bims-crepig 2024-07-14 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2024‒07‒14
33 papers selected by
Connor Rogerson, University of Cambridge

Polymerization of ZBTB transcription factors regulates chromatin occupancy.
Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.
Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.
A single-cell atlas of chromatin accessibility in mouse organogenesis.
macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast.
Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia.
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.
Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.
sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden.
SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.
Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals.
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.
TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.
Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq.
An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.
Feedforward cysteine regulation maintains melanoma differentiation state and limits metastatic spread.
Chromosome compaction is triggered by an autonomous DNA-binding module within condensin.
Histone H3.3 chaperone HIRA renders stress-responsive genes poised for prospective lethal stresses in acquired tolerance.
YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment.
The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis.
Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice.
PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.
TET1 displays catalytic and non-catalytic functions in the adult mouse cortex.
PICKLE and HISTONE DEACETYLASE6 coordinately regulate genes and transposable elements in Arabidopsis.
Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a.
DNA methylation enables recurrent endogenization of giant viruses in an animal relative.
Accurate allocation of multimapped reads enables regulatory element analysis at repeats.
The Hippo pathway transcription factors YAP and TAZ play HPV-type dependent roles in cervical cancer.
Evolutionary conservation of VSX2 super-enhancer modules in retinal development.
KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription.
Bromodomain protein BRD4 directs mitotic cell division of mouse fibroblasts by inhibiting DNA damage.
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings.

Mol Cell. 2024 Jul 11. pii: S1097-2765(24)00513-6. [Epub ahead of print]84(13): 2511-2524.e8

Polymerization of ZBTB transcription factors regulates chromatin occupancy.

Paul M C Park, Jiho Park, Jared Brown, Moritz Hunkeler, Shourya S Roy Burman, Katherine A Donovan, Hojong Yoon, Radosław P Nowak, Mikołaj Słabicki, Benjamin L Ebert, Eric S Fischer.

  BCL6, an oncogenic transcription factor (TF), forms polymers in the presence of a small-molecule molecular glue that stabilizes a complementary interface between homodimers of BCL6's broad-complex, tramtrack, and bric-à-brac (BTB) domain. The BTB domains of other proteins, including a large class of TFs, have similar architectures and symmetries, raising the possibility that additional BTB proteins self-assemble into higher-order structures. Here, we surveyed 189 human BTB proteins with a cellular fluorescent reporter assay and identified 18 ZBTB TFs that show evidence of polymerization. Through biochemical and cryoelectron microscopy (cryo-EM) studies, we demonstrate that these ZBTB TFs polymerize into filaments. We found that BTB-domain-mediated polymerization of ZBTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites, leading to repression of target genes. Our results reveal a role of higher-order structures in regulating ZBTB TFs and suggest an underappreciated role for TF polymerization in modulating gene expression.

Keywords:  BTB domain; ZBTB proteins; higher-order assembly; homotypic clusters; protein polymerization; transcription factors

DOI:  https://doi.org/10.1016/j.molcel.2024.06.010
Nat Commun. 2024 Jul 11. 15(1): 5187

Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.

Akihisa Osakabe, Yoshimasa Takizawa, Naoki Horikoshi, Suguru Hatazawa, Lumi Negishi, Shoko Sato, Frédéric Berger, Tetsuji Kakutani, Hitoshi Kurumizaka.

The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.

DOI: https://doi.org/10.1038/s41467-024-49465-w
Nucleic Acids Res. 2024 Jul 11. pii: gkae605. [Epub ahead of print]

BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.

Takayuki Hoshii, Sota Kikuchi, Tomoya Kujirai, Takeshi Masuda, Tomoko Ito, Satoshi Yasuda, Makoto Matsumoto, Bahityar Rahmutulla, Masaki Fukuyo, Takeshi Murata, Hitoshi Kurumizaka, Atsushi Kaneda.

The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.

DOI: https://doi.org/10.1093/nar/gkae605
Genes Cells. 2024 Jul 07.

Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.

Tomoaki Kimura, Seiya Hirai, Tomoya Kujirai, Risa Fujita, Mitsuo Ogasawara, Haruhiko Ehara, Shun-Ichi Sekine, Yoshimasa Takizawa, Hitoshi Kurumizaka.

  The Lys mutation of the canonical histone H3.1 Glu97 residue (H3E97K) is found in cancer cells. Previous biochemical analyses revealed that the nucleosome containing the H3E97K mutation is extremely unstable as compared to the wild-type nucleosome. However, the mechanism by which the H3E97K mutation causes nucleosome instability has not been clarified yet. In the present study, the cryo-electron microscopy structure of the nucleosome containing the H3E97K mutation revealed that the entry/exit DNA regions of the H3E97K nucleosome are disordered, probably by detachment of the nucleosomal DNA from the H3 N-terminal regions. This may change the intra-molecular amino acid interactions with the replaced H3 Lys97 residue, inducing structural distortion around the mutated position in the nucleosome. Consistent with the nucleosomal DNA end flexibility and the nucleosome instability, the H3E97K mutation exhibited reduced binding of linker histone H1 to the nucleosome, defective activation of PRC2 (the essential methyltransferase for facultative heterochromatin formation) with a poly-nucleosome, and enhanced nucleosome transcription by RNA polymerase II.

Keywords:  cancer; chromatin; cryo‐EM; epigenetics; histone mutation; nucleosome

DOI:  https://doi.org/10.1111/gtc.13143
Nat Cell Biol. 2024 Jul 08.

A single-cell atlas of chromatin accessibility in mouse organogenesis.

Keyong Sun, Xin Liu, Xun Lan.

Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis.

DOI: https://doi.org/10.1038/s41556-024-01435-6
Cell Rep. 2024 Jul 10. pii: S2211-1247(24)00801-5. [Epub ahead of print]43(7): 114472

macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast.

Max A B Haase, Luciana Lazar-Stefanita, Guðjón Ólafsson, Aleksandra Wudzinska, Michael J Shen, David M Truong, Jef D Boeke.

  In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones, providing additional layers of structural and epigenetic regulation. Here, we systematically replace individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. We show that variants H2A.J, TsH2B, and H3.5 complement their respective replicative counterparts. However, macroH2A1 fails to complement, and its overexpression is toxic in yeast, negatively interacting with yeast's native histones and kinetochore genes. To isolate yeast with macroH2A1 chromatin, we uncouple the effects of its macro and histone fold domains, revealing that both domains suffice to override native nucleosome positioning. Furthermore, both uncoupled constructs of macroH2A1 exhibit lower nucleosome occupancy, decreased short-range chromatin interactions (<20 kb), disrupted centromeric clustering, and increased chromosome instability. Our observations demonstrate that lack of a canonical histone H2A dramatically alters chromatin organization in yeast, leading to genome instability and substantial fitness defects.

Keywords:  CP: Molecular biology; chromatin; genome instability; histone variants; humanization; linker length; macroH2A; nucleosome; yeast

DOI:  https://doi.org/10.1016/j.celrep.2024.114472
Nat Commun. 2024 Jul 07. 15(1): 5693

Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia.

Roger Mulet-Lazaro, Stanley van Herk, Margit Nuetzel, Aniko Sijs-Szabo, Noelia Díaz, Katherine Kelly, Claudia Erpelinck-Verschueren, Lucia Schwarzfischer-Pfeilschifter, Hanna Stanewsky, Ute Ackermann, Dagmar Glatz, Johanna Raithel, Alexander Fischer, Sandra Pohl, Anita Rijneveld, Juan M Vaquerizas, Christian Thiede, Christoph Plass, Bas J Wouters, Ruud Delwel, Michael Rehli, Claudia Gebhard.

Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.

DOI: https://doi.org/10.1038/s41467-024-49811-y
Elife. 2024 Jul 08. pii: RP92764. [Epub ahead of print]13

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.

Joshua D Eaton, Jessica Board, Lee Davidson, Chris Estell, Steven West.

  RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial promoter directionality. After transcription begins, the opposing functions of the endonucleolytic subunit of Integrator, INTS11, and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.

Keywords:  CDK9; INTS11; Integrator; RNA polymerase II; chromosomes; cleavage and polyadenylation; gene expression; human; promoter; transcription; transcription initiation; transcription termination

DOI:  https://doi.org/10.7554/eLife.92764
Cell Genom. 2024 Jul 09. pii: S2666-979X(24)00200-3. [Epub ahead of print] 100606

Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.

Katelyn R Titus, Zoltan Simandi, Harshini Chandrashekar, Dominik Paquet, Jennifer E Phillips-Cremins.

DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.

DOI: https://doi.org/10.1016/j.xgen.2024.100606
Genome Biol. 2024 Jul 10. 25(1): 186

sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden.

Sonia N Acharya, Ruth V Nichols, Lauren E Rylaarsdam, Brendan L O'Connell, Theodore P Braun, Andrew C Adey.

  DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Accumulated off-target coverage enables genome-wide differentially methylated region (DMR) calling for clusters with as few as 115 cells. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).

Keywords:  DNA methylation; Epigenetics; Single-cell

DOI:  https://doi.org/10.1186/s13059-024-03306-7
Commun Biol. 2024 Jul 09. 7(1): 834

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.

Hongyu Yu, Daiqing Wu, Shreya Mishra, Guning Shen, Huaigu Sun, Ming Hu, Yun Li.

Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE .

DOI: https://doi.org/10.1038/s42003-024-06428-7
Elife. 2024 Jul 12. pii: RP93194. [Epub ahead of print]13

Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals.

Lisa Baumgartner, Jonathan J Ipsaro, Ulrich Hohmann, Dominik Handler, Alexander Schleiffer, Peter Duchek, Julius Brennecke.

  Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the Drosophila PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C2H2 zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino's chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino's chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.

Keywords:  D. melanogaster; HP1 proteins; chromodomain; chromosomes; gene expression; genetics; genomics; heterochromatin; piRNA pathway; transposon silencing; zinc finger protein

DOI:  https://doi.org/10.7554/eLife.93194
Cell. 2024 Jul 11. pii: S0092-8674(24)00642-1. [Epub ahead of print]187(14): 3541-3562.e51

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Marcela Sandoval-Velasco, Olga Dudchenko, Juan Antonio Rodríguez, Cynthia Pérez Estrada, Marianne Dehasque, Claudia Fontsere, Sarah S T Mak, Ruqayya Khan, Vinícius G Contessoto, Antonio B Oliveira Junior, Achyuth Kalluchi, Bernardo J Zubillaga Herrera, Jiyun Jeong, Renata P Roy, Ishawnia Christopher, David Weisz, Arina D Omer, Sanjit S Batra, Muhammad S Shamim, Neva C Durand, Brendan O'Connell, Alfred L Roca, Maksim V Plikus, Mariya A Kusliy, Svetlana A Romanenko, Natalya A Lemskaya, Natalya A Serdyukova, Svetlana A Modina, Polina L Perelman, Elena A Kizilova, Sergei I Baiborodin, Nikolai B Rubtsov, Gur Machol, Krisha Rath, Ragini Mahajan, Parwinder Kaur, Andreas Gnirke, Isabel Garcia-Treviño, Rob Coke, Joseph P Flanagan, Kelcie Pletch, Aurora Ruiz-Herrera, Valerii Plotnikov, Innokentiy S Pavlov, Naryya I Pavlova, Albert V Protopopov, Michele Di Pierro, Alexander S Graphodatsky, Eric S Lander, M Jordan Rowley, Peter G Wolynes, José N Onuchic, Love Dalén, Marc A Marti-Renom, M Thomas P Gilbert, Erez Lieberman Aiden.

  Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

Keywords:  Hi-C; X inactivation; ancient DNA; chromatin loops; fossil; genome architecture; genome assembly; glass transition; vitrification; woolly mammoth

DOI:  https://doi.org/10.1016/j.cell.2024.06.002
Genome Biol. 2024 Jul 10. 25(1): 187

TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.

Raphaël Romero, Christophe Menichelli, Christophe Vroland, Jean-Michel Marin, Sophie Lèbre, Charles-Henri Lecellier, Laurent Bréhélin.

Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learning approach that identifies sequence features explaining the binding differences observed between two ChIP-seq experiments targeting either the same TF in two conditions or two TFs with similar motifs (paralogous TFs). TFscope systematically investigates differences in the core motif, nucleotide environment and co-factor motifs, and provides the contribution of each key feature in the two experiments. TFscope was applied to > 305 ChIP-seq pairs, and several examples are discussed.

DOI: https://doi.org/10.1186/s13059-024-03321-8
Nat Cell Biol. 2024 Jul 08.

Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq.

Keyong Sun, Xin Liu, Runda Xu, Chang Liu, Anming Meng, Xun Lan.

Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis.

DOI: https://doi.org/10.1038/s41556-024-01449-0
Cancer Res. 2024 Jul 11.

An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.

Raunak Shrestha, Lisa N Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Su C/Pcf West Coast Prostate Cancer Dream Team, Joshi J Alumkal, Rahul Aggarwal, Eric J Small, Mathieu Lupien, David A Quigley, Felix Y Feng.

Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease that resists therapy targeting androgen signaling, the primary driver of prostate cancer. mCRPC resists androgen receptor (AR) inhibitors by amplifying AR signaling or by evolving into therapy-resistant subtypes that do not depend on AR. Elucidation of the epigenetic underpinnings of these subtypes could provide important insights into the drivers of therapy resistance. In this study, we produced chromatin accessibility maps linked to the binding of lineage-specific transcription factors (TF) by performing ATAC sequencing on 70 mCRPC tissue biopsies integrated with transcriptome and whole genome sequencing. mCRPC had a distinct global chromatin accessibility profile linked to AR function. Analysis of TF occupancy across accessible chromatin revealed 203 TFs associated with mCRPC subtypes. Notably, ZNF263 was identified as a putative prostate cancer TF with a significant impact on gene activity in the double-negative (AR- neuroendocrine-) subtype, potentially activating MYC targets. Overall, this analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during progression to mCRPC.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0890
Cell Rep. 2024 Jul 10. pii: S2211-1247(24)00813-1. [Epub ahead of print]43(7): 114484

Feedforward cysteine regulation maintains melanoma differentiation state and limits metastatic spread.

Deyang Yu, Jiaxin Liang, Hans R Widlund, Pere Puigserver.

  The inherent ability of melanoma cells to alter the differentiation-associated transcriptional repertoire to evade treatment and facilitate metastatic spread is well accepted and has been termed phenotypic switching. However, how these facets of cellular behavior are controlled remains largely elusive. Here, we show that cysteine availability, whether from lysosomes (CTNS-dependent) or exogenously derived (SLC7A11-dependent or as N-acetylcysteine), controls melanoma differentiation-associated pathways by acting on the melanocyte master regulator MITF. Functional data indicate that low cysteine availability reduces MITF levels and impairs lysosome functions, which affects tumor ferroptosis sensitivity but improves metastatic spread in vivo. Mechanistically, cysteine-restrictive conditions reduce acetyl-CoA levels to decrease p300-mediated H3K27 acetylation at the melanocyte-restricted MITF promoter, thus forming a cysteine feedforward regulation that controls MITF levels and downstream lysosome functions. These findings collectively suggest that cysteine homeostasis governs melanoma differentiation by maintaining MITF levels and lysosome functions, which protect against ferroptosis and limit metastatic spread.

Keywords:  CP: Cancer; cell death; cysteine; lysosome; melanoma; metastasis

DOI:  https://doi.org/10.1016/j.celrep.2024.114484
Cell Rep. 2024 Jul 08. pii: S2211-1247(24)00748-4. [Epub ahead of print]43(7): 114419

Chromosome compaction is triggered by an autonomous DNA-binding module within condensin.

Alyssa Pastic, Michael L Nosella, Annahat Kochhar, Zi Hao Liu, Julie D Forman-Kay, Damien D'Amours.

  The compaction of chromatin into mitotic chromosomes is essential for faithful transmission of the genome during cell division. In eukaryotes, chromosome morphogenesis is regulated by the condensin complex, though the exact mechanism used to target condensin to chromatin and initiate condensation is not understood. Here, we reveal that condensin contains an intrinsically disordered region (IDR) that modulates its association with chromatin in early mitosis and exhibits phase separation. We describe DNA-binding motifs within the IDR that, upon deletion, inflict striking defects in chromosome condensation and segregation, ill-timed condensin turnover on chromatin, and cell death. Importantly, we demonstrate that the condensin IDR can impart cell cycle regulatory functions when transferred to other subunits within the complex, indicating its autonomous nature. Collectively, our study unveils the molecular basis for the initiation of chromosome condensation in early mitosis and how this process ultimately promotes genomic stability and faultless cell division.

Keywords:  CP: Molecular biology; IDR; Smc4; chromatin; chromosome condensation; condensin complex; genomic stability; intrinsically disordered protein region; mitosis; phase separation

DOI:  https://doi.org/10.1016/j.celrep.2024.114419
Genes Cells. 2024 Jul 08.

Histone H3.3 chaperone HIRA renders stress-responsive genes poised for prospective lethal stresses in acquired tolerance.

Yoshikazu Nagagaki, Yuji Kozakura, Theventhiran Mahandaran, Yukiko Fumoto, Ryuichiro Nakato, Katsuhiko Shirahige, Fuyuki Ishikawa.

  Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress-responsive genes, including HSP70, by depositing histone H3.3 following low-dose stresses. These genes are also marked with histone H3 Lys-4 trimethylation and H3 Lys-9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.

Keywords:  Chromatin remodeling; HIRA; acquired tolerance; heat shock protein; histone H3.3; histone chaperone; hormesis; stress response

DOI:  https://doi.org/10.1111/gtc.13140
Cell Rep. 2024 Jul 09. pii: S2211-1247(24)00785-X. [Epub ahead of print]43(7): 114456

YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment.

Yutthaphong Phongbunchoo, Fatima-Zohra Braikia, Cecilia Pessoa-Rodrigues, Senthilkumar Ramamoorthy, Haribaskar Ramachandran, Anna Grosschedl, Fei Ma, Pierre Cauchy, Asifa Akhtar, Ranjan Sen, Gerhard Mittler, Rudolf Grosschedl.

  The rearrangement and expression of the immunoglobulin μ heavy chain (Igh) gene require communication of the intragenic Eμ and 3' regulatory region (RR) enhancers with the variable (VH) gene promoter. Eμ binding of the transcription factor YY1 has been implicated in enhancer-promoter communication, but the YY1 protein network remains obscure. By analyzing the comprehensive proteome of the 1-kb Eμ wild-type enhancer and that of Eμ lacking the YY1 binding site, we identified the male-specific lethal (MSL)/MOF complex as a component of the YY1 protein network. We found that MSL2 recruitment depends on YY1 and that gene knockout of Msl2 in primary pre-B cells reduces μ gene expression and chromatin looping of Eμ to the 3' RR enhancer and VH promoter. Moreover, Mof heterozygosity in mice impaired μ expression and early B cell differentiation. Together, these data suggest that the MSL/MOF complex regulates Igh gene expression by augmenting YY1-mediated enhancer-promoter communication.

Keywords:  CP: Immunology; Eμ enhancer; MSL/MOF; YY1; enhancer proteome; enhancer-promoter communication; gene dosage compensation; immunoglobulin μ gene; pre-B cell

DOI:  https://doi.org/10.1016/j.celrep.2024.114456
Nat Commun. 2024 Jul 11. 15(1): 5585

The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis.

Jayne E Murray, Emanuele Valli, Giorgio Milazzo, Chelsea Mayoh, Andrew J Gifford, Jamie I Fletcher, Chengyuan Xue, Nisitha Jayatilleke, Firoozeh Salehzadeh, Laura D Gamble, Jourdin R C Rouaen, Daniel R Carter, Helen Forgham, Eric O Sekyere, Joanna Keating, Georgina Eden, Sophie Allan, Stephanie Alfred, Frances K Kusuma, Ashleigh Clark, Hannah Webber, Amanda J Russell, Antoine de Weck, Benjamin T Kile, Martina Santulli, Piergiuseppe De Rosa, Emmy D G Fleuren, Weiman Gao, Lorna Wilkinson-White, Jason K K Low, Joel P Mackay, Glenn M Marshall, Douglas J Hilton, Federico M Giorgi, Jan Koster, Giovanni Perini, Michelle Haber, Murray D Norris.

MYCN oncogene amplification is frequently observed in aggressive childhood neuroblastoma. Using an unbiased large-scale mutagenesis screen in neuroblastoma-prone transgenic mice, we identify a single germline point mutation in the transcriptional corepressor Runx1t1, which abolishes MYCN-driven tumorigenesis. This loss-of-function mutation disrupts a highly conserved zinc finger domain within Runx1t1. Deletion of one Runx1t1 allele in an independent Runx1t1 knockout mouse model is also sufficient to prevent MYCN-driven neuroblastoma development, and reverse ganglia hyperplasia, a known pre-requisite for tumorigenesis. Silencing RUNX1T1 in human neuroblastoma cells decreases colony formation in vitro, and inhibits tumor growth in vivo. Moreover, RUNX1T1 knockdown inhibits the viability of PAX3-FOXO1 fusion-driven rhabdomyosarcoma and MYC-driven small cell lung cancer cells. Despite the role of Runx1t1 in MYCN-driven tumorigenesis neither gene directly regulates the other. We show RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex recruited by HAND2 to enhancer regions to regulate chromatin accessibility and cell-fate pathway genes.

DOI: https://doi.org/10.1038/s41467-024-49871-0
Plant J. 2024 Jul 08.

Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice.

Fei Wang, Zengde Xi, Mengyao Wang, Linyou Wang, Jianbo Wang.

  The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.

Keywords:  DNA methylation; allele‐specific expression; chromatin accessibility; heterosis; inter‐subspecific hybrid rice; transcriptional regulation

DOI:  https://doi.org/10.1111/tpj.16920
Sci Rep. 2024 Jul 12. 14(1): 16074

PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression.

Christin Schmidt, Sarah Cohen, Brian L Gudenas, Sarah Husain, Annika Carlson, Samantha Westelman, Linyu Wang, Joanna J Phillips, Paul A Northcott, William A Weiss, Bjoern Schwer.

SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.

DOI: https://doi.org/10.1038/s41598-024-66811-6
Epigenetics. 2024 Dec;19(1): 2374979

TET1 displays catalytic and non-catalytic functions in the adult mouse cortex.

Yee Hoon Foong, Blake Caldwell, Joanne L Thorvaldsen, Christopher Krapp, Clementina A Mesaros, Wanding Zhou, Rahul M Kohli, Marisa S Bartolomei.

  TET1/2/3 dioxygenases iteratively demethylate 5-methylcytosine, beginning with the formation of 5-hydroxymethylcytosine (5hmC). The post-mitotic brain maintains higher levels of 5hmC than most peripheral tissues, and TET1 ablation studies have underscored the critical role of TET1 in brain physiology. However, deletion of Tet1 precludes the disentangling of the catalytic and non-catalytic functions of TET1. Here, we dissect these functions of TET1 by comparing adult cortex of Tet1 wildtype (Tet1 WT), a novel Tet1 catalytically dead mutant (Tet1 HxD), and Tet1 knockout (Tet1 KO) mice. Using DNA methylation array, we uncover that Tet1 HxD and KO mutations perturb the methylation status of distinct subsets of CpG sites. Gene ontology (GO) analysis on specific differential 5hmC regions indicates that TET1's catalytic activity is linked to neuronal-specific functions. RNA-Seq further shows that Tet1 mutations predominantly impact the genes that are associated with alternative splicing. Lastly, we performed High-performance Liquid Chromatography Mass-Spectrometry lipidomics on WT and mutant cortices and uncover accumulation of lysophospholipids lysophosphatidylethanolamine and lysophosphatidylcholine in Tet1 HxD cortex. In summary, we show that Tet1 HxD does not completely phenocopy Tet1 KO, providing evidence that TET1 modulates distinct cortical functions through its catalytic and non-catalytic roles.

Keywords:  DNA demethylation; DNA hydroxymethylcytosine; Infinium BeadChip array; TET1; adult mouse cortex; dioxygenases

DOI:  https://doi.org/10.1080/15592294.2024.2374979
Plant Physiol. 2024 Jul 08. pii: kiae369. [Epub ahead of print]

PICKLE and HISTONE DEACETYLASE6 coordinately regulate genes and transposable elements in Arabidopsis.

Wenjuan Li, Xiaoling Zhang, Qingche Zhang, Qingzhu Li, Yanzhuo Li, Yanfang Lv, Yue Liu, Ying Cao, Huamei Wang, Xiangsong Chen, Hongchun Yang.

  Chromatin dynamics play essential roles in transcriptional regulation. The chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler PICKLE (PKL) and HISTONE DEACETYLASE6 (HDA6) are required for transcriptional gene silencing, but their coordinated function in gene repression requires further study. Through a genetic suppressor screen, we found that a point mutation at PKL could partially restore the developmental defects of a weak Polycomb repressive complex 1 (PRC1) mutant (ring1a-2 ring1b-3), in which RING1A expression is suppressed by a T-DNA insertion at the promoter. Compared to ring1a-2 ring1b-3, the expression of RING1A is increased, nucleosome occupancy is reduced, and the histone 3 lysine 9 acetylation (H3K9ac) level is increased at the RING1A locus in the pkl ring1a-2 ring1b-3 triple mutant. HDA6 interacts with PKL and represses RING1A expression similarly to PKL genetically and molecularly in the ring1a-2 ring1b-3 background. Furthermore, we show that PKL and HDA6 suppress the expression of a set of genes and transposable elements (TEs) by increasing nucleosome density and reducing H3K9ac. Genome-wide analysis indicated they possibly coordinately maintain DNA methylation as well. Our findings suggest that PKL and HDA6 function together to reduce H3K9ac and increase nucleosome occupancy, thereby facilitating gene/TE regulation in Arabidopsis (Arabidopsis thaliana).

Keywords:  HDA6; PKL; chromatin remodeling; histone deacetylation; transcriptional regulation; transposable elements

DOI:  https://doi.org/10.1093/plphys/kiae369
Nat Commun. 2024 Jul 06. 15(1): 5674

Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a.

Ting Zhao, Yan Hong, Bowen Yan, Suming Huang, Guo-Li Ming, Hongjun Song.

Quiescence, a hallmark of adult neural stem cells (NSCs), is required for maintaining the NSC pool to support life-long continuous neurogenesis in the adult dentate gyrus (DG). Whether long-lasting epigenetic modifications maintain NSC quiescence over the long term in the adult DG is not well-understood. Here we show that mice with haploinsufficiency of Setd1a, a schizophrenia risk gene encoding a histone H3K4 methyltransferase, develop an enlarged DG with more dentate granule cells after young adulthood. Deletion of Setd1a specifically in quiescent NSCs in the adult DG promotes their activation and neurogenesis, which is countered by inhibition of the histone demethylase LSD1. Mechanistically, RNA-sequencing and CUT & RUN analyses of cultured quiescent adult NSCs reveal Setd1a deletion-induced transcriptional changes and many Setd1a targets, among which down-regulation of Bhlhe40 promotes quiescent NSC activation in the adult DG in vivo. Together, our study reveals a Setd1a-dependent epigenetic mechanism that sustains NSC quiescence in the adult DG.

DOI: https://doi.org/10.1038/s41467-024-50010-y
Sci Adv. 2024 Jul 12. 10(28): eado6406

DNA methylation enables recurrent endogenization of giant viruses in an animal relative.

Luke A Sarre, Iana V Kim, Vladimir Ovchinnikov, Marine Olivetta, Hiroshi Suga, Omaya Dudin, Arnau Sebé-Pedrós, Alex de Mendoza.

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.

DOI: https://doi.org/10.1126/sciadv.ado6406
Genome Res. 2024 Jul 10.

Accurate allocation of multimapped reads enables regulatory element analysis at repeats.

Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony.

Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multimapped" reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multimapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multimapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multimapping read assignment. Allo also provides read-level output in the form of a corrected alignment file, making it compatible with existing regulatory genomics analysis pipelines and downstream peak-finders. In a demonstration application on CTCF ChIP-seq data, we show that Allo results in the discovery of thousands of new CTCF peaks. Many of these peaks contain the expected cognate motif and/or serve as TAD boundaries. We additionally apply Allo to a diverse collection of ENCODE ChIP-seq data sets, resulting in multiple previously unidentified interactions between transcription factors and repetitive element families. Finally, we show that Allo may be particularly beneficial in identifying ChIP-seq peaks at centromeres, near segmentally duplicated genes, and in younger TEs, enabling new regulatory analyses in these regions.

DOI: https://doi.org/10.1101/gr.278638.123
Nat Commun. 2024 Jul 10. 15(1): 5809

The Hippo pathway transcription factors YAP and TAZ play HPV-type dependent roles in cervical cancer.

Molly R Patterson, Joseph A Cogan, Rosa Cassidy, Daisy A Theobald, Miao Wang, James A Scarth, Chinedu A Anene, Adrian Whitehouse, Ethan L Morgan, Andrew Macdonald.

Human papillomaviruses (HPVs) cause most cervical cancers and an increasing number of anogenital and oral carcinomas, with most cases caused by HPV16 or HPV18. HPV hijacks host signalling pathways to promote carcinogenesis. Understanding these interactions could permit identification of much-needed therapeutics for HPV-driven malignancies. The Hippo signalling pathway is important in HPV+ cancers, with the downstream effector YAP playing a pro-oncogenic role. In contrast, the significance of its paralogue TAZ remains largely uncharacterised in these cancers. We demonstrate that TAZ is dysregulated in a HPV-type dependent manner by a distinct mechanism to that of YAP and controls proliferation via alternative cellular targets. Analysis of cervical cancer cell lines and patient biopsies revealed that TAZ expression was only significantly increased in HPV18+ and HPV18-like cells and TAZ knockdown reduced proliferation, migration and invasion only in HPV18+ cells. RNA-sequencing of HPV18+ cervical cells revealed that YAP and TAZ have distinct targets, suggesting they promote carcinogenesis by different mechanisms. Thus, in HPV18+ cancers, YAP and TAZ play non-redundant roles. This analysis identified TOGARAM2 as a previously uncharacterised TAZ target and demonstrates its role as a key effector of TAZ-mediated proliferation, migration and invasion in HPV18+ cancers.

DOI: https://doi.org/10.1038/s41467-024-49965-9
Development. 2024 Jul 01. pii: dev202435. [Epub ahead of print]151(13):

Evolutionary conservation of VSX2 super-enhancer modules in retinal development.

Victoria Honnell, Shannon Sweeney, Jackie Norrie, Madison Parks, Cody Ramirez, Asha Jacob Jannu, Beisi Xu, Brett Teubner, Ah Young Lee, Claire Bell, Michael A Dyer.

  Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. We recently identified developmental stage- and cell type-specific modules within the murine Vsx2 SE. Here, we show that the human VSX2 SE modules have similar developmental stage- and cell type-specific activity in reporter gene assays. By inserting the human sequence of one VSX2 SE module into a mouse with microphthalmia, eye size was rescued. To understand the function of these SE modules during human retinal development, we deleted individual modules in human embryonic stem cells and generated retinal organoids. Deleting one module results in small organoids, recapitulating the small-eyed phenotype of mice with microphthalmia, while deletion of the other module led to disruptions in bipolar neuron development. This prototypical SE serves as a model for understanding developmental stage- and cell type-specific effects of neurogenic transcription factors with complex expression patterns. Moreover, by elucidating the gene regulatory mechanisms, we can begin to examine how dysregulation of these mechanisms contributes to phenotypic diversity and disease.

Keywords:  Organoid; Retina; Retinal development; Super-enhancer

DOI:  https://doi.org/10.1242/dev.202435
Nat Commun. 2024 Jul 12. 15(1): 5859

KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription.

Usman Hyder, Ashwini Challa, Micah Thornton, Tulip Nandu, W Lee Kraus, Iván D'Orso.

Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.

DOI: https://doi.org/10.1038/s41467-024-49905-7
iScience. 2024 Jul 19. 27(7): 109797

Bromodomain protein BRD4 directs mitotic cell division of mouse fibroblasts by inhibiting DNA damage.

Tiyun Wu, Haitong Hou, Anup Dey, Mahesh Bachu, Xiongfong Chen, Jan Wisniewski, Fuki Kudoh, Chao Chen, Sakshi Chauhan, Hua Xiao, Richard Pan, Keiko Ozato.

  Bromodomain protein BRD4 binds to acetylated histones to regulate transcription. BRD4 also drives cancer cell proliferation. However, the role of BRD4 in normal cell growth has remained unclear. Here, we investigated this question by using mouse embryonic fibroblasts with conditional Brd4 knockout (KO). We found that Brd4KO cells grow more slowly than wild type cells; they do not complete replication, fail to achieve mitosis, and exhibit extensive DNA damage throughout all cell cycle stages. BRD4 was required for expression of more than 450 cell cycle genes including genes encoding core histones and centromere/kinetochore proteins that are critical for genome replication and chromosomal segregation. Moreover, we show that many genes controlling R-loop formation and DNA damage response (DDR) require BRD4 for expression. Finally, BRD4 constitutively occupied genes controlling R-loop, DDR and cell cycle progression. In summary, BRD4 epigenetically marks above genes and serves as a master regulator of normal cell growth.

Keywords:  Biochemistry; Biological sciences; Cancer; Cell biology; Natural sciences

DOI:  https://doi.org/10.1016/j.isci.2024.109797
NAR Genom Bioinform. 2024 Sep;6(3): lqae073

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings.

Nathan J LeRoy, Jason P Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E Brown, Aidong Zhang, Nathan C Sheffield.

Data from the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) are now widely available. One major computational challenge is dealing with high dimensionality and inherent sparsity, which is typically addressed by producing lower dimensional representations of single cells for downstream clustering tasks. Current approaches produce such individual cell embeddings directly through a one-step learning process. Here, we propose an alternative approach by building embedding models pre-trained on reference data. We argue that this provides a more flexible analysis workflow that also has computational performance advantages through transfer learning. We implemented our approach in scEmbed, an unsupervised machine-learning framework that learns low-dimensional embeddings of genomic regulatory regions to represent and analyze scATAC-seq data. scEmbed performs well in terms of clustering ability and has the key advantage of learning patterns of region co-occurrence that can be transferred to other, unseen datasets. Moreover, models pre-trained on reference data can be exploited to build fast and accurate cell-type annotation systems without the need for other data modalities. scEmbed is implemented in Python and it is available to download from GitHub. We also make our pre-trained models available on huggingface for public use. scEmbed is open source and available at https://github.com/databio/geniml. Pre-trained models from this work can be obtained on huggingface: https://huggingface.co/databio.

DOI: https://doi.org/10.1093/nargab/lqae073