Occupancy maps of 208 chromatin-associated proteins in one human cell type

Abstract

Transcription factors are DNA-binding proteins that have key roles in gene regulation 1,2. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes 3-6. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatinassociated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP-seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium. There are an estimated 1,639 transcription factors (TFs) in the human genome 2 , and up to 2,500 CAPs when we include transcriptional cofactors, RNA polymerase-associated proteins, histone-binding regulators, and chromatin-modifying enzymes 1,7. A typical TF binds to a short DNA sequence motif, and, in vivo, some TFs exhibit additional chromosomal occupancy mediated by their interactions with other CAPs 8-10. CAPs are vital for orchestrating cell type-and cell state-specific gene regulation, including the temporal coordination of gene expression in developmental processes, environmental responses, and disease states 3-6,11-13. Identifying genomic regions with which a TF is physically associated, referred to as TF binding sites (TFBSs), is an important step towards understanding its biological roles. The most common genome-wide assay for identifying TFBSs is ChIP-seq 14-16. In addition to highlighting potentially active regulatory DNA elements by direct measurement, ChIP-seq data can define DNA sequence motifs that can be used, often in conjunction with expression data and chromatin accessibility maps, to infer likely binding events in other cellular contexts without performing direct assays. Although motifs identified by ChIP-seq are often representative of direct binding, this is not always the case, as co-occurrence of other TFs could ...

Expanded encyclopaedias of DNA elements in the human and mouse genomes

“…These new data not only expand our knowledge of the binding patterns of TFs, but also reveal patterns of extensive co-occupancy among human TFs. Furthermore, the integration of ENCODE TF binding elements with chromatin and RNA transcription data provides connections with key biological features of promoters and distal enhancers and insights into the organization of chromatin loops and gene domains 10 .…”

“…Across multiple data types, the increase in the scale of experimental data has provided new insights into genome organization and function, and catalysed new capabilities for deriving biological understandings and principles, as illustrated below and detailed in accompanying papers [7][8][9][10][11][12][13][14][15][16] . In summary, we:…”

“…• Describe an expansive new genomic compartment of DNA elements that encode recognition sites for RNA-binding proteins, providing new insights into post-transcriptional regulation 9 . • Deeply map the co-occupancy patterns of human transcription factors in reference cell types and connect these with key biological features of promoters and distal enhancers 10 . • Greatly increase the cell and tissue range, genomic resolution, and biological annotation of human DNase I-hypersensitive sites 11 and transcription factor footprints 12 .…”

Perspectives on ENCODE

“…An important part of ENCODE 3 is that the regulatory mapping efforts have now been integrated and synthesized into the first version of an encyclopedia, highlighting a registry of 0.9 million cCREs in human and 0.3 million cCREs in mouse. Details can be found in the accompanying ENCODE paper 8 and companion papers in this issue and other journals [9][10][11][12][13][14] .…”

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

“…A subset of DAPs was further classified into sequence-specific transcription factors (ssTFs; N = 117) and non-sequence-specific DAPs (nssDAPs; N = 85). ssTFs were conservatively defined as those that had an in vitro-derived motif in the Cis-BP database (Weirauch et al 2014), and nssDAPs were defined as DAPs without in vitro-derived motifs that had previously been characterized as non-sequence-specific chromatin regulators or transcription cofactors (Lambert et al 2018;Partridge et al 2020). As a second method to assess transcription factor associations, we used the protein interaction quantitation (PIQ) algorithm and in vitro-derived (SELEX, protein binding microarray, or B1H) motifs from 555 TFs in the Cis-BP database to identify DAP footprints that were present in ENCODE DNase I hypersensitivity (DHS) footprints (Supplemental Table S2; Sherwood et al 2014).…”