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs. Here, we integrated 620 TF ChIP-seq datasets produced by the ENCODE project for 168 TFs in 79 different cell/tissue types and predicted an unprecedentedly completely map of CREs in CRMs in the human genome at single nucleotide resolution. The map includes 305 912 CRMs containing a total of 1 178 913 CREs belonging to 736 unique TF binding motifs. The predicted CREs and CRMs tend to be subject to either purifying selection or positive selection, thus are likely to be functional. Based on the results, we also examined the status of available ChIP-seq datasets for predicting the entire regulatory genome of humans. Oxford University Press 2018-06-20 2018-05-04 /pmc/articles/PMC6009671/ /pubmed/29733395 http://dx.doi.org/10.1093/nar/gky338 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Computational Biology Niu, Meng Tabari, Ehsan Ni, Pengyu Su, Zhengchang Towards a map of cis-regulatory sequences in the human genome |
title | Towards a map of cis-regulatory sequences in the human genome |
title_full | Towards a map of cis-regulatory sequences in the human genome |
title_fullStr | Towards a map of cis-regulatory sequences in the human genome |
title_full_unstemmed | Towards a map of cis-regulatory sequences in the human genome |
title_short | Towards a map of cis-regulatory sequences in the human genome |
title_sort | towards a map of cis-regulatory sequences in the human genome |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009671/ https://www.ncbi.nlm.nih.gov/pubmed/29733395 http://dx.doi.org/10.1093/nar/gky338 |
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