Genome-wide map of regulatory interactions in the human genome
- Nastaran Heidari1,5,
- Douglas H. Phanstiel1,5,
- Chao He2,
- Fabian Grubert1,
- Fereshteh Jahanbani1,
- Maya Kasowski1,3,
- Michael Q. Zhang2,4 and
- Michael P. Snyder1
- 1Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
- 2MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China;
- 3Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA;
- 4Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080-3021, USA
- Corresponding author: mpsnyder{at}stanford.edu
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↵5 These authors contributed equally to this work.
Abstract
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.176586.114.
Freely available online through the Genome Research Open Access option.
- Received March 31, 2014.
- Accepted September 11, 2014.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
