bims-crepig 2023-12-10 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–12–10
fourteen papers selected by
Connor Rogerson, University of Cambridge

The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes.
Chromatin state transitions in the Drosophila intestinal lineage identify principles of cell-type specification.
Combinatorial single-cell profiling of major chromatin types with MAbID.
High-capacity sample multiplexing for single cell chromatin accessibility profiling.
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids.
3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.
The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer.
Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment.
A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.
Transcription induces context-dependent remodeling of chromatin architecture during differentiation.
Multimodal interactions drive chromatin phase separation and compaction.
Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase.
Rational optimization of a transcription factor activation domain inhibitor.
Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks.

Nat Genet. 2023 Dec 04.

The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes.

Sandipan Brahma, Steven Henikoff.

Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which is carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, nucleosome remodeling and chromatin accessibility are unclear. Here, we used a chemical-genetic approach coupled with time-resolved chromatin profiling to dissect the interplay between RNA Polymerase II (RNAPII), BAF and DNA-sequence-specific transcription factors in mouse embryonic stem cells. We show that BAF dynamically unwraps and evicts nucleosomes at accessible chromatin regions, while RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances ATP-dependent nucleosome eviction by BAF. We find that although RNAPII and BAF dynamically probe both transcriptionally active and Polycomb-repressed genomic regions, pluripotency transcription factor chromatin binding confers locus specificity for productive chromatin remodeling and nucleosome eviction by BAF. Our study suggests a paradigm for how functional synergy between dynamically acting chromatin factors regulates locus-specific nucleosome organization and chromatin accessibility.

DOI: https://doi.org/10.1038/s41588-023-01603-8
Dev Cell. 2023 Nov 30. pii: S1534-5807(23)00581-6. [Epub ahead of print]

Chromatin state transitions in the Drosophila intestinal lineage identify principles of cell-type specification.

Manon Josserand, Natalia Rubanova, Marine Stefanutti, Spyridon Roumeliotis, Marion Espenel, Owen J Marshall, Nicolas Servant, Louis Gervais, Allison J Bardin.

  Tissue homeostasis relies on rewiring of stem cell transcriptional programs into those of differentiated cells. Here, we investigate changes in chromatin occurring in a bipotent adult stem cells. Combining mapping of chromatin-associated factors with statistical modeling, we identify genome-wide transitions during differentiation in the adult Drosophila intestinal stem cell (ISC) lineage. Active, stem-cell-enriched genes transition to a repressive heterochromatin protein-1-enriched state more prominently in enteroendocrine cells (EEs) than in enterocytes (ECs), in which the histone H1-enriched Black state is preeminent. In contrast, terminal differentiation genes associated with metabolic functions follow a common path from a repressive, primed, histone H1-enriched Black state in ISCs to active chromatin states in EE and EC cells. Furthermore, we find that lineage priming has an important function in adult ISCs, and we identify histone H1 as a mediator of this process. These data define underlying principles of chromatin changes during adult multipotent stem cell differentiation.

Keywords:  adult stem cells; chromatin; lineage differentiation; tissue homeostasis

DOI:  https://doi.org/10.1016/j.devcel.2023.11.005
Nat Methods. 2023 Dec 04.

Combinatorial single-cell profiling of major chromatin types with MAbID.

Silke J A Lochs, Robin H van der Weide, Kim L de Luca, Tessy Korthout, Ramada E van Beek, Hiroshi Kimura, Jop Kind.

Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.

DOI: https://doi.org/10.1038/s41592-023-02090-9
BMC Genomics. 2023 Dec 04. 24(1): 737

High-capacity sample multiplexing for single cell chromatin accessibility profiling.

Gregory T Booth, Riza M Daza, Sanjay R Srivatsan, José L McFaline-Figueroa, Rula Green Gladden, Andrew C Mullen, Scott N Furlan, Jay Shendure, Cole Trapnell.

  Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, sciPlex-ATAC-seq, which uses unmodified DNA oligos as sample-specific nuclear labels, enabling the concurrent profiling of chromatin accessibility within single nuclei from virtually unlimited specimens or experimental conditions. We first demonstrate our method with a chemical epigenomics screen, in which we identify drug-altered distal regulatory sites predictive of compound- and dose-dependent effects on transcription. We then analyze cell type-specific chromatin changes in PBMCs from multiple donors responding to synthetic and allogeneic immune stimulation. We quantify stimulation-altered immune cell compositions and isolate the unique effects of allogeneic stimulation on chromatin accessibility specific to T-lymphocytes. Finally, we observe that impaired global chromatin decondensation often coincides with chemical inhibition of allogeneic T-cell activation.

Keywords:  Chromatin; Genomics; Perturbation; Screening; Sequencing; Single-cell

DOI:  https://doi.org/10.1186/s12864-023-09832-1
Cell Rep. 2023 Dec 02. pii: S2211-1247(23)01555-3. [Epub ahead of print]42(12): 113543

Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids.

Zepeng Qu, Zachary Batz, Nivedita Singh, Claire Marchal, Anand Swaroop.

  We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.

Keywords:  3D chromatin structure; CP: Neuroscience; CP: Stem cell research; Hi-C; chromatin looping; gene regulation; organogenesis; organoid; retinal development; stem cells; topologically associated domains; transcription factor

DOI:  https://doi.org/10.1016/j.celrep.2023.113543
Nat Struct Mol Biol. 2023 Dec 05.

3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.

Dylan Murphy, Eralda Salataj, Dafne Campigli Di Giammartino, Javier Rodriguez-Hernaez, Andreas Kloetgen, Vidur Garg, Erin Char, Christopher M Uyehara, Ly-Sha Ee, UkJin Lee, Matthias Stadtfeld, Anna-Katerina Hadjantonakis, Aristotelis Tsirigos, Alexander Polyzos, Effie Apostolou.

Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.

DOI: https://doi.org/10.1038/s41594-023-01130-4
Nat Commun. 2023 Dec 06. 14(1): 8084

The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer.

Alexandros Armaos, François Serra, Iker Núñez-Carpintero, Ji-Heui Seo, Sylvan C Baca, Stefano Gustincich, Alfonso Valencia, Matthew L Freedman, Davide Cirillo, Claudia Giambartolomei, Gian Gaetano Tartaglia.

We introduce Promoter-Enhancer-Guided Interaction Networks (PENGUIN), a method for studying protein-protein interaction (PPI) networks within enhancer-promoter interactions. PENGUIN integrates H3K27ac-HiChIP data with tissue-specific PPIs to define enhancer-promoter PPI networks (EPINs). We validated PENGUIN using cancer (LNCaP) and benign (LHSAR) prostate cell lines. Our analysis detected EPIN clusters enriched with the architectural protein CTCF, a regulator of enhancer-promoter interactions. CTCF presence was coupled with the prevalence of prostate cancer (PrCa) single nucleotide polymorphisms (SNPs) within the same EPIN clusters, suggesting functional implications in PrCa. Within the EPINs displaying enrichments in both CTCF and PrCa SNPs, we also show enrichment in oncogenes. We substantiated our identified SNPs through CRISPR/Cas9 knockout and RNAi screens experiments. Here we show that PENGUIN provides insights into the intricate interplay between enhancer-promoter interactions and PPI networks, which are crucial for identifying key genes and potential intervention targets. A dedicated server is available at https://penguin.life.bsc.es/ .

DOI: https://doi.org/10.1038/s41467-023-43767-1
Nat Cell Biol. 2023 Dec 04.

Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment.

Jenna M Giafaglione, Preston D Crowell, Amelie M L Delcourt, Takao Hashimoto, Sung Min Ha, Aishwarya Atmakuri, Nicholas M Nunley, Rachel M A Dang, Mao Tian, Johnny A Diaz, Elisavet Tika, Marie C Payne, Deborah L Burkhart, Dapei Li, Nora M Navone, Eva Corey, Peter S Nelson, Neil Y C Lin, Cedric Blanpain, Leigh Ellis, Paul C Boutros, Andrew S Goldstein.

Lineage transitions are a central feature of prostate development, tumourigenesis and treatment resistance. While epigenetic changes are well known to drive prostate lineage transitions, it remains unclear how upstream metabolic signalling contributes to the regulation of prostate epithelial identity. To fill this gap, we developed an approach to perform metabolomics on primary prostate epithelial cells. Using this approach, we discovered that the basal and luminal cells of the prostate exhibit distinct metabolomes and nutrient utilization patterns. Furthermore, basal-to-luminal differentiation is accompanied by increased pyruvate oxidation. We establish the mitochondrial pyruvate carrier and subsequent lactate accumulation as regulators of prostate luminal identity. Inhibition of the mitochondrial pyruvate carrier or supplementation with exogenous lactate results in large-scale chromatin remodelling, influencing both lineage-specific transcription factors and response to antiandrogen treatment. These results establish reciprocal regulation of metabolism and prostate epithelial lineage identity.

DOI: https://doi.org/10.1038/s41556-023-01274-x
Dev Cell. 2023 Nov 30. pii: S1534-5807(23)00583-X. [Epub ahead of print]

A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.

David J Falvo, Adrien Grimont, Paul Zumbo, William B Fall, Julie L Yang, Alexa Osterhoudt, Grace Pan, Andre F Rendeiro, Yinuo Meng, John E Wilkinson, Friederike Dündar, Olivier Elemento, Rhonda K Yantiss, Erika Hissong, Richard Koche, Doron Betel, Rohit Chandwani.

  Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible.

Keywords:  ATAC-seq; CUT&TAG; cell fate; epigenetic memory; inflammatory injury; lineage plasticity; pancreatic cancer; pancreatitis; single-cell RNA sequencing; tumorigenesis

DOI:  https://doi.org/10.1016/j.devcel.2023.11.008
PLoS Biol. 2023 Dec 04. 21(12): e3002424

Transcription induces context-dependent remodeling of chromatin architecture during differentiation.

Sanjay Chahar, Yousra Ben Zouari, Hossein Salari, Dominique Kobi, Manon Maroquenne, Cathie Erb, Anne M Molitor, Audrey Mossler, Nezih Karasu, Daniel Jost, Tom Sexton.

Metazoan chromosomes are organized into discrete spatial domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between domain organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow chromatin architecture changes during development, we used Capture Hi-C to interrogate the domains around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and subdomains were formed around some activated genes without changes in CTCF binding. The ectopic induction of some genes was sufficient to recapitulate domain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex chromosome folding patterns that can be important in certain genomic contexts.

DOI: https://doi.org/10.1371/journal.pbio.3002424
Proc Natl Acad Sci U S A. 2023 Dec 12. 120(50): e2308858120

Multimodal interactions drive chromatin phase separation and compaction.

Tina Ukmar-Godec, Maria-Sol Cima-Omori, Zhadyra Yerkesh, Karthik Eswara, Taekyung Yu, Reshma Ramesh, Gwladys Riviere, Alain Ibanez de Opakua, Wolfgang Fischle, Markus Zweckstetter.

  Gene silencing is intimately connected to DNA condensation and the formation of transcriptionally inactive heterochromatin by Heterochromatin Protein 1α (HP1α). Because heterochromatin foci are dynamic and HP1α can promote liquid-liquid phase separation, HP1α-mediated phase separation has been proposed as a mechanism of chromatin compaction. The molecular basis of HP1α-driven phase separation and chromatin compaction and the associated regulation by trimethylation of lysine 9 in histone 3 (H3K9me3), which is the hallmark of constitutive heterochromatin, is however largely unknown. Using a combination of chromatin compaction and phase separation assays, site-directed mutagenesis, and NMR-based interaction analysis, we show that human HP1α can compact chromatin in the absence of liquid-liquid phase separation. We further demonstrate that H3K9-trimethylation promotes compaction of chromatin arrays through multimodal interactions. The results provide molecular insights into HP1α-mediated chromatin compaction and thus into the role of human HP1α in the regulation of gene silencing.

Keywords:  H3K9-trimethylation; Heterochromatin Protein 1α (HP1α); chromatin compaction; phase separation

DOI:  https://doi.org/10.1073/pnas.2308858120
Cell Discov. 2023 Dec 05. 9(1): 120

Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase.

Folan Lin, Ruxin Zhang, Weihan Shao, Cong Lei, Mingxi Ma, Ying Zhang, Zengqi Wen, Wanqiu Li.

Histone lysine methyltransferase SUV420H1, which is responsible for site-specific di-/tri-methylation of histone H4 lysine 20 (H4K20), has crucial roles in DNA-templated processes, including DNA replication, DNA damage repair, and chromatin compaction. Its mutations frequently occur in human cancers. Nucleosomes containing the histone variant H2A.Z enhance the catalytic activities of SUV420H1 on H4K20 di-methylation deposition, regulating early replication origins. However, the molecular mechanism by which SUV420H1 specifically recognizes and deposits H4K20 methyl marks on nucleosomes remains poorly understood. Here we report the cryo-electron microscopy structures of SUV420H1 associated with H2A-containing nucleosome core particles (NCPs), and H2A.Z-containing NCPs. We find that SUV420H1 makes extensive site-specific contacts with histone and DNA regions. SUV420H1 C-terminal domain recognizes the H2A-H2B acidic patch of NCPs through its two arginine anchors, thus enabling H4K20 insertion for catalysis specifically. We also identify important residues increasing the catalytic activities of SUV420H1 bound to H2A.Z NCPs. In vitro and in vivo functional analyses reveal that multiple disease-associated mutations at the interfaces are essential for its catalytic activity and chromatin state regulation. Together, our study provides molecular insights into the nucleosome-based recognition and methylation mechanisms of SUV420H1, and a structural basis for understanding SUV420H1-related human disease.

DOI: https://doi.org/10.1038/s41421-023-00620-5
Nat Struct Mol Biol. 2023 Dec 04.

Rational optimization of a transcription factor activation domain inhibitor.

Shaon Basu, Paula Martínez-Cristóbal, Marta Frigolé-Vivas, Mireia Pesarrodona, Michael Lewis, Elzbieta Szulc, C Adriana Bañuelos, Carolina Sánchez-Zarzalejo, Stasė Bielskutė, Jiaqi Zhu, Karina Pombo-García, Carla Garcia-Cabau, Levente Zodi, Hannes Dockx, Jordann Smak, Harpreet Kaur, Cristina Batlle, Borja Mateos, Mateusz Biesaga, Albert Escobedo, Lídia Bardia, Xavier Verdaguer, Alessandro Ruffoni, Nasrin R Mawji, Jun Wang, Jon K Obst, Teresa Tam, Isabelle Brun-Heath, Salvador Ventura, David Meierhofer, Jesús García, Paul Robustelli, Travis H Stracker, Marianne D Sadar, Antoni Riera, Denes Hnisz, Xavier Salvatella.

Transcription factors are among the most attractive therapeutic targets but are considered largely 'undruggable' in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.

DOI: https://doi.org/10.1038/s41594-023-01159-5
BMC Genomics. 2023 Dec 04. 24(1): 736

Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks.

Sebastian Proft, Janna Leiz, Udo Heinemann, Dominik Seelow, Kai M Schmidt-Ott, Maria Rutkiewicz.

   BACKGROUND: Transcription factors regulate gene expression by binding to transcription factor binding sites (TFBSs). Most models for predicting TFBSs are based on position weight matrices (PWMs), which require a specific motif to be present in the DNA sequence and do not consider interdependencies of nucleotides. Novel approaches such as Transcription Factor Flexible Models or recurrent neural networks consequently provide higher accuracies. However, it is unclear whether such approaches can uncover novel non-canonical, hitherto unexpected TFBSs relevant to human transcriptional regulation.
RESULTS: In this study, we trained a convolutional recurrent neural network with HT-SELEX data for GRHL1 binding and applied it to a set of GRHL1 binding sites obtained from ChIP-Seq experiments from human cells. We identified 46 non-canonical GRHL1 binding sites, which were not found by a conventional PWM approach. Unexpectedly, some of the newly predicted binding sequences lacked the CNNG core motif, so far considered obligatory for GRHL1 binding. Using isothermal titration calorimetry, we experimentally confirmed binding between the GRHL1-DNA binding domain and predicted GRHL1 binding sites, including a non-canonical GRHL1 binding site. Mutagenesis of individual nucleotides revealed a correlation between predicted binding strength and experimentally validated binding affinity across representative sequences. This correlation was neither observed with a PWM-based nor another deep learning approach.
CONCLUSIONS: Our results show that convolutional recurrent neural networks may uncover unanticipated binding sites and facilitate quantitative transcription factor binding predictions.

Keywords:  Genetics; Grainyhead-like 1; Machine learning; Neural networks; Transcription factor binding

DOI:  https://doi.org/10.1186/s12864-023-09830-3