Cofactors for estrogen receptor α (ERα) can modulate gene activity by posttranslationally modifying histone tails at target promoters. Here, we found that stimulation of ERα-positive cells with 17β-estradiol (E2) promotes global citrullination of histone H3 arginine 26 (H3R26) on chromatin. Additionally, we found that the H3 citrulline 26 (H3Cit26) modification colocalizes with ERα at decondensed chromatin loci surrounding the estrogen-response elements of target promoters. Surprisingly, we also found that citrullination of H3R26 is catalyzed by peptidylarginine deiminase (PAD) 2 and not by PAD4 (which citrullinates H4R3). Further, we showed that PAD2 interacts with ERα after E2 stimulation and that inhibition of either PAD2 or ERα strongly suppresses E2-induced H3R26 citrullination and ERα recruitment at target gene promoters. Collectively, our data suggest that E2 stimulation induces the recruitment of PAD2 to target promoters by ERα, whereby PAD2 then citrullinates H3R26, which leads to local chromatin decondensation and transcriptional activation. C ancers of the female reproductive system are serious human health problems, and estrogen plays a critical role in the initiation and progression of these diseases (1). Despite decades of research into mechanisms of 17β-estradiol (E2)-responsive gene transcription, our understanding of this process is far from complete (2). It is generally believed that, upon E2 binding, the nuclear hormone receptor estrogen receptor α (hereafter called ER) undergoes major structural reorganization, associates with estrogen-response elements (ERE) within target gene promoters, and recruits a range of coactivators including histone modification enzymes (3-6). After deposition, the resulting histone modifications can then modulate target gene activity by affecting local chromatin structure and regulating the accessibility of chromatin to transcription factors (2, 5, 7-9).Peptidylarginine deiminase (PAD) enzymes convert arginine and methylarginine residues to citrulline via a hydrolytic process termed citrullination or deimination (10, 11). We and others have shown that one such PAD, PAD4, appears to play a repressive role in regulating the expression of the canonical ER target gene, TFF1, via citrullination of histone H4 methylarginine 3, thus suggesting that PADs potentially function as ER cofactors (12, 13). Given that these previous studies were limited to a single ER target promoter, we chose to take a more comprehesive approach to test whether PAD-mediated histone tail citrullination may be more fundamental to ER target gene regulation than previously realized. In this study, we show that citrullination of histone H3R26 at ER targets is closely associated with gene transcription and that citrullination at this residue is catalyzed by PAD2, as opposed to PAD4. Additionally, we show that PAD2 interacts with ER and that PAD2-mediated citrullination of H3R26 likely facilitates transcriptional activation by creating an open, permissive, chromatin architecture around the EREs of E2-i...

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ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.

Summary Environmental exposures to chemically heterogeneous endocrine disrupting chemicals (EDCs) mimic or interfere with hormone actions, and negatively impact human health. Despite public interest and the prevalence of EDCs in the environment, methods to mechanistically classify these diverse chemicals in a high throughput (HT) manner have not been actively explored. Here, we describe the use of multi-parametric, HT microscopy-based platforms to examine how a prototypical EDC, Bisphenol A (BPA), and eighteen poorly studied analogs (BPXs), affect estrogen receptor (ER). We show that short exposure to BPA and most BPXs induce ERα and/or ERβ and change levels of target gene transcription. Many BPXs exhibit higher affinity for ERβ and act as ERβ antagonists, while they act largely as agonists or mixed agonists/antagonists on ERα. Finally, despite binding to ERs, some BPXs exhibit lower levels of activity. Our comprehensive view of BPXs activities allows their classification and evaluation of potential harmful effects. The strategy described here used on a large scale basis likely offers a faster, more cost-effective way to identify safer BPA alternatives.