HiChIRP reveals RNA-associated chromosome conformation

Mumbach, Maxwell R.; Granja, Jeffrey M.; Flynn, Ryan A.; Roake, Caitlin M.; Satpathy, Ansuman T.; Rubin, Adam J.; Qi, Yanyan; Jiang, Zhaozhao; Shams, Shadi; Louie, Brent; Guo, Jimmy K.; Gennert, David; Corces, M. Ryan; Khavari, Paul A.; Atianand, Maninjay K.; Artandi, Steven E.; Fitzgerald, Katherine A.; Greenleaf, William J.; Chang, Howard Y.

doi:10.1038/s41592-019-0407-x

Cited by 75 publications

(62 citation statements)

References 33 publications

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“…We performed HiChIP 12,13 in mESCs using antibodies against two opposing histone modifications: repressive H3K27me3 deposited by PcG or the enhancer-associated H3K27 acetylation (H3K27ac) 34 . We observed 1D signal enrichment that recapitulated publicly available H3K27me3 and H3K27ac ChIP-seq datasets 35 ( Figure 1A) and enrichment of 1D HiChIP signal at corresponding H3K27me3 and H3K27ac ChIP-seq peaks ( Supplementary Figure 1a).…”

Section: Resultsmentioning

confidence: 99%

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

Kraft

Yost

Murphy

et al. 2020

Preprint

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SUMMARYPolycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction1-5. This process is essential for embryonic stem cell (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling progressive spread of H3K27me3 on the linear genome6. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear7-10. Here, we apply H3K27me3 HiChIP11-13, a protein-directed chromosome conformation method, and optical reconstruction of chromatin architecture14 to profile long-range Polycomb-associated DNA loops that span tens to hundreds of megabases across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells7-10. We find that H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors revealed a coupling of Polycomb-associated genome architecture and H3K27me3 deposition evidenced by disruption of spatial contact between distant loci and altered H3K27me3 in cis, both locally and megabases away on the same chromosome. Further, we find that global alterations in PRC2 occupancy resulting from an EZH2 mutant15 selectively deficient in RNA binding is accompanied by loss of Polycomb-associated DNA looping. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Additionally, developmental gene loci have novel roles in Polycomb spreading, emerging as important architectural elements of the epigenome.

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Section: Resultsmentioning

confidence: 99%

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

Kraft

Yost

Murphy

et al. 2020

Preprint

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“…First, we explored RNA-DNA contacts captured in our data and compared their interactions to those of several ncRNAs that have been previously mapped to chromatin that reflect a range of known cis and trans localization patterns. Specifically, we observed strong enrichment of: (i) Xist over the inactive X (Xi), but not the active X chromosome (Xa) 46,56 (Figure 1B, Supplemental Figure 1D); (ii) Malat1 and U1 over actively transcribed RNA Polymerase II genes 57,58 ( Figure 1B); and (iii) telomerase RNA component (Terc) over telomere-proximal regions of all chromosomes (Supplemental Figure 1E) 59,60 .…”

Section: Rd-sprite Generates Accurate Maps Of Higher-order Rna and Dnmentioning

confidence: 99%

RNA promotes the formation of spatial compartments in the nucleus

Quinodoz

Bhat

Ollikainen

et al. 2020

Preprint

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The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions.

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“…Xist RNA is one of the well-studied lncRNAs involved in epigenetic regulation and gene silencing. It is a 17-kb lncRNA that is expressed from the inactive Xchromosome (Xi) [53], coating the entire X chromosome to repress gene expression through its ability to recruit repressive complexes such as polycomb complexes PRC1 and PRC2 [54][55][56]. In addition, Xist plays an important role in three-dimensional (3D) conformation and maintains the heterochromatin structure in Xi (Fig.…”

Section: Xist Rna Regulates Gene Silencing and Chromatin Conformationmentioning

confidence: 99%

Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

2020

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Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.

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HiChIRP reveals RNA-associated chromosome conformation

Cited by 75 publications

References 33 publications

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

RNA promotes the formation of spatial compartments in the nucleus

Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

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