bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–03–12
thirteen papers selected by
Connor Rogerson, University of Cambridge
  1. Transcription shapes 3D chromatin organization by interacting with loop extrusion.
  2. High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding.
  3. SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry.
  4. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
  5. Comprehensive characterization of the embryonic factor LEUTX.
  6. CTCF controls three-dimensional enhancer network underlying the inflammatory response of bone marrow-derived dendritic cells.
  7. UV irradiation remodels the specificity landscape of transcription factors.
  8. Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer.
  9. Conserved and plant-specific histone acetyltransferase complexes cooperate to regulate gene transcription and plant development.
  10. Non-canonical functions of SNAIL drive context-specific cancer progression.
  11. A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis.
  12. Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans.
  13. Histone malonylation is regulated by SIRT5 and KAT2A.
  1. Proc Natl Acad Sci U S A. 2023 Mar 14. 120(11): e2210480120
    Transcription shapes 3D chromatin organization by interacting with loop extrusion.
    Edward J Banigan, Wen Tang, Aafke A van den Berg, Roman R Stocsits, Gordana Wutz, Hugo B Brandão, Georg A Busslinger, Jan-Michael Peters, Leonid A Mirny.
      Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded by chromatin-bound factors, such as CTCF, which generates characteristic and functional chromatin organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin and that active promoters are cohesin loading sites. However, the effects of transcription on cohesin have not been reconciled with observations of active extrusion by cohesin. To determine how transcription modulates extrusion, we studied mouse cells in which we could alter cohesin abundance, dynamics, and localization by genetic "knockouts" of the cohesin regulators CTCF and Wapl. Through Hi-C experiments, we discovered intricate, cohesin-dependent contact patterns near active genes. Chromatin organization around active genes exhibited hallmarks of interactions between transcribing RNA polymerases (RNAPs) and extruding cohesins. These observations could be reproduced by polymer simulations in which RNAPs were moving barriers to extrusion that obstructed, slowed, and pushed cohesins. The simulations predicted that preferential loading of cohesin at promoters is inconsistent with our experimental data. Additional ChIP-seq experiments showed that the putative cohesin loader Nipbl is not predominantly enriched at promoters. Therefore, we propose that cohesin is not preferentially loaded at promoters and that the barrier function of RNAP accounts for cohesin accumulation at active promoters. Altogether, we find that RNAP is an extrusion barrier that is not stationary, but rather, translocates and relocalizes cohesin. Loop extrusion and transcription might interact to dynamically generate and maintain gene interactions with regulatory elements and shape functional genomic organization.
    Keywords:  chromatin organization; cohesin; genome organization; loop extrusion; transcription
    DOI:  https://doi.org/10.1073/pnas.2210480120
  2. Nat Commun. 2023 Mar 06. 14(1): 1250
    High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding.
    Jia-Yong Zhong, Longjian Niu, Zhuo-Bin Lin, Xin Bai, Ying Chen, Feng Luo, Chunhui Hou, Chuan-Le Xiao.
      Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.
    DOI:  https://doi.org/10.1038/s41467-023-36899-x
  3. Nat Commun. 2023 Mar 07. 14(1): 1267
    SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry.
    Bieke Decaesteker, Amber Louwagie, Siebe Loontiens, Fanny De Vloed, Sarah-Lee Bekaert, Juliette Roels, Suzanne Vanhauwaert, Sara De Brouwer, Ellen Sanders, Alla Berezovskaya, Geertrui Denecker, Eva D'haene, Stéphane Van Haver, Wouter Van Loocke, Jo Van Dorpe, David Creytens, Nadine Van Roy, Tim Pieters, Christophe Van Neste, Matthias Fischer, Pieter Van Vlierberghe, Stephen S Roberts, Johannes Schulte, Sara Ek, Rogier Versteeg, Jan Koster, Johan van Nes, Mark Zimmerman, Katleen De Preter, Frank Speleman.
      The pediatric extra-cranial tumor neuroblastoma displays a low mutational burden while recurrent copy number alterations are present in most high-risk cases. Here, we identify SOX11 as a dependency transcription factor in adrenergic neuroblastoma based on recurrent chromosome 2p focal gains and amplifications, specific expression in the normal sympatho-adrenal lineage and adrenergic neuroblastoma, regulation by multiple adrenergic specific (super-)enhancers and strong dependency on high SOX11 expression in adrenergic neuroblastomas. SOX11 regulated direct targets include genes implicated in epigenetic control, cytoskeleton and neurodevelopment. Most notably, SOX11 controls chromatin regulatory complexes, including 10 SWI/SNF core components among which SMARCC1, SMARCA4/BRG1 and ARID1A. Additionally, the histone deacetylase HDAC2, PRC1 complex component CBX2, chromatin-modifying enzyme KDM1A/LSD1 and pioneer factor c-MYB are regulated by SOX11. Finally, SOX11 is identified as a core transcription factor of the core regulatory circuitry (CRC) in adrenergic high-risk neuroblastoma with a potential role as epigenetic master regulator upstream of the CRC.
    DOI:  https://doi.org/10.1038/s41467-023-36735-2
  4. Nat Commun. 2023 Mar 10. 14(1): 1326
    Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
    Dácil Alonso-Gil, Ana Cuadrado, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Ana Losada.
      Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesin's ATPase and is essential for loop extrusion, but its requirement for cohesin loading is unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data are consistent with a model in which NIPBL may not be required for chromatin association of cohesin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 binds chromatin and becomes stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.
    DOI:  https://doi.org/10.1038/s41467-023-36900-7
  5. iScience. 2023 Mar 17. 26(3): 106172
    Comprehensive characterization of the embryonic factor LEUTX.
    Lisa Gawriyski, Eeva-Mari Jouhilahti, Masahito Yoshihara, Liangru Fei, Jere Weltner, Tomi T Airenne, Ras Trokovic, Shruti Bhagat, Mari H Tervaniemi, Yasuhiro Murakawa, Kari Salokas, Xiaonan Liu, Sini Miettinen, Thomas R Bürglin, Biswajyoti Sahu, Timo Otonkoski, Mark S Johnson, Shintaro Katayama, Markku Varjosalo, Juha Kere.
      The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.
    Keywords:  Molecular biology; Omics; Reproductive medicine
    DOI:  https://doi.org/10.1016/j.isci.2023.106172
  6. Nat Commun. 2023 Mar 08. 14(1): 1277
    CTCF controls three-dimensional enhancer network underlying the inflammatory response of bone marrow-derived dendritic cells.
    Bobae Yang, Sueun Kim, Woong-Jae Jung, Kyungwoo Kim, Sugyung Kim, Yong-Jin Kim, Tae-Gyun Kim, Eun-Chong Lee, Jung-Sik Joo, Chae Gyu Park, Sumin Oh, Kyung Hyun Yoo, Hyoung-Pyo Kim.
      Dendritic cells are antigen-presenting cells orchestrating innate and adaptive immunity. The crucial role of transcription factors and histone modifications in the transcriptional regulation of dendritic cells has been extensively studied. However, it is not been well understood whether and how three-dimensional chromatin folding controls gene expression in dendritic cells. Here we demonstrate that activation of bone marrow-derived dendritic cells induces extensive reprogramming of chromatin looping as well as enhancer activity, both of which are implicated in the dynamic changes in gene expression. Interestingly, depletion of CTCF attenuates GM-CSF-mediated JAK2/STAT5 signaling, resulting in defective NF-κB activation. Moreover, CTCF is necessary for establishing NF-κB-dependent chromatin interactions and maximal expression of pro-inflammatory cytokines, which prime Th1 and Th17 cell differentiation. Collectively, our study provides mechanistic insights into how three-dimensional enhancer networks control gene expression during bone marrow-derived dendritic cells activation, and offers an integrative view of the complex activities of CTCF in the inflammatory response of bone marrow-derived dendritic cells.
    DOI:  https://doi.org/10.1038/s41467-023-36948-5
  7. Proc Natl Acad Sci U S A. 2023 Mar 14. 120(11): e2217422120
    UV irradiation remodels the specificity landscape of transcription factors.
    Zachery Mielko, Yuning Zhang, Harshit Sahay, Yiling Liu, Matthew A Schaich, Brittani Schnable, Abigail M Morrison, Debbie Burdinski, Sheera Adar, Miles Pufall, Bennett Van Houten, Raluca Gordân, Ariel Afek.
      Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hypermutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all the TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs, we identified a surprising but reproducible effect at certain nonconsensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and nonconsensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.
    Keywords:  UV photoproducts; protein-DNA binding; transcription factors
    DOI:  https://doi.org/10.1073/pnas.2217422120
  8. Gut. 2023 Mar 08. pii: gutjnl-2022-328154. [Epub ahead of print]
    Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer.
    Feda H Hamdan, Amro M Abdelrahman, Ana Patricia Kutschat, Xin Wang, Thomas L Ekstrom, Nidhi Jalan-Sakrikar, Catherine Wegner Wippel, Negar Taheri, Liezel Tamon, Waltraut Kopp, Joana Aggrey-Fynn, Aditya V Bhagwate, Roberto Alva-Ruiz, Isaac Lynch, Jennifer Yonkus, Robyn Laura Kosinsky, Jochen Gaedcke, Stephan A Hahn, Jens T Siveke, Rondell Graham, Zeynab Najafova, Elisabeth Hessmann, Mark J Truty, Steven A Johnsen.
       OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) displays a remarkable propensity towards therapy resistance. However, molecular epigenetic and transcriptional mechanisms enabling this are poorly understood. In this study, we aimed to identify novel mechanistic approaches to overcome or prevent resistance in PDAC.
    DESIGN: We used in vitro and in vivo models of resistant PDAC and integrated epigenomic, transcriptomic, nascent RNA and chromatin topology data. We identified a JunD-driven subgroup of enhancers, called interactive hubs (iHUBs), which mediate transcriptional reprogramming and chemoresistance in PDAC.
    RESULTS: iHUBs display characteristics typical for active enhancers (H3K27ac enrichment) in both therapy sensitive and resistant states but exhibit increased interactions and production of enhancer RNA (eRNA) in the resistant state. Notably, deletion of individual iHUBs was sufficient to decrease transcription of target genes and sensitise resistant cells to chemotherapy. Overlapping motif analysis and transcriptional profiling identified the activator protein 1 (AP1) transcription factor JunD as a master transcription factor of these enhancers. JunD depletion decreased iHUB interaction frequency and transcription of target genes. Moreover, targeting either eRNA production or signaling pathways upstream of iHUB activation using clinically tested small molecule inhibitors decreased eRNA production and interaction frequency, and restored chemotherapy responsiveness in vitro and in vivo. Representative iHUB target genes were found to be more expressed in patients with poor response to chemotherapy compared with responsive patients.
    CONCLUSION: Our findings identify an important role for a subgroup of highly connected enhancers (iHUBs) in regulating chemotherapy response and demonstrate targetability in sensitisation to chemotherapy.
    Keywords:  chemotherapy; drug resistance; gene regulation; molecular oncology; pancreatic cancer
    DOI:  https://doi.org/10.1136/gutjnl-2022-328154
  9. Nat Plants. 2023 Mar 06.
    Conserved and plant-specific histone acetyltransferase complexes cooperate to regulate gene transcription and plant development.
    Chan-Juan Wu, Dan-Yang Yuan, Zhen-Zhen Liu, Xin Xu, Long Wei, Xue-Wei Cai, Yin-Na Su, Lin Li, She Chen, Xin-Jian He.
      Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryza sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL and EAF6). We find that PAGA and SAGA can independently mediate moderate and high levels of histone acetylation, respectively, thereby promoting transcriptional activation. Moreover, PAGA and SAGA can also repress gene transcription via the antagonistic effect between PAGA and SAGA. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.
    DOI:  https://doi.org/10.1038/s41477-023-01359-3
  10. Nat Commun. 2023 Mar 07. 14(1): 1201
    Non-canonical functions of SNAIL drive context-specific cancer progression.
    Mariel C Paul, Christian Schneeweis, Chiara Falcomatà, Chuan Shan, Daniel Rossmeisl, Stella Koutsouli, Christine Klement, Magdalena Zukowska, Sebastian A Widholz, Moritz Jesinghaus, Konstanze K Heuermann, Thomas Engleitner, Barbara Seidler, Katia Sleiman, Katja Steiger, Markus Tschurtschenthaler, Benjamin Walter, Sören A Weidemann, Regina Pietsch, Angelika Schnieke, Roland M Schmid, Maria S Robles, Geoffroy Andrieux, Melanie Boerries, Roland Rad, Günter Schneider, Dieter Saur.
      SNAIL is a key transcriptional regulator in embryonic development and cancer. Its effects in physiology and disease are believed to be linked to its role as a master regulator of epithelial-to-mesenchymal transition (EMT). Here, we report EMT-independent oncogenic SNAIL functions in cancer. Using genetic models, we systematically interrogated SNAIL effects in various oncogenic backgrounds and tissue types. SNAIL-related phenotypes displayed remarkable tissue- and genetic context-dependencies, ranging from protective effects as observed in KRAS- or WNT-driven intestinal cancers, to dramatic acceleration of tumorigenesis, as shown in KRAS-induced pancreatic cancer. Unexpectedly, SNAIL-driven oncogenesis was not associated with E-cadherin downregulation or induction of an overt EMT program. Instead, we show that SNAIL induces bypass of senescence and cell cycle progression through p16INK4A-independent inactivation of the Retinoblastoma (RB)-restriction checkpoint. Collectively, our work identifies non-canonical EMT-independent functions of SNAIL and unravel its complex context-dependent role in cancer.
    DOI:  https://doi.org/10.1038/s41467-023-36505-0
  11. Nat Plants. 2023 Mar 06.
    A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis.
    Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolomé, Zheng Li, Suhua Feng, Hsuan Yu Kuo, Ryan L Kan, Hoiyan Lam, John Curtis Richey, Linli Tang, Jessica Zhou, Mukun Liu, Yasaman Jami-Alahmadi, James Wohlschlegel, Steven E Jacobsen.
      DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain-of-function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression through DNA methylation, histone H3K27me3 deposition, H3K4me3 demethylation, histone deacetylation, inhibition of RNA polymerase II transcription elongation or Ser-5 dephosphorylation. These proteins also silenced many other genes with different efficacies, and a machine learning model could accurately predict the efficacy of each silencer on the basis of various chromatin features of the target loci. Furthermore, some proteins were also able to target gene silencing when used in a dCas9-SunTag system. These results provide a more comprehensive understanding of epigenetic regulatory pathways in plants and provide an armament of tools for targeted gene manipulation.
    DOI:  https://doi.org/10.1038/s41477-023-01362-8
  12. Nat Commun. 2023 Mar 06. 14(1): 1254
    Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans.
    Xinhao Hou, Mingjing Xu, Chengming Zhu, Jianing Gao, Meili Li, Xiangyang Chen, Cheng Sun, Björn Nashan, Jianye Zang, Ying Zhou, Shouhong Guang, Xuezhu Feng.
      The chromatin organization modifier domain (chromodomain) is an evolutionally conserved motif across eukaryotic species. The chromodomain mainly functions as a histone methyl-lysine reader to modulate gene expression, chromatin spatial conformation and genome stability. Mutations or aberrant expression of chromodomain proteins can result in cancer and other human diseases. Here, we systematically tag chromodomain proteins with green fluorescent protein (GFP) using CRISPR/Cas9 technology in C. elegans. By combining ChIP-seq analysis and imaging, we delineate a comprehensive expression and functional map of chromodomain proteins. We then conduct a candidate-based RNAi screening and identify factors that regulate the expression and subcellular localization of the chromodomain proteins. Specifically, we reveal an H3K9me1/2 reader, CEC-5, both by in vitro biochemistry and in vivo ChIP assays. MET-2, an H3K9me1/2 writer, is required for CEC-5 association with heterochromatin. Both MET-2 and CEC-5 are required for the normal lifespan of C. elegans. Furthermore, a forward genetic screening identifies a conserved Arginine124 of CEC-5's chromodomain, which is essential for CEC-5's association with chromatin and life span regulation. Thus, our work will serve as a reference to explore chromodomain functions and regulation in C. elegans and allow potential applications in aging-related human diseases.
    DOI:  https://doi.org/10.1038/s41467-023-36898-y
  13. iScience. 2023 Mar 17. 26(3): 106193
    Histone malonylation is regulated by SIRT5 and KAT2A.
    Ran Zhang, Joanna Bons, Grace Scheidemantle, Xiaojing Liu, Olga Bielska, Chris Carrico, Jacob Rose, Indra Heckenbach, Morten Scheibye-Knudsen, Birgit Schilling, Eric Verdin.
      The posttranslational modification lysine malonylation is found in many proteins, including histones. However, it remains unclear whether histone malonylation is regulated or functionally relevant. Here, we report that availability of malonyl-co-enzyme A (malonyl-CoA), an endogenous malonyl donor, affects lysine malonylation, and that the deacylase SIRT5 selectively reduces malonylation of histones. To determine if histone malonylation is enzymatically catalyzed, we knocked down each of the 22 lysine acetyltransferases (KATs) to test their malonyltransferase potential. KAT2A knockdown in particular reduced histone malonylation levels. By mass spectrometry, H2B_K5 was highly malonylated and regulated by SIRT5 in mouse brain and liver. Acetyl-CoA carboxylase (ACC), the malonyl-CoA producing enzyme, was partly localized in the nucleolus, and histone malonylation increased nucleolar area and ribosomal RNA expression. Levels of global lysine malonylation and ACC expression were higher in older mouse brains than younger mice. These experiments highlight the role of histone malonylation in ribosomal gene expression.
    Keywords:  Biological sciences; Molecular biology; Omics; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2023.106193
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