bims-crepig 2023-11-12 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–11–12
twenty-six papers selected by
Connor Rogerson, University of Cambridge

ZMYM2 controls human transposable element transcription through distinct co-regulatory complexes.
Global identification of SWI/SNF targets reveals compensation by EP400.
NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos.
GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers.
The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development.
Molecular basis for SOX2-dependent regulation of super-enhancer activity.
Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos.
Structure of the transcribing RNA polymerase II-Elongin complex.
Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity.
HNF1α maintains pancreatic α and β cell functions in primary human islets.
Multi-level regulation of even-skipped stripes by the ubiquitous factor Zelda.
PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.
Transcriptional reprogramming by mutated IRF4 in lymphoma.
RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes.
eRNA co-expression network uncovers TF dependency and convergent cooperativity.
Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation.
Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations.
Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms.
Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants.
Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer.
Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease.
Scalable single-cell profiling of chromatin modifications with sciCUT&Tag.
scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.
Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements.
Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis.
Histone removal in sperm protects paternal chromosomes from premature division at fertilization.

Elife. 2023 11 07. pii: RP86669. [Epub ahead of print]12

ZMYM2 controls human transposable element transcription through distinct co-regulatory complexes.

Danielle J Owen, Elisa Aguilar-Martinez, Zongling Ji, Yaoyong Li, Andrew D Sharrocks.

  ZMYM2 is a zinc finger transcriptional regulator that plays a key role in promoting and maintaining cell identity. It has been implicated in several diseases such as congenital anomalies of the kidney where its activity is diminished and cancer where it participates in oncogenic fusion protein events. ZMYM2 is thought to function through promoting transcriptional repression and here we provide more evidence to support this designation. Here we studied ZMYM2 function in human cells and demonstrate that ZMYM2 is part of distinct chromatin-bound complexes including the established LSD1-CoREST-HDAC1 corepressor complex. We also identify new functional and physical interactions with ADNP and TRIM28/KAP1. The ZMYM2-TRIM28 complex forms in a SUMO-dependent manner and is associated with repressive chromatin. ZMYM2 and TRIM28 show strong functional similarity and co-regulate a large number of genes. However, there are no strong links between ZMYM2-TRIM28 binding events and nearby individual gene regulation. Instead, ZMYM2-TRIM28 appears to regulate genes in a more regionally defined manner within TADs where it can directly regulate co-associated retrotransposon expression. We find that different types of ZMYM2 binding complex associate with and regulate distinct subclasses of retrotransposons, with ZMYM2-ADNP complexes at SINEs and ZMYM2-TRIM28 complexes at LTR elements. We propose a model whereby ZMYM2 acts directly through retrotransposon regulation, which may then potentially affect the local chromatin environment and associated coding gene expression.

Keywords:  ADNP; TRIM28; ZMYM2; chromatin; chromosomes; gene expression; human; transcription; transposable element

DOI:  https://doi.org/10.7554/eLife.86669
Cell. 2023 Oct 29. pii: S0092-8674(23)01088-7. [Epub ahead of print]

Global identification of SWI/SNF targets reveals compensation by EP400.

Benjamin J E Martin, Eileen F Ablondi, Christine Goglia, Claudia A Mimoso, Piero R Espinel-Cabrera, Karen Adelman.

  Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.

Keywords:  BRG1; EP400; PRO-seq; RNAPII; SWI/SNF; chromatin accessibility; chromatin remodeling; combination therapies; epigenetic regulators; transcription

DOI:  https://doi.org/10.1016/j.cell.2023.10.006
Cell Res. 2023 Nov 07.

NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos.

Fangnong Lai, Lijia Li, Xiaoyu Hu, Bofeng Liu, Ziqi Zhu, Ling Liu, Qiang Fan, Huabin Tian, Kai Xu, Xukun Lu, Qing Li, Kong Feng, Lijuan Wang, Zili Lin, Hongyu Deng, Jinsong Li, Wei Xie.

Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to the inner cell mass (ICM) where pluripotent epiblast arises, and extraembryonic trophectoderm. However, how ZGA is connected to the first lineage segregation in mammalian embryos remains elusive. Here, we investigated the role of nuclear receptor (NR) transcription factors (TFs), whose motifs are highly enriched and accessible from the 2-cell (2C) to 8-cell (8C) stages in mouse embryos. We found that NR5A2, an NR TF strongly induced upon ZGA, was required for this connection. Upon Nr5a2 knockdown or knockout, embryos developed beyond 2C normally with the zygotic genome largely activated. However, 4-8C-specific gene activation was substantially impaired and Nr5a2-deficient embryos subsequently arrested at the morula stage. Genome-wide chromatin binding analysis showed that NR5A2-bound cis-regulatory elements in both 2C and 8C embryos are strongly enriched for B1 elements where its binding motif is embedded. NR5A2 was not required for the global opening of its binding sites in 2C embryos but was essential to the opening of its 8C-specific binding sites. These 8C-specific, but not 2C-specific, binding sites are enriched near genes involved in blastocyst and stem cell regulation, and are often bound by master pluripotency TFs in blastocysts and embryonic stem cells (ESCs). Importantly, NR5A2 regulated key pluripotency genes Nanog and Pou5f1/Oct4, and primitive endoderm regulatory genes including Gata6 among many early ICM genes, as well as key trophectoderm regulatory genes including Tead4 and Gata3 at the 8C stage. By contrast, master pluripotency TFs NANOG, SOX2, and OCT4 targeted both early and late ICM genes in mouse ESCs. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that bridges ZGA to the first lineage segregation during mouse early development.

DOI: https://doi.org/10.1038/s41422-023-00887-z
Nat Cell Biol. 2023 Nov;25(11): 1704-1715

GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers.

Liat Ravid Lustig, Abhishek Sampath Kumar, Till Schwämmle, Ilona Dunkel, Gemma Noviello, Elodie Limberg, Raha Weigert, Guido Pacini, René Buschow, Afrah Ghauri, Maximilian Stötzel, Lars Wittler, Alexander Meissner, Edda G Schulz.

X-chromosome inactivation (XCI) balances gene expression between the sexes in female mammals. Shortly after fertilization, upregulation of Xist RNA from one X chromosome initiates XCI, leading to chromosome-wide gene silencing. XCI is maintained in all cell types, except the germ line and the pluripotent state where XCI is reversed. The mechanisms triggering Xist upregulation have remained elusive. Here we identify GATA transcription factors as potent activators of Xist. Through a pooled CRISPR activation screen in murine embryonic stem cells, we demonstrate that GATA1, as well as other GATA transcription factors can drive ectopic Xist expression. Moreover, we describe GATA-responsive regulatory elements in the Xist locus bound by different GATA factors. Finally, we show that GATA factors are essential for XCI induction in mouse preimplantation embryos. Deletion of GATA1/4/6 or GATA-responsive Xist enhancers in mouse zygotes effectively prevents Xist upregulation. We propose that the activity or complete absence of various GATA family members controls initial Xist upregulation, XCI maintenance in extra-embryonic lineages and XCI reversal in the epiblast.

DOI: https://doi.org/10.1038/s41556-023-01266-x
Genetics. 2023 Nov 09. pii: iyad196. [Epub ahead of print]

The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development.

Matthew J Niederhuber, Mary Leatham-Jensen, Daniel J McKay.

  Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of nucleosome remodelers in control of dynamic enhancer activity. We find that the Drosophila SWI/SNF complex, BAP, is required for repression of a temporally dynamic enhancer, brdisc. Contrary to expectations, we find that the BAP-specific subunit Osa is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels of brdisc activity when the enhancer is normally active. Genome-wide profiling reveals that Osa directly binds brdisc as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. Transgenic reporter analyses demonstrate that Osa is required for activation and for constraint of different sets of target enhancers in the same cells. Moreover, Osa loss results in hyperactivation of the Notch ligand Delta and development of ectopic sensory structures patterned by Notch signaling early in development. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.

Keywords:  chromatin; developmental gene regulation; enhancer; nucleosome remodeler

DOI:  https://doi.org/10.1093/genetics/iyad196
Nucleic Acids Res. 2023 Nov 01. pii: gkad908. [Epub ahead of print]

Molecular basis for SOX2-dependent regulation of super-enhancer activity.

Wanki Yoo, Yi Wei Song, Jihyun Kim, Jihye Ahn, Jaehoon Kim, Yongdae Shin, Je-Kyung Ryu, Kyeong Kyu Kim.

Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn't fully understood. To address SOX2's role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078's enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.

DOI: https://doi.org/10.1093/nar/gkad908
Elife. 2023 11 07. pii: e85997. [Epub ahead of print]12

Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos.

Sahla Syed, Yifei Duan, Bomyi Lim.

  It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the overall competency of the enhancer has yet to be fully understood. In this study, we utilized the MS2-MCP live imaging technique to quantitatively analyze the regulatory logic of the snail distal enhancer in early Drosophila embryos. Through systematic modulation of Dorsal and Twist binding motifs in this enhancer, we found that a mutation in any one of these binding sites causes a drastic reduction in transcriptional amplitude, resulting in a reduction in mRNA production of the target gene. We provide evidence of synergy, such that multiple binding sites with moderate affinities cooperatively recruit more TFs to drive stronger transcriptional activity than a single site. Moreover, a Hidden Markov-based stochastic model of transcription reveals that embryos with mutated binding sites have a higher probability of returning to the inactive promoter state. We propose that TF-DNA binding regulates spatial and temporal gene expression and drives robust pattern formation by modulating transcriptional kinetics and tuning bursting rates.

Keywords:  D. melanogaster; Drosophila embryos; MS2-MCP; chromosomes; developmental biology; gene expression; hidden-markov model; live imaging; transcription bursting; transcription factors; transcription kinetics

DOI:  https://doi.org/10.7554/eLife.85997
Nat Struct Mol Biol. 2023 Nov 06.

Structure of the transcribing RNA polymerase II-Elongin complex.

Ying Chen, Goran Kokic, Christian Dienemann, Olexandr Dybkov, Henning Urlaub, Patrick Cramer.

Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.

DOI: https://doi.org/10.1038/s41594-023-01138-w
Nat Commun. 2023 Nov 06. 14(1): 6943

Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity.

Zhi Liu, Dong-Sung Lee, Yuqiong Liang, Ye Zheng, Jesse R Dixon.

Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

DOI: https://doi.org/10.1038/s41467-023-42647-y
JCI Insight. 2023 Nov 09. pii: e170884. [Epub ahead of print]

HNF1α maintains pancreatic α and β cell functions in primary human islets.

Mollie F Qian, Romina J Bevacqua, Vy Mn Coykendall, Xiong Liu, Weichen Zhao, Charles A Chang, Xueying Gu, Xiao-Qing Dai, Patrick E MacDonald, Seung K Kim.

  HNF1A haploinsufficiency underlies the most common form of human monogenic diabetes (HNF1A-MODY) and hypomorphic HNF1A variants confer type 2 diabetes risk, but a lack of experimental systems for interrogating mature human islets has limited our understanding of how the transcription factor HNF1α regulates adult islet function. Here, we combined conditional genetic targeting in human islet cells, RNA sequencing, chromatin mapping with Cleavage Under Targets & Release Using Nuclease (CUT&RUN), and transplantation-based assays to determine HNF1α-regulated mechanisms in adult human pancreatic α and β cells. Short hairpin RNA-mediated (shRNA) suppression of HNF1A in primary human pseudoislets led to blunted insulin output and dysregulated glucagon secretion after transplantation in mice, recapitulating phenotypes observed in diabetic patients. These deficits corresponded with altered expression of genes encoding factors critical for hormone secretion, including calcium channel subunits, ATPase transporters and extracellular matrix constituents. Additionally, HNF1A loss led to upregulation of transcriptional repressors, providing evidence for a mechanism of transcriptional de-repression through HNF1α. CUT&RUN mapping of HNF1α DNA-binding sites in primary human islets imputed a subset of HNF1α-regulated genes as direct targets. These data elucidate mechanistic links between HNF1A loss and diabetic phenotypes in mature human α and β cells.

Keywords:  Beta cells; Diabetes; Endocrinology; Genetics; Monogenic diseases

DOI:  https://doi.org/10.1172/jci.insight.170884
Development. 2023 Nov 08. pii: dev.201860. [Epub ahead of print]

Multi-level regulation of even-skipped stripes by the ubiquitous factor Zelda.

Timothy R Bishop, Pinar Onal, Zhe Xu, Michael Zheng, Himari Gunasinghe, Chung-Yi Nien, Stephen Small, Rhea R Datta.

  The zinc-finger protein Zelda (Zld) is a key activator of zygotic transcription in early Drosophila embryos. Here we study Zld-dependent regulation of the seven-striped pattern of the pair-rule gene even-skipped (eve). Individual stripes are regulated by discrete enhancers that respond to broadly distributed activators; stripe boundaries are formed by localized repressors encoded by the gap genes. Zld's strongest effects are on stripes 2, 3, and 7, which are regulated by two enhancers in a 3.8 kb genomic fragment that includes the eve basal promoter. We show that Zld facilitates binding of the activator Bicoid and the gap repressors to this fragment, consistent with its proposed role as a pioneer protein. To test whether Zld's effects are direct, we mutated all canonical Zld sites in the 3.8 kb fragment, which reduced expression but failed to phenocopy the abolishment of stripes caused by removing Zld in trans. We show that Zld also indirectly regulates the eve stripes by establishing specific gap gene expression boundaries, which provides the embryonic spacing required for proper stripe activation.

Keywords:  Cis regulation; Cross-repression; Embryogenesis; Even-skipped; Transcriptional regulation; Zelda

DOI:  https://doi.org/10.1242/dev.201860
Nat Commun. 2023 Nov 03. 14(1): 7039

PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.

Anniina Vihervaara, Philip Versluis, Samu V Himanen, John T Lis.

RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. Pol II CTD is predominantly unphosphorylated from initiation until the early pause-region, whereas serine-2- and serine-5-phosphorylations are preferentially deposited in the later pause-region. Upon pause-release, serine-7-phosphorylation rapidly increases and dominates over the region where Pol II assembles elongation factors and accelerates to its full elongational speed. Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes.

DOI: https://doi.org/10.1038/s41467-023-42715-3
Nat Commun. 2023 Nov 07. 14(1): 6947

Transcriptional reprogramming by mutated IRF4 in lymphoma.

Nikolai Schleussner, Pierre Cauchy, Vedran Franke, Maciej Giefing, Oriol Fornes, Naveen Vankadari, Salam A Assi, Mariantonia Costanza, Marc A Weniger, Altuna Akalin, Ioannis Anagnostopoulos, Thomas Bukur, Marco G Casarotto, Frederik Damm, Oliver Daumke, Benjamin Edginton-White, J Christof M Gebhardt, Michael Grau, Stephan Grunwald, Martin-Leo Hansmann, Sylvia Hartmann, Lionel Huber, Eva Kärgel, Simone Lusatis, Daniel Noerenberg, Nadine Obier, Ulrich Pannicke, Anja Fischer, Anja Reisser, Andreas Rosenwald, Klaus Schwarz, Srinivasan Sundararaj, Andre Weilemann, Wiebke Winkler, Wendan Xu, Georg Lenz, Klaus Rajewsky, Wyeth W Wasserman, Peter N Cockerill, Claus Scheidereit, Reiner Siebert, Ralf Küppers, Rudolf Grosschedl, Martin Janz, Constanze Bonifer, Stephan Mathas.

Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.

DOI: https://doi.org/10.1038/s41467-023-41954-8
Mol Cell Biol. 2023 Nov 08. 1-15

RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes.

Preeti Khan, Priyabrata Singha, Ronita Nag Chaudhuri.

  Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.

Keywords:  H3K56; H4K16; RNA polymerase II; gene expression; histone acetylation; transcription regulation

DOI:  https://doi.org/10.1080/10985549.2023.2270912
Sci Rep. 2023 11 04. 13(1): 19085

eRNA co-expression network uncovers TF dependency and convergent cooperativity.

Seungha Alisa Lee, Katla Kristjánsdóttir, Hojoong Kwak.

Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of "bivalent" TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs.

DOI: https://doi.org/10.1038/s41598-023-46415-2
Mol Cell. 2023 Nov 02. pii: S1097-2765(23)00806-7. [Epub ahead of print]83(21): 3801-3817.e8

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation.

Corina Pascal, Jonathan Zonszain, Ofir Hameiri, Chen Gargi-Levi, Galit Lev-Maor, Luna Tammer, Tamar Levy, Anan Tarabeih, Vanessa Rachel Roy, Stav Ben-Salmon, Liraz Elbaz, Mireille Eid, Tamar Hakim, Salima Abu Rabe'a, Nana Shalev, Albert Jordan, Eran Meshorer, Gil Ast.

  Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.

Keywords:  ChIP-seq; GC content; H1 histones; PRO-seq; RNA polymerase II elongation; RNA-seq; alternative splicing; exon skipping; intron retention

DOI:  https://doi.org/10.1016/j.molcel.2023.10.003
Cell Syst. 2023 Nov 03. pii: S2405-4712(23)00299-5. [Epub ahead of print]

Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations.

Amy Briffa, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D Moore, David B Lyons, Martin Howard, Daniel Zilberman.

  Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.

Keywords:  DNA methylation dynamics; MET1; epigenetic inheritance; gene body methylation; population genetics; stochastic mathematical model

DOI:  https://doi.org/10.1016/j.cels.2023.10.007
PLoS Genet. 2023 Nov 08. 19(11): e1010492

Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms.

Sarah MacKinnon, Viviane Pagé, Jennifer J Chen, Ali Shariat-Panahi, Ryan D Martin, Terence E Hébert, Jason C Tanny.

Heterochromatin is a condensed chromatin structure that represses transcription of repetitive DNA elements and developmental genes, and is required for genome stability. Paradoxically, transcription of heterochromatic sequences is required for establishment of heterochromatin in diverse eukaryotic species. As such, components of the transcriptional machinery can play important roles in establishing heterochromatin. How these factors coordinate with heterochromatin proteins at nascent heterochromatic transcripts remains poorly understood. In the model eukaryote Schizosaccharomyces pombe (S. pombe), heterochromatin nucleation can be coupled to processing of nascent transcripts by the RNA interference (RNAi) pathway, or to other post-transcriptional mechanisms that are RNAi-independent. Here we show that the RNA polymerase II processivity factor Spt5 negatively regulates heterochromatin in S. pombe through its C-terminal domain (CTD). The Spt5 CTD is analogous to the CTD of the RNA polymerase II large subunit, and is comprised of multiple repeats of an amino acid motif that is phosphorylated by Cdk9. We provide evidence that genetic ablation of Spt5 CTD phosphorylation results in aberrant RNAi-dependent nucleation of heterochromatin at an ectopic location, as well as inappropriate spread of heterochromatin proximal to centromeres. In contrast, truncation of Spt5 CTD repeat number enhanced RNAi-independent heterochromatin formation and bypassed the requirement for RNAi. We relate these phenotypes to the known Spt5 CTD-binding factor Prf1/Rtf1. This separation of function argues that Spt5 CTD phosphorylation and CTD length restrict heterochromatin through unique mechanisms. More broadly, our findings argue that length and phosphorylation of the Spt5 CTD repeat array have distinct regulatory effects on transcription.

DOI: https://doi.org/10.1371/journal.pgen.1010492
EMBO J. 2023 Nov 08. e113595

Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants.

Loris Pratx, Philipp Wendering, Christian Kappel, Zoran Nikoloski, Isabel Bäurle.

  Plants often experience recurrent stressful events, for example, during heat waves. They can be primed by heat stress (HS) to improve the survival of more severe heat stress conditions. At certain genes, sustained expression is induced for several days beyond the initial heat stress. This transcriptional memory is associated with hyper-methylation of histone H3 lysine 4 (H3K4me3), but it is unclear how this is maintained for extended periods. Here, we determined histone turnover by measuring the chromatin association of HS-induced histone H3.3. Genome-wide histone turnover was not homogenous; in particular, H3.3 was retained longer at heat stress memory genes compared to HS-induced non-memory genes during the memory phase. While low nucleosome turnover retained H3K4 methylation, methylation loss did not affect turnover, suggesting that low nucleosome turnover sustains H3K4 methylation, but not vice versa. Together, our results unveil the modulation of histone turnover as a mechanism to retain environmentally mediated epigenetic modifications.

Keywords:  heat stress; histone retention; histone turnover; priming; transcriptional memory

DOI:  https://doi.org/10.15252/embj.2023113595
Elife. 2023 Nov 08. pii: RP89993. [Epub ahead of print]12

Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer.

Robert A Phillips, Ethan Wan, Jennifer J Tuscher, David Reid, Olivia R Drake, Lara Ianov, Jeremy J Day.

  Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 hr) enriched for inducible transcription factors and later changes (4 hr) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 hr, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 hr after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.

Keywords:  CRISPR; chromatin; enhancer; gene regulation; human; neuroscience; rat; striatum; transcription

DOI:  https://doi.org/10.7554/eLife.89993
Cell Rep. 2023 Nov 04. pii: S2211-1247(23)01404-3. [Epub ahead of print]42(11): 113392

Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease.

Min Yu, Yage Nie, Jiawen Yang, Shilun Yang, Rui Li, Varsha Rao, Xiaoyan Hu, Cheng Fang, Simeng Li, Dengpan Song, Fuyou Guo, Michael P Snyder, Howard Y Chang, Calvin J Kuo, Jin Xu, Junlei Chang.

  The blood-brain barrier (BBB) is primarily manifested by a variety of physiological properties of brain endothelial cells (ECs), but the molecular foundation for these properties remains incompletely clear. Here, we generate a comprehensive molecular atlas of adult brain ECs using acutely purified mouse ECs and integrated multi-omics. Using RNA sequencing (RNA-seq) and proteomics, we identify the transcripts and proteins selectively enriched in brain ECs and demonstrate that they are partially correlated. Using single-cell RNA-seq, we dissect the molecular basis of functional heterogeneity of brain ECs. Using integrative epigenomics and transcriptomics, we determine that TCF/LEF, SOX, and ETS families are top-ranked transcription factors regulating the BBB. We then validate the identified brain-EC-enriched proteins and transcription factors in normal mouse and human brain tissue and assess their expression changes in mice with Alzheimer's disease. Overall, we present a valuable resource with broad implications for regulation of the BBB and treatment of neurological disorders.

Keywords:  Alzheimer's disease; CP: Neuroscience; blood-brain barrier; endothelial cells; multi-omics; proteomics

DOI:  https://doi.org/10.1016/j.celrep.2023.113392
Nat Protoc. 2023 Nov 07.

Scalable single-cell profiling of chromatin modifications with sciCUT&Tag.

Derek H Janssens, Jacob E Greene, Steven J Wu, Christine A Codomo, Samuel S Minot, Scott N Furlan, Kami Ahmad, Steven Henikoff.

Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.

DOI: https://doi.org/10.1038/s41596-023-00905-9
Elife. 2023 Nov 10. pii: e87772. [Epub ahead of print]12

scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.

Yong-Il Kim, Rebecca O'Rourke, Charles G Sagerström.

  Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires resolution of mixed transcription and chromatin states.

Keywords:  developmental biology; zebrafish

DOI:  https://doi.org/10.7554/eLife.87772
Nature. 2023 Nov 08.

Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements.

Zhiming Li, Shoufu Duan, Xu Hua, Xiaowei Xu, Yinglu Li, Demis Menolfi, Hui Zhou, Chao Lu, Shan Zha, Stephen P Goff, Zhiguo Zhang.

In eukaryotes, repetitive DNA sequences are transcriptionally silenced through histone H3 lysine 9 trimethylation (H3K9me3). Loss of silencing of the repeat elements leads to genome instability and human diseases, including cancer and ageing1-3. Although the role of H3K9me3 in the establishment and maintenance of heterochromatin silencing has been extensively studied4-6, the pattern and mechanism that underlie the partitioning of parental H3K9me3 at replicating DNA strands are unknown. Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. Mechanistically, the human silencing hub (HUSH) complex interacts with the leading-strand DNA polymerase Pol ε and contributes to the asymmetric segregation of H3K9me3. Cells deficient in Pol ε subunits (POLE3 and POLE4) or the HUSH complex (MPP8 and TASOR) show compromised H3K9me3 asymmetry and increased LINE expression. Similar results were obtained in cells expressing a MPP8 mutant defective in H3K9me3 binding and in TASOR mutants with reduced interactions with Pol ε. These results reveal an unexpected mechanism whereby the HUSH complex functions with Pol ε to promote asymmetric H3K9me3 distribution at head-on LINEs to suppress their expression in S phase.

DOI: https://doi.org/10.1038/s41586-023-06711-3
Nat Commun. 2023 Nov 08. 14(1): 7209

Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis.

W Dean Pontius, Ellen S Hong, Zachary J Faber, Jeremy Gray, Craig D Peacock, Ian Bayles, Katreya Lovrenert, Diana H Chin, Berkley E Gryder, Cynthia F Bartels, Peter C Scacheri.

The metastasis-invasion cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor and ultimately grow within a secondary organ. Despite metastasis being a dynamic, multistep process, most omics studies to date have focused on comparing primary tumors to the metastatic deposits that define end-stage disease. This static approach means we lack information about the genomic and epigenomic changes that occur during the majority of tumor progression. One particularly understudied phase of tumor progression is metastatic colonization, during which cells must adapt to the new microenvironment of the secondary organ. Through temporal profiling of chromatin accessibility and gene expression in vivo, we identify dynamic changes in the epigenome that occur as osteosarcoma tumors form and grow within the lung microenvironment. Furthermore, we show through paired in vivo and in vitro CRISPR drop-out screens and pharmacological validation that the upstream transcription factors represent a class of metastasis-specific dependency genes. While current models depict lung colonization as a discrete step within the metastatic cascade, our study shows it is a defined trajectory through multiple epigenetic states, revealing new therapeutic opportunities undetectable with standard approaches.

DOI: https://doi.org/10.1038/s41467-023-42656-x
Science. 2023 Nov 10. 382(6671): 725-731

Histone removal in sperm protects paternal chromosomes from premature division at fertilization.

Raphaëlle Dubruille, Marion Herbette, Maxime Revel, Béatrice Horard, Ching-Ho Chang, Benjamin Loppin.

The global replacement of histones with protamines in sperm chromatin is widespread in animals, including insects, but its actual function remains enigmatic. We show that in the Drosophila paternal effect mutant paternal loss (pal), sperm chromatin retains germline histones H3 and H4 genome wide without impairing sperm viability. However, after fertilization, pal sperm chromosomes are targeted by the egg chromosomal passenger complex and engage into a catastrophic premature division in synchrony with female meiosis II. We show that pal encodes a rapidly evolving transition protein specifically required for the eviction of (H3-H4)2 tetramers from spermatid DNA after the removal of H2A-H2B dimers. Our study thus reveals an unsuspected role of histone eviction from insect sperm chromatin: safeguarding the integrity of the male pronucleus during female meiosis.

DOI: https://doi.org/10.1126/science.adh0037