bims-crepig 2023-07-16 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023‒07‒16
29 papers selected by
Connor Rogerson
University of Cambridge

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila.
Ultra-long-range interactions between active regulatory elements.
RNA polymerase II dynamics shape enhancer-promoter interactions.
Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation.
Transcriptional network governing extraembryonic endoderm cell fate choice.
The Mediator complex regulates enhancer-promoter interactions.
The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks.
Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction.
Regulation of chromatin microphase separation by binding of protein complexes.
Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn.
Single-cell transcriptome atlas of Drosophila gastrula 2.0.
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation.
RNA polymerase II CTD is dispensable for transcription and required for termination in human cells.
Hidden modes of DNA binding by human nuclear receptors.
High-throughput Oligopaint screen identifies druggable 3D genome regulators.
Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.
G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture.
MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia.
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes.
DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.
Spontaneous Histone Exchange Between Nucleosomes.
An extended transcription factor regulatory network controls hepatocyte identity.
Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase.
Complementary Alu sequences mediate enhancer-promoter selectivity.
Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging.
Inferring regulators of cell identity in the human adult pancreas.
A novel transcription factor combination for direct reprogramming to a spontaneously contracting human cardiomyocyte-like state.
How enhancers regulate wavelike gene expression patterns.

Science. 2023 Jul 14. 381(6654): 198-204

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila.

Jelle Jacobs, Michaela Pagani, Christoph Wenzl, Alexander Stark.

Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors (CoRs) to silence transcription, even in the presence of activating cues. However, whether CoRs can dominantly silence all enhancers or display distinct specificities is unclear. In this work, we report that most enhancers in Drosophila can be repressed by only a subset of CoRs, and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Distinct TF motifs render enhancers more resistant or sensitive to specific CoRs, as we demonstrate by motif mutagenesis and addition. These CoR-enhancer compatibilities constitute an additional layer of regulatory specificity that allows differential regulation at close genomic distances and is indicative of distinct mechanisms of transcriptional repression.

DOI: https://doi.org/10.1126/science.adf6149
Genome Res. 2023 Jul 14. pii: gr.277567.122. [Epub ahead of print]

Ultra-long-range interactions between active regulatory elements.

Elias T Friman, Ilya M Flyamer, Davide Marenduzzo, Shelagh Boyle, Wendy A Bickmore.

Contacts between enhancers and promoters are thought to relate to their ability to activate transcription. Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture datasets and analyzed a collection of hundreds of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of tens of megabases in vertebrate and invertebrate genomes and that interactions correlate and change with activity. However, these ultra-long-range interactions are not dependent on RNA polymerase II transcription or individual transcription cofactors. Using simulations, we show that a model of chromatin and multivalent binding factors can give rise to long-range interactions via bridging-induced clustering. We propose that long-range interactions between cis-regulatory elements are driven by at least three distinct processes - cohesin-mediated loop extrusion, polycomb contacts, and clustering of active regions.

DOI: https://doi.org/10.1101/gr.277567.122
Nat Genet. 2023 Jul 10.

RNA polymerase II dynamics shape enhancer-promoter interactions.

Gilad Barshad, James J Lewis, Alexandra G Chivu, Abderhman Abuhashem, Nils Krietenstein, Edward J Rice, Yitian Ma, Zhong Wang, Oliver J Rando, Anna-Katerina Hadjantonakis, Charles G Danko.

How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer-promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer-promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer-promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer-promoter communication.

DOI: https://doi.org/10.1038/s41588-023-01442-7
Mol Cell. 2023 Jul 10. pii: S1097-2765(23)00508-7. [Epub ahead of print]

Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation.

Bin Zheng, Sarah Gold, Marta Iwanaszko, Benjamin Charles Howard, Lu Wang, Ali Shilatifard.

  The BET family protein BRD4, which forms the CDK9-containing BRD4-PTEFb complex, is considered to be a master regulator of RNA polymerase II (Pol II) pause release. Because its tandem bromodomains interact with acetylated histone lysine residues, it has long been thought that BRD4 requires these bromodomains for its recruitment to chromatin and transcriptional regulatory function. Here, using rapid depletion and genetic complementation with domain deletion mutants, we demonstrate that BRD4 bromodomains are dispensable for Pol II pause release. A minimal, bromodomain-less C-terminal BRD4 fragment containing the PTEFb-interacting C-terminal motif (CTM) is instead both necessary and sufficient to mediate Pol II pause release in the absence of full-length BRD4. Although BRD4-PTEFb can associate with chromatin through acetyl recognition, our results indicate that a distinct, active BRD4-PTEFb population functions to regulate transcription independently of bromodomain-mediated chromatin association. These findings may enable more effective pharmaceutical modulation of BRD4-PTEFb activity.

Keywords:  BRD4; JQ1; PTEFb; Pol II; bromodomains; dBET6; elongation; pause release; rapid depletion

DOI:  https://doi.org/10.1016/j.molcel.2023.06.032
Dev Biol. 2023 Jul 07. pii: S0012-1606(23)00128-8. [Epub ahead of print]

Transcriptional network governing extraembryonic endoderm cell fate choice.

Paula Duyen Pham, Hanbin Lu, Han Han, Jeff Jiajing Zhou, Aarushi Madan, Wenqi Wang, Cornelis Murre, Ken W Y Cho.

  The mechanism by which transcription factor (TF) network instructs cell-type-specific transcriptional programs to drive primitive endoderm (PrE) progenitors to commit to parietal endoderm (PE) versus visceral endoderm (VE) cell fates remains poorly understood. To address the question, we analyzed the single-cell transcriptional signatures defining PrE, PE, and VE cell states during the onset of the PE-VE lineage bifurcation. By coupling with the epigenomic comparison of active enhancers unique to PE and VE cells, we identified GATA6, SOX17, and FOXA2 as central regulators for the lineage divergence. Transcriptomic analysis of cXEN cells, an in vitro model for PE cells, after the acute depletion of GATA6 or SOX17 demonstrated that these factors induce Mycn, imparting the self-renewal properties of PE cells. Concurrently, they suppress the VE gene program, including key genes like Hnf4a and Ttr, among others. We proceeded with RNA-seq analysis on cXEN cells with FOXA2 knockout, in conjunction with GATA6 or SOX17 depletion. We found FOXA2 acts as a potent suppressor of Mycn while simultaneously activating the VE gene program. The antagonistic gene regulatory activities of GATA6/SOX17 and FOXA2 in promoting alternative cell fates, and their physical co-bindings at the enhancers provide molecular insights to the plasticity of the PrE lineage. Finally, we show that the external cue, BMP signaling, promotes the VE cell fate by activation of VE TFs and repression of PE TFs including GATA6 and SOX17. These data reveal a putative core gene regulatory module that underpins PE and VE cell fate choice.

Keywords:  BMP signaling; Degron tags; FoxA2; Gata6; Mycn; Parietal endoderm; Primitive endoderm; Sox17; Transcription factors; Visceral endoderm

DOI:  https://doi.org/10.1016/j.ydbio.2023.07.002
Nat Struct Mol Biol. 2023 Jul 10.

The Mediator complex regulates enhancer-promoter interactions.

Shyam Ramasamy, Abrar Aljahani, Magdalena A Karpinska, T B Ngoc Cao, Taras Velychko, J Neos Cruz, Michael Lidschreiber, A Marieke Oudelaar.

Enhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy at enhancers. Together, our results indicate that the Mediator and Cohesin complexes contribute to enhancer-promoter interactions and provide insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.

DOI: https://doi.org/10.1038/s41594-023-01027-2
Nat Commun. 2023 07 12. 14(1): 4135

The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.

Zheng Li, Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolomé, Suhua Feng, Yasaman Jami-Alahmadi, Xinyi Wang, James Wohlschlegel, Sylvain Bischof, Jeff A Long, Steven E Jacobsen.

MORPHEUS' MOLECULE1 (MOM1) is an Arabidopsis factor previously shown to mediate transcriptional silencing independent of major DNA methylation changes. Here we find that MOM1 localizes with sites of RNA-directed DNA methylation (RdDM). Tethering MOM1 with an artificial zinc finger to an unmethylated FWA promoter leads to establishment of DNA methylation and FWA silencing. This process is blocked by mutations in components of the Pol V arm of the RdDM machinery, as well as by mutation of MICRORCHIDIA 6 (MORC6). We find that at some endogenous RdDM sites, MOM1 is required to maintain DNA methylation and a closed chromatin state. In addition, efficient silencing of newly introduced FWA transgenes is impaired in the mom1 mutant. In addition to RdDM sites, we identify a group of MOM1 peaks at active chromatin near genes that colocalized with MORC6. These findings demonstrate a multifaceted role of MOM1 in genome regulation.

DOI: https://doi.org/10.1038/s41467-023-39751-4
Nat Methods. 2023 Jul 13.

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks.

Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, Stein Aerts.

Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .

DOI: https://doi.org/10.1038/s41592-023-01938-4
Nat Commun. 2023 07 10. 14(1): 4081

Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction.

Cuifang Liu, Juan Yu, Aoqun Song, Min Wang, Jiansen Hu, Ping Chen, Jicheng Zhao, Guohong Li.

During cell renewal, epigenetic information needs to be precisely restored to maintain cell identity and genome integrity following DNA replication. The histone mark H3K27me3 is essential for the formation of facultative heterochromatin and the repression of developmental genes in embryonic stem cells. However, how the restoration of H3K27me3 is precisely achieved following DNA replication is still poorly understood. Here we employ ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We find that the restoration rate of H3K27me3 is highly correlated with dense chromatin states. In addition, we reveal that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressed genes and the restoration rate of H3K27me3 on nascent DNA is greatly compromised after partial depletion of H1. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication.

DOI: https://doi.org/10.1038/s41467-023-39846-y
Elife. 2023 07 12. pii: e82983. [Epub ahead of print]12

Regulation of chromatin microphase separation by binding of protein complexes.

Omar Adame-Arana, Gaurav Bajpai, Dana Lorber, Talila Volk, Samuel Safran.

  We show evidence of the association of RNA polymerase II (RNAP) with chromatin in a core-shell organization, reminiscent of microphase separation where the cores comprise dense chromatin and the shell, RNAP and chromatin with low density. These observations motivate our physical model for the regulation of core-shell chromatin organization. Here, we model chromatin as a multiblock copolymer, comprising active and inactive regions (blocks) that are both in poor solvent and tend to be condensed in the absence of binding proteins. However, we show that the solvent quality for the active regions of chromatin can be regulated by the binding of protein complexes (e.g., RNAP and transcription factors). Using the theory of polymer brushes, we find that such binding leads to swelling of the active chromatin regions which in turn modifies the spatial organization of the inactive regions. In addition, we use simulations to study spherical chromatin micelles, whose cores comprise inactive regions and shells comprise active regions and bound protein complexes. In spherical micelles the swelling increases the number of inactive cores and controls their size. Thus, genetic modifications affecting the binding strength of chromatin-binding protein complexes may modulate the solvent quality experienced by chromatin and regulate the physical organization of the genome.

Keywords:  D. melanogaster; active and inactive chromatin; chromatin organization; chromatin-binding protein complexes; chromosomes; gene expression; microphase separation; physics of living systems

DOI:  https://doi.org/10.7554/eLife.82983
Cell Rep. 2023 Jul 11. pii: S2211-1247(23)00814-8. [Epub ahead of print]42(7): 112803

Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn.

Aki K Braceros, Megan D Schertzer, Arina Omer, Jackson B Trotman, Eric S Davis, Jill M Dowen, Douglas H Phanstiel, Erez Lieberman Aiden, J Mauro Calabrese.

  During mouse embryogenesis, expression of the long non-coding RNA (lncRNA) Airn leads to gene repression and recruitment of Polycomb repressive complexes (PRCs) to varying extents over a 15-Mb domain. The mechanisms remain unclear. Using high-resolution approaches, we show in mouse trophoblast stem cells that Airn expression induces long-range changes to chromatin architecture that coincide with PRC-directed modifications and center around CpG island promoters that contact the Airn locus even in the absence of Airn expression. Intensity of contact between the Airn lncRNA and chromatin correlated with underlying intensity of PRC recruitment and PRC-directed modifications. Deletion of CpG islands that contact the Airn locus altered long-distance repression and PRC activity in a manner that correlated with changes in chromatin architecture. Our data imply that the extent to which Airn expression recruits PRCs to chromatin is controlled by DNA regulatory elements that modulate proximity of the Airn lncRNA product to its target DNA.

Keywords:  Airn; CHART-seq; CP: Molecular biology; ChIP-seq; Hi-C; Xist; chromatin archtecture; epigenetics; long noncoding RNA; polycomb repressive complex; transcription

DOI:  https://doi.org/10.1016/j.celrep.2023.112803
Cell Rep. 2023 Jul 03. pii: S2211-1247(23)00718-0. [Epub ahead of print] 112707

Single-cell transcriptome atlas of Drosophila gastrula 2.0.

Shunta Sakaguchi, Sonoko Mizuno, Yasushi Okochi, Chiharu Tanegashima, Osamu Nishimura, Tadashi Uemura, Mitsutaka Kadota, Honda Naoki, Takefumi Kondo.

  During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing accurate spatial and lineage information are still lacking. Here, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. We find that the expression profiles of plasma-membrane-related genes, but not those of transcription-factor genes, represent each germ layer, supporting the nonequivalent contribution of each transcription-factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstruct the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.

Keywords:  CP: Developmental biology; ▪▪▪

DOI:  https://doi.org/10.1016/j.celrep.2023.112707
Sci Adv. 2023 Jul 14. 9(28): eadf9460

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation.

Laura M Pikkupeura, Raul B Bressan, Jordi Guiu, Yun Chen, Martti Maimets, Daniela Mayer, Pawel J Schweiger, Stine L Hansen, Grzegorz J Maciag, Hjalte L Larsen, Kadi Lõhmussaar, Marianne Terndrup Pedersen, Joji M Yap Teves, Jette Bornholdt, Vladimir Benes, Albin Sandelin, Kim B Jensen.

During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue. While the morphological changes associated with the transition are well characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation, and three-dimensional (3D) chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility, and methylation between the two cellular states. Using integrative analyses, we identified sustained Yes-Associated Protein (YAP) transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization and likely to be coordinated by changes in extracellular matrix composition. Together, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

DOI: https://doi.org/10.1126/sciadv.adf9460
EMBO Rep. 2023 Jul 10. e56150

RNA polymerase II CTD is dispensable for transcription and required for termination in human cells.

Yousra Yahia, Alexia Pigeot, Amal Zine El Aabidine, Nilay Shah, Nezih Karasu, Ignasi Forné, Stefan Krebs, Helmut Blum, Cyril Esnault, Tom Sexton, Axel Imhof, Dirk Eick, Jean-Christophe Andrau.

  The largest subunit of RNA polymerase (Pol) II harbors an evolutionarily conserved C-terminal domain (CTD), composed of heptapeptide repeats, central to the transcriptional process. Here, we analyze the transcriptional phenotypes of a CTD-Δ5 mutant that carries a large CTD truncation in human cells. Our data show that this mutant can transcribe genes in living cells but displays a pervasive phenotype with impaired termination, similar to but more severe than previously characterized mutations of CTD tyrosine residues. The CTD-Δ5 mutant does not interact with the Mediator and Integrator complexes involved in the activation of transcription and processing of RNAs. Examination of long-distance interactions and CTCF-binding patterns in CTD-Δ5 mutant cells reveals no changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate onto DNA but becomes pervasive once engaged in transcription, resulting in a defect in termination.

Keywords:  Pol II interactome; RNA polymerase II (Pol II); carboxy-terminal domain (CTD); mammalian transcription; termination

DOI:  https://doi.org/10.15252/embr.202256150
Nat Commun. 2023 Jul 13. 14(1): 4179

Hidden modes of DNA binding by human nuclear receptors.

Devesh Bhimsaria, José A Rodríguez-Martínez, Jacqui L Mendez-Johnson, Debostuti Ghoshdastidar, Ashwin Varadarajan, Manju Bansal, Danette L Daniels, Parameswaran Ramanathan, Aseem Z Ansari.

Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that have central roles in cellular function. Their malfunction is linked to numerous diseases, and the ability to modulate their activity with synthetic ligands has yielded 16% of all FDA-approved drugs. NRs regulate distinct gene networks, however they often function from genomic sites that lack known binding motifs. Here, to annotate genomic binding sites of known and unexamined NRs more accurately, we use high-throughput SELEX to comprehensively map DNA binding site preferences of all full-length human NRs, in complex with their ligands. Furthermore, to identify non-obvious binding sites buried in DNA-protein interactomes, we develop MinSeq Find, a search algorithm based on the MinTerm concept from electrical engineering and digital systems design. The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cells. MinSeqs also unmask binding sites created or disrupted by 52,106 single-nucleotide polymorphisms associated with human diseases. By implicating druggable NRs as hidden drivers of multiple human diseases, our results not only reveal new biological roles of NRs, but they also provide a resource for drug-repurposing and precision medicine.

DOI: https://doi.org/10.1038/s41467-023-39577-0
Nature. 2023 Jul 12.

High-throughput Oligopaint screen identifies druggable 3D genome regulators.

Daniel S Park, Son C Nguyen, Randi Isenhart, Parisha P Shah, Wonho Kim, R Jordan Barnett, Aditi Chandra, Jennifer M Luppino, Jailynn Harke, May Wai, Patrick J Walsh, Richard J Abdill, Rachel Yang, Yemin Lan, Sora Yoon, Rebecca Yunker, Masato T Kanemaki, Golnaz Vahedi, Jennifer E Phillips-Cremins, Rajan Jain, Eric F Joyce.

The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions1-3. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.

DOI: https://doi.org/10.1038/s41586-023-06340-w
Nat Commun. 2023 Jul 14. 14(1): 4129

Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.

Nozomu Takata, Jason M Miska, Marc A Morgan, Priyam Patel, Leah K Billingham, Neha Joshi, Matthew J Schipma, Zachary J Dumar, Nikita R Joshi, Alexander V Misharin, Ryan B Embry, Luciano Fiore, Peng Gao, Lauren P Diebold, Gregory S McElroy, Ali Shilatifard, Navdeep S Chandel, Guillermo Oliver.

Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. We report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing, we identify specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determine that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we show that removal of Glucose transporter 1 and Lactate dehydrogenase A gene activity from developing retinal progenitors arrests eye morphogenesis. Surprisingly, we uncover that lactate-mediated upregulation of key eye-field transcription factors is controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase activity. Our results identify an unexpected bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.

DOI: https://doi.org/10.1038/s41467-023-39672-2
Nucleic Acids Res. 2023 Jul 10. pii: gkad588. [Epub ahead of print]

G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture.

Jun Yuan, Xiaomei He, Yinsheng Wang.

High-order chromatin organization plays an important role in biological processes and disease development. Previous studies revealed a widespread occurrence of guanine quadruplex (G4) structures in the human genome, with enrichment in gene regulatory regions, especially in promoters. However, it remains unclear whether G4 structures contribute to RNA polymerase II (RNAPII)-mediated long-range DNA interactions and transcription activity. In this study, we conducted an intuitive overlapping analysis of previously published RNAPII ChIA-PET (chromatin interaction analysis with paired-end tag) and BG4 ChIP-seq (chromatin immunoprecipitation followed by sequencing using a G4 structure-specific antibody) data. We observed a strong positive correlation between RNAPII-linked DNA loops and G4 structures in chromatin. Additionally, our RNAPII HiChIP-seq (in situ Hi-C followed by ChIP-seq) results showed that treatment of HepG2 cells with pyridostatin (PDS), a small-molecule G4-binding ligand, could diminish RNAPII-linked long-range DNA contacts, with more pronounced diminutions being observed for those contacts involving G4 structure loci. RNA sequencing data revealed that PDS treatment modulates the expression of not only genes with G4 structures in their promoters, but also those with promoters being connected with distal G4s through RNAPII-linked long-range DNA interactions. Together, our data substantiate the function of DNA G4s in RNAPII-associated DNA looping and transcription regulation.

DOI: https://doi.org/10.1093/nar/gkad588
Elife. 2023 07 10. pii: e82597. [Epub ahead of print]12

MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia.

Courtney A Copeland, Benjamin A Olenchock, David Ziehr, Sarah McGarrity, Kevin Leahy, Jamey D Young, Joseph Loscalzo, William M Oldham.

  Hypoxia requires metabolic adaptations to sustain energetically demanding cellular activities. While the metabolic consequences of hypoxia have been studied extensively in cancer cell models, comparatively little is known about how primary cell metabolism responds to hypoxia. Thus, we developed metabolic flux models for human lung fibroblast and pulmonary artery smooth muscle cells proliferating in hypoxia. Unexpectedly, we found that hypoxia decreased glycolysis despite activation of hypoxia-inducible factor 1α (HIF-1α) and increased glycolytic enzyme expression. While HIF-1α activation in normoxia by prolyl hydroxylase (PHD) inhibition did increase glycolysis, hypoxia blocked this effect. Multi-omic profiling revealed distinct molecular responses to hypoxia and PHD inhibition, and suggested a critical role for MYC in modulating HIF-1α responses to hypoxia. Consistent with this hypothesis, MYC knockdown in hypoxia increased glycolysis and MYC over-expression in normoxia decreased glycolysis stimulated by PHD inhibition. These data suggest that MYC signaling in hypoxia uncouples an increase in HIF-dependent glycolytic gene transcription from glycolytic flux.

Keywords:  MYC; biochemistry; cell biology; chemical biology; human; hypoxia; hypoxia-inducible factor; metabolic flux analysis; prolyl hydroxylase

DOI:  https://doi.org/10.7554/eLife.82597
Nat Commun. 2023 Jul 14. 14(1): 4214

Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes.

Kristina M Garske, Asha Kar, Caroline Comenho, Brunilda Balliu, David Z Pan, Yash V Bhagat, Gregory Rosenberg, Amogha Koka, Sankha Subhra Das, Zong Miao, Janet S Sinsheimer, Jaakko Kaprio, Kirsi H Pietiläinen, Päivi Pajukanta.

Obesity-induced adipose tissue dysfunction can cause low-grade inflammation and downstream obesity comorbidities. Although preadipocytes may contribute to this pro-inflammatory environment, the underlying mechanisms are unclear. We used human primary preadipocytes from body mass index (BMI) -discordant monozygotic (MZ) twin pairs to generate epigenetic (ATAC-sequence) and transcriptomic (RNA-sequence) data for testing whether increased BMI alters the subnuclear compartmentalization of open chromatin in the twins' preadipocytes, causing downstream inflammation. Here we show that the co-accessibility of open chromatin, i.e. compartmentalization of chromatin activity, is altered in the higher vs lower BMI MZ siblings for a large subset ( ~ 88.5 Mb) of the active subnuclear compartments. Using the UK Biobank we show that variants within these regions contribute to systemic inflammation through interactions with BMI on C-reactive protein. In summary, open chromatin co-accessibility in human preadipocytes is disrupted among the higher BMI siblings, suggesting a mechanism how obesity may lead to inflammation via gene-environment interactions.

DOI: https://doi.org/10.1038/s41467-023-39919-y
PLoS Comput Biol. 2023 Jul 13. 19(7): e1011307

DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.

Tong Liu, Zheng Wang.

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein. The ChIA-PET experiments have been applied to explore the key roles of different protein factors in chromatin folding and transcription regulation. However, compared with widely available Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature. A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab experiments. Here we present DeepChIA-PET, a supervised deep learning approach that can accurately predict ChIA-PET interactions by learning the latent relationships between ChIA-PET and two widely used data types: Hi-C and ChIP-seq. We trained our deep models with CTCF-mediated ChIA-PET of GM12878 as ground truth, and the deep network contains 40 dilated residual convolutional blocks. We first showed that DeepChIA-PET with only Hi-C as input significantly outperforms Peakachu, another computational method for predicting ChIA-PET from Hi-C but using random forests. We next proved that adding ChIP-seq as one extra input does improve the classification performance of DeepChIA-PET, but Hi-C plays a more prominent role in DeepChIA-PET than ChIP-seq. Our evaluation results indicate that our learned models can accurately predict not only CTCF-mediated ChIA-ET in GM12878 and HeLa but also non-CTCF ChIA-PET interactions, including RNA polymerase II (RNAPII) ChIA-PET of GM12878, RAD21 ChIA-PET of GM12878, and RAD21 ChIA-PET of K562. In total, DeepChIA-PET is an accurate tool for predicting the ChIA-PET interactions mediated by various chromatin-associated proteins from different cell types.

DOI: https://doi.org/10.1371/journal.pcbi.1011307
J Biol Chem. 2023 Jul 11. pii: S0021-9258(23)02065-3. [Epub ahead of print] 105037

Spontaneous Histone Exchange Between Nucleosomes.

Subhra Kanti Das, Mai Thao Huynh, Tae-Hee Lee.

  The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4)2 tetramer. The strong yet flexible DNA-histone interactions are the physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions also implies that nucleosomes dissociate DNA-histone contacts both transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At high nucleosome concentration, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely event, where nucleosomes could act as their own histone chaperone. This spontaneous histone exchange could serve as a mechanism for maintaining overall chromatin stability, although it has never been reported. Here we employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes on a time scale of a few tens of seconds at a physiological nucleosome concentration. We show that the rate of histone exchange increases at a higher monovalent salt concentration, with histone-acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support the notion of histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.

Keywords:  DNA methylation; histone acetylation; histone chaperone; histone exchange; nucleosome; single-molecule FRET

DOI:  https://doi.org/10.1016/j.jbc.2023.105037
EMBO Rep. 2023 Jul 10. e57020

An extended transcription factor regulatory network controls hepatocyte identity.

Julie Dubois-Chevalier, Céline Gheeraert, Alexandre Berthier, Clémence Boulet, Vanessa Dubois, Loïc Guille, Marie Fourcot, Guillemette Marot, Karine Gauthier, Laurent Dubuquoy, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute.

  Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID)CONNECT TFs. Besides controlling identity effector genes, Hep-IDCONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-IDCONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-IDCONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-IDCONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammation-induced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC.

Keywords:  cell identity; core regulatory network; hepatocyte dedifferentiation; liver disease; transcription factors

DOI:  https://doi.org/10.15252/embr.202357020
Science. 2023 Jul 14. 381(6654): eadf8822

Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase.

Fei Huang, Xiao Luo, Yang Ou, Zhaoxu Gao, Qiming Tang, Zhenzhen Chu, Xinguang Zhu, Yuehui He.

Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.

DOI: https://doi.org/10.1126/science.adf8822
Nature. 2023 Jul 12.

Complementary Alu sequences mediate enhancer-promoter selectivity.

Liang Liang, Changchang Cao, Lei Ji, Zhaokui Cai, Di Wang, Rong Ye, Juan Chen, Xiaohua Yu, Jie Zhou, Zhibo Bai, Ruoyan Wang, Xianguang Yang, Ping Zhu, Yuanchao Xue.

Enhancers determine spatiotemporal gene expression programs by engaging with long-range promoters1-4. However, it remains unknown how enhancers find their cognate promoters. We recently developed a RNA in situ conformation sequencing technology to identify enhancer-promoter connectivity using pairwise interacting enhancer RNAs and promoter-derived noncoding RNAs5,6. Here we apply this technology to generate high-confidence enhancer-promoter RNA interaction maps in six additional cell lines. Using these maps, we discover that 37.9% of the enhancer-promoter RNA interaction sites are overlapped with Alu sequences. These pairwise interacting Alu and non-Alu RNA sequences tend to be complementary and potentially form duplexes. Knockout of Alu elements compromises enhancer-promoter looping, whereas Alu insertion or CRISPR-dCasRx-mediated Alu tethering to unregulated promoter RNAs can create new loops to homologous enhancers. Mapping 535,404 noncoding risk variants back to the enhancer-promoter RNA interaction maps enabled us to construct variant-to-function maps for interpreting their molecular functions, including 15,318 deletions or insertions in 11,677 Alu elements that affect 6,497 protein-coding genes. We further demonstrate that polymorphic Alu insertion at the PTK2 enhancer can promote tumorigenesis. Our study uncovers a principle for determining enhancer-promoter pairing specificity and provides a framework to link noncoding risk variants to their molecular functions.

DOI: https://doi.org/10.1038/s41586-023-06323-x
Nat Aging. 2023 Jul 13.

Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging.

Robin W Yeo, Olivia Y Zhou, Brian L Zhong, Eric D Sun, Paloma Navarro Negredo, Surag Nair, Mahfuza Sharmin, Tyson J Ruetz, Mikaela Wilson, Anshul Kundaje, Alexander R Dunn, Anne Brunet.

The regenerative potential of brain stem cell niches deteriorates during aging. Yet the mechanisms underlying this decline are largely unknown. Here we characterize genome-wide chromatin accessibility of neurogenic niche cells in vivo during aging. Interestingly, chromatin accessibility at adhesion and migration genes decreases with age in quiescent neural stem cells (NSCs) but increases with age in activated (proliferative) NSCs. Quiescent and activated NSCs exhibit opposing adhesion behaviors during aging: quiescent NSCs become less adhesive, whereas activated NSCs become more adhesive. Old activated NSCs also show decreased migration in vitro and diminished mobilization out of the niche for neurogenesis in vivo. Using tension sensors, we find that aging increases force-producing adhesions in activated NSCs. Inhibiting the cytoskeletal-regulating kinase ROCK reduces these adhesions, restores migration in old activated NSCs in vitro, and boosts neurogenesis in vivo. These results have implications for restoring the migratory potential of NSCs and for improving neurogenesis in the aged brain.

DOI: https://doi.org/10.1038/s43587-023-00449-3
NAR Genom Bioinform. 2023 Sep;5(3): lqad068

Inferring regulators of cell identity in the human adult pancreas.

Lotte Vanheer, Federica Fantuzzi, San Kit To, Andrea Schiavo, Matthias Van Haele, Tessa Ostyn, Tine Haesen, Xiaoyan Yi, Adrian Janiszewski, Joel Chappell, Adrien Rihoux, Toshiaki Sawatani, Tania Roskams, Francois Pattou, Julie Kerr-Conte, Miriam Cnop, Vincent Pasque.

Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity and cell states in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. BHLHE41 depletion induced apoptosis in primary pancreatic islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity and cell states in the human adult pancreas.

DOI: https://doi.org/10.1093/nargab/lqad068
J Mol Cell Cardiol. 2023 Jul 06. pii: S0022-2828(23)00106-2. [Epub ahead of print]

A novel transcription factor combination for direct reprogramming to a spontaneously contracting human cardiomyocyte-like state.

Marisol Romero-Tejeda, Hananeh Fonoudi, Carly J Weddle, Jean-Marc DeKeyser, Brian Lenny, K Ashley Fetterman, Tarek Magdy, Yadav Sapkota, Conrad Epting, Paul W Burridge.

  The reprogramming of somatic cells to a spontaneously contracting cardiomyocyte-like state using defined transcription factors has proven successful in mouse fibroblasts. However, this process has been less successful in human cells, thus limiting the potential clinical applicability of this technology in regenerative medicine. We hypothesized that this issue is due to a lack of cross-species concordance between the required transcription factor combinations for mouse and human cells. To address this issue, we identified novel transcription factor candidates to induce cell conversion between human fibroblasts and cardiomyocytes, using the network-based algorithm Mogrify. We developed an automated, high-throughput method for screening transcription factor, small molecule, and growth factor combinations, utilizing acoustic liquid handling and high-content kinetic imaging cytometry. Using this high-throughput platform, we screened the effect of 4960 unique transcription factor combinations on direct conversion of 24 patient-specific primary human cardiac fibroblast samples to cardiomyocytes. Our screen revealed the combination of MYOCD, SMAD6, and TBX20 (MST) as the most successful direct reprogramming combination, which consistently produced up to 40% TNNT2+ cells in just 25 days. Addition of FGF2 and XAV939 to the MST cocktail resulted in reprogrammed cells with spontaneous contraction and cardiomyocyte-like calcium transients. Gene expression profiling of the reprogrammed cells also revealed the expression of cardiomyocyte associated genes. Together, these findings indicate that cardiac direct reprogramming in human cells can be achieved at similar levels to those attained in mouse fibroblasts. This progress represents a step forward towards the clinical application of the cardiac direct reprogramming approach.

Keywords:  Calcium cycling; Cardiomyocyte; Direct reprogramming; Fibroblast; High-throughput; Spontaneous contraction

DOI:  https://doi.org/10.1016/j.yjmcc.2023.06.005
Elife. 2023 Jul 11. pii: e84969. [Epub ahead of print]12

How enhancers regulate wavelike gene expression patterns.

Christine Mau, Heike Rudolf, Frederic Strobl, Benjamin Schmid, Timo Regensburger, Ralf Palmisano, Ernst H K Stelzer, Leila Taher, Ezzat El-Sherif.

  A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called 'enhancers'. Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expression patterns in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here we establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several Tribolium enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expression patterns (that we call 'dynamic enhancers') and enhancers that stabilizes gene expression patterns (that we call 'static enhancers'). However, more data is needed for a strong support for this or any other alternative models.

Keywords:  computational biology; developmental biology; systems biology

DOI:  https://doi.org/10.7554/eLife.84969