bims-crepig 2023-03-05 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–03–05
nineteen papers selected by
Connor Rogerson, University of Cambridge

Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation.
Oncogenic YAP mediates changes in chromatin accessibility and activity that drive cell cycle gene expression and cell migration.
Gene silencing dynamics are modulated by transiently active regulatory elements.
H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.
GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development.
DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network.
Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis.
Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions.
The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency.
The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy.
Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing.
Transcription of MERVL retrotransposons is required for preimplantation embryo development.
Enhancer co-amplification and hijacking promote oncogene expression in liposarcoma.
Structural basis of Janus kinase trans-activation.
Cohesin regulates alternative splicing.
ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.
Linking chromatin acylation mark-defined proteome and genome in living cells.
HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.
Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury.

Genome Biol. 2023 Mar 03. 24(1): 41

Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation.

Ryan M Boileau, Kevin X Chen, Robert Blelloch.

   BACKGROUND: Enhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers including the monomethylation of H3K4 (H3K4me1) by MLL3 (KMT2C) and MLL4 (KMT2D). MLL3/4 are thought to be critical for enhancer activation and cognate gene expression including through the recruitment of acetyltransferases for H3K27.
RESULTS: Here we test this model by evaluating the impact of MLL3/4 loss on chromatin and transcription during early differentiation of mouse embryonic stem cells. We find that MLL3/4 activity is required at most if not all sites that gain or lose H3K4me1 but is largely dispensable at sites that remain stably methylated during this transition. This requirement extends to H3K27 acetylation (H3K27ac) at most transitional sites. However, many sites gain H3K27ac independent of MLL3/4 or H3K4me1 including enhancers regulating key factors in early differentiation. Furthermore, despite the failure to gain active histone marks at thousands of enhancers, transcriptional activation of nearby genes is largely unaffected, thus uncoupling the regulation of these chromatin events from transcriptional changes during this transition. These data challenge current models of enhancer activation and imply distinct mechanisms between stable and dynamically changing enhancers.
CONCLUSIONS: Collectively, our study highlights gaps in knowledge about the steps and epistatic relationships of enzymes necessary for enhancer activation and cognate gene transcription.

Keywords:  Differentiation; Enhancer; Epistasis; H3K27ac; H3K4me1; MLL3; MLL4; P300; Pluripotency; Transcription

DOI:  https://doi.org/10.1186/s13059-023-02883-3
Nucleic Acids Res. 2023 Mar 02. pii: gkad107. [Epub ahead of print]

Oncogenic YAP mediates changes in chromatin accessibility and activity that drive cell cycle gene expression and cell migration.

Maria Camila Fetiva, Franziska Liss, Dörthe Gertzmann, Julius Thomas, Benedikt Gantert, Magdalena Vogl, Nataliia Sira, Grit Weinstock, Susanne Kneitz, Carsten P Ade, Stefan Gaubatz.

YAP, the key protein effector of the Hippo pathway, is a transcriptional co-activator that controls the expression of cell cycle genes, promotes cell growth and proliferation and regulates organ size. YAP modulates gene transcription by binding to distal enhancers, but the mechanisms of gene regulation by YAP-bound enhancers remain poorly understood. Here we show that constitutive active YAP5SA leads to widespread changes in chromatin accessibility in untransformed MCF10A cells. Newly accessible regions include YAP-bound enhancers that mediate activation of cycle genes regulated by the Myb-MuvB (MMB) complex. By CRISPR-interference we identify a role for YAP-bound enhancers in phosphorylation of Pol II at Ser5 at MMB-regulated promoters, extending previously published studies that suggested YAP primarily regulates the pause-release step and transcriptional elongation. YAP5SA also leads to less accessible 'closed' chromatin regions, which are not directly YAP-bound but which contain binding motifs for the p53 family of transcription factors. Diminished accessibility at these regions is, at least in part, a consequence of reduced expression and chromatin-binding of the p53 family member ΔNp63 resulting in downregulation of ΔNp63-target genes and promoting YAP-mediated cell migration. In summary, our studies uncover changes in chromatin accessibility and activity that contribute to the oncogenic activities of YAP.

DOI: https://doi.org/10.1093/nar/gkad107
Mol Cell. 2023 Mar 02. pii: S1097-2765(23)00085-0. [Epub ahead of print]83(5): 715-730.e6

Gene silencing dynamics are modulated by transiently active regulatory elements.

Marit W Vermunt, Jing Luan, Zhe Zhang, A Josephine Thrasher, Anran Huang, Megan S Saari, Eugene Khandros, Robert A Beagrie, Shiping Zhang, Pranay Vemulamada, Matilda Brilleman, Kiwon Lee, Jennifer A Yano, Belinda M Giardine, Cheryl A Keller, Ross C Hardison, Gerd A Blobel.

  Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via the FOG1/NuRD deacetylase complex, as revealed by the study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.

Keywords:  FOG1/NuRD complex; GATA1; erythroid differentiation; gene silencing; transcriptional regulation; transient enhancer

DOI:  https://doi.org/10.1016/j.molcel.2023.02.006
Nature. 2023 Mar 01.

H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.

Hua Wang, Zheng Fan, Pavel V Shliaha, Matthew Miele, Ronald C Hendrickson, Xuejun Jiang, Kristian Helin.

Trimethylation of histone H3 lysine 4 (H3K4me3) is associated with transcriptional start sites and has been proposed to regulate transcription initiation1,2. However, redundant functions of the H3K4 SET1/COMPASS methyltransferase complexes complicate the elucidation of the specific role of H3K4me3 in transcriptional regulation3,4. Here, using mouse embryonic stem cells as a model system, we show that acute ablation of shared subunits of the SET1/COMPASS complexes leads to a complete loss of all H3K4 methylation. Turnover of H3K4me3 occurs more rapidly than that of H3K4me1 and H3K4me2 and is dependent on KDM5 demethylases. Notably, acute loss of H3K4me3 does not have detectable effects on transcriptional initiation but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II (RNAPII) pausing and slower elongation. We show that H3K4me3 is required for the recruitment of the integrator complex subunit 11 (INTS11), which is essential for the eviction of paused RNAPII and transcriptional elongation. Thus, our study demonstrates a distinct role for H3K4me3 in transcriptional pause-release and elongation rather than transcriptional initiation.

DOI: https://doi.org/10.1038/s41586-023-05780-8
iScience. 2023 Mar 17. 26(3): 106125

GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development.

Ann E Collier, Samantha N Piekos, Angela Liu, Jillian M Pattison, Franco Felix, Alessandro A Bailetti, Egor Sedov, Sadhana Gaddam, Hanson Zhen, Anthony E Oro.

  Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.

Keywords:  Biological sciences; Cell biology; Developmental biology

DOI:  https://doi.org/10.1016/j.isci.2023.106125
Mol Cell. 2023 Feb 23. pii: S1097-2765(23)00107-7. [Epub ahead of print]

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network.

Massimo Carraro, Ivo A Hendriks, Colin M Hammond, Victor Solis-Mezarino, Moritz Völker-Albert, Jonas D Elsborg, Melanie B Weisser, Christos Spanos, Guillermo Montoya, Juri Rappsilber, Axel Imhof, Michael L Nielsen, Anja Groth.

  A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.

Keywords:  ASF1; DAXX; HJURP; NASP; epigenetic; gene silencing; heterochromatin; histone chaperone; nucleosome assembly; protein network; proteomics

DOI:  https://doi.org/10.1016/j.molcel.2023.02.009
Nat Commun. 2023 Mar 03. 14(1): 1209

Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis.

Yu Zhang, Min Ma, Meng Liu, Aiqing Sun, Xiaoyun Zheng, Kunpeng Liu, Chunmei Yin, Chuanshun Li, Cizhong Jiang, Xiaoyu Tu, Yuda Fang.

Histone H2A monoubiquitination (H2Aub1) functions as a conserved posttranslational modification in eukaryotes to maintain gene expression and guarantee cellular identity. Arabidopsis H2Aub1 is catalyzed by the core components AtRING1s and AtBMI1s of polycomb repressive complex 1 (PRC1). Because PRC1 components lack known DNA binding domains, it is unclear how H2Aub1 is established at specific genomic locations. Here, we show that the Arabidopsis cohesin subunits AtSYN4 and AtSCC3 interact with each other, and AtSCC3 binds to AtBMI1s. H2Aub1 levels are reduced in atsyn4 mutant or AtSCC3 artificial microRNA knockdown plants. ChIP-seq assays indicate that most binding events of AtSYN4 and AtSCC3 are associated with H2Aub1 along the genome where transcription is activated independently of H3K27me3. Finally, we show that AtSYN4 binds directly to the G-box motif and directs H2Aub1 to these sites. Our study thus reveals a mechanism for cohesin-mediated recruitment of AtBMI1s to specific genomic loci to mediate H2Aub1.

DOI: https://doi.org/10.1038/s41467-023-36788-3
iScience. 2023 Mar 17. 26(3): 106106

Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions.

Ester Marina-Zárate, Ana Rodríguez-Ronchel, Manuel J Gómez, Fátima Sánchez-Cabo, Almudena R Ramiro.

  CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS). Using a conditional mouse model, we have identified one set of CBSs that are lost upon CTCF depletion (lost CBSs) and another set that persists (retained CBSs). Retained CBSs are more similar to the consensus CTCF-binding sequence and usually span tandem CTCF peaks. Lost CBSs are enriched at enhancers and promoters and associate with active chromatin marks and higher transcriptional activity. In contrast, retained CBSs are enriched at TAD and loop boundaries. Integration of ChIP-seq and RNA-seq data has revealed that retained CBSs are located at the boundaries between distinct chromatin states, acting as chromatin barriers. Our results provide evidence that transient, lost CBSs are involved in transcriptional regulation, whereas retained CBSs are critical for establishing higher-order chromatin architecture.

Keywords:  Components of the immune system; Molecular Structure; Molecular mechanism of gene regulation

DOI:  https://doi.org/10.1016/j.isci.2023.106106
Nat Commun. 2023 Mar 03. 14(1): 1210

The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency.

Paraskevi Athanasouli, Martina Balli, Anchel De Jaime-Soguero, Annekatrien Boel, Sofia Papanikolaou, Bernard K van der Veer, Adrian Janiszewski, Tijs Vanhessche, Annick Francis, Youssef El Laithy, Antonio Lo Nigro, Francesco Aulicino, Kian Peng Koh, Vincent Pasque, Maria Pia Cosma, Catherine Verfaillie, An Zwijsen, Björn Heindryckx, Christoforos Nikolaou, Frederic Lluis.

Early during preimplantation development and in heterogeneous mouse embryonic stem cells (mESC) culture, pluripotent cells are specified towards either the primed epiblast or the primitive endoderm (PE) lineage. Canonical Wnt signaling is crucial for safeguarding naive pluripotency and embryo implantation, yet the role and relevance of canonical Wnt inhibition during early mammalian development remains unknown. Here, we demonstrate that transcriptional repression exerted by Wnt/TCF7L1 promotes PE differentiation of mESCs and in preimplantation inner cell mass. Time-series RNA sequencing and promoter occupancy data reveal that TCF7L1 binds and represses genes encoding essential naive pluripotency factors and indispensable regulators of the formative pluripotency program, including Otx2 and Lef1. Consequently, TCF7L1 promotes pluripotency exit and suppresses epiblast lineage formation, thereby driving cells into PE specification. Conversely, TCF7L1 is required for PE specification as deletion of Tcf7l1 abrogates PE differentiation without restraining epiblast priming. Taken together, our study underscores the importance of transcriptional Wnt inhibition in regulating lineage specification in ESCs and preimplantation embryo development as well as identifies TCF7L1 as key regulator of this process.

DOI: https://doi.org/10.1038/s41467-023-36914-1
PLoS Genet. 2023 Mar 03. 19(3): e1010654

The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy.

Madeleine L Ball, Stefan A Koestler, Leila Muresan, Sohaib Abdul Rehman, Kevin O'Holleran, Robert White.

While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription.

DOI: https://doi.org/10.1371/journal.pgen.1010654
Sci Adv. 2023 Mar;9(9): eadf2451

Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing.

Harmony R Salzler, Vasudha Vandadi, Benjamin D McMichael, John C Brown, Sally A Boerma, Mary P Leatham-Jensen, Kirsten M Adams, Michael P Meers, Jeremy M Simon, Robert J Duronio, Daniel J McKay, A Gregory Matera.

Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or replication-independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive Polycomb response elements located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes using different mechanisms.

DOI: https://doi.org/10.1126/sciadv.adf2451
Nat Genet. 2023 Mar 02.

Transcription of MERVL retrotransposons is required for preimplantation embryo development.

Akihiko Sakashita, Tomohiro Kitano, Hirotsugu Ishizu, Youjia Guo, Harumi Masuda, Masaru Ariura, Kensaku Murano, Haruhiko Siomi.

Zygotic genome activation (ZGA) is a critical postfertilization step that promotes totipotency and allows different cell fates to emerge in the developing embryo. MERVL (murine endogenous retrovirus-L) is transiently upregulated at the two-cell stage during ZGA. Although MERVL expression is widely used as a marker of totipotency, the role of this retrotransposon in mouse embryogenesis remains elusive. Here, we show that full-length MERVL transcripts, but not encoded retroviral proteins, are essential for accurate regulation of the host transcriptome and chromatin state during preimplantation development. Both knockdown and CRISPRi-based repression of MERVL result in embryonic lethality due to defects in differentiation and genomic stability. Furthermore, transcriptome and epigenome analysis revealed that loss of MERVL transcripts led to retention of an accessible chromatin state at, and aberrant expression of, a subset of two-cell-specific genes. Taken together, our results suggest a model in which an endogenous retrovirus plays a key role in regulating host cell fate potential.

DOI: https://doi.org/10.1038/s41588-023-01324-y
Cancer Res. 2023 Feb 27. pii: CAN-22-1858. [Epub ahead of print]

Enhancer co-amplification and hijacking promote oncogene expression in liposarcoma.

Tingting Liu, Juan Wang, Hongbo Yang, Qiushi Jin, Xiaotao Wang, Yihao Fu, Yu Luan, Qixuan Wang, Mark W Youngblood, Xinyan Lu, Lucia Casadei, Raphael Pollock, Feng Yue.

Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults with two major subtypes, well differentiated and dedifferentiated. Both subtypes are characterized with the pathognomonic giant ring or marker chromosomes that harbor high copy-numbers of known oncogenes. Here, we reported a comprehensive molecular characterization of both tumor and normal tissues from the same LPS patients, including whole genome sequencing (WGS), transcriptome, enhancer landscape, and genome-wide 3D genome structure by Hi-C. Tumor-specific transcripts and regulatory elements were identified, and enhancer co-amplification and hijacking events were discovered as novel mechanisms upregulating oncogenes such as MDM2, CDK4 and HMGA2. Combining Hi-C, optical mapping, nanopore long reads and WGS data partially resolved complex structural variations and reconstructed the local genome and the giant chromosome. Overall, this study provides a comprehensive resource for LPS research and offers insights into how altered enhancers and the 3D genome contribute to gene dysregulation in cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1858
Cell Rep. 2023 Mar 01. pii: S2211-1247(23)00212-7. [Epub ahead of print]42(3): 112201

Structural basis of Janus kinase trans-activation.

Nathanael A Caveney, Robert A Saxton, Deepa Waghray, Caleb R Glassman, Naotaka Tsutsumi, Stevan R Hubbard, K Christopher Garcia.

  Janus kinases (JAKs) mediate signal transduction downstream of cytokine receptors. Cytokine-dependent dimerization is conveyed across the cell membrane to drive JAK dimerization, trans-phosphorylation, and activation. Activated JAKs in turn phosphorylate receptor intracellular domains (ICDs), resulting in the recruitment, phosphorylation, and activation of signal transducer and activator of transcription (STAT)-family transcription factors. The structural arrangement of a JAK1 dimer complex with IFNλR1 ICD was recently elucidated while bound by stabilizing nanobodies. While this revealed insights into the dimerization-dependent activation of JAKs and the role of oncogenic mutations in this process, the tyrosine kinase (TK) domains were separated by a distance not compatible with the trans-phosphorylation events between the TK domains. Here, we report the cryoelectron microscopy structure of a mouse JAK1 complex in a putative trans-activation state and expand these insights to other physiologically relevant JAK complexes, providing mechanistic insight into the crucial trans-activation step of JAK signaling and allosteric mechanisms of JAK inhibition.

Keywords:  CP: Molecular biology; cryo-EM; cytokine; janus kinase; phosphorylation

DOI:  https://doi.org/10.1016/j.celrep.2023.112201
Sci Adv. 2023 Mar;9(9): eade3876

Cohesin regulates alternative splicing.

Amit K Singh, Qingrong Chen, Cu Nguyen, Daoud Meerzaman, Dinah S Singer.

Cohesin, a trimeric complex that establishes sister chromatid cohesion, has additional roles in chromatin organization and transcription. We report that among those roles is the regulation of alternative splicing through direct interactions and in situ colocalization with splicing factors. Degradation of cohesin results in marked changes in splicing, independent of its effects on transcription. Introduction of a single cohesin point mutation in embryonic stem cells alters splicing patterns, demonstrating causality. In primary human acute myeloid leukemia, mutations in cohesin are highly correlated with distinct patterns of alternative splicing. Cohesin also directly interacts with BRD4, another splicing regulator, to generate a pattern of splicing that is distinct from either factor alone, documenting their functional interaction. These findings identify a role for cohesin in regulating alternative splicing in both normal and leukemic cells and provide insights into the role of cohesin mutations in human disease.

DOI: https://doi.org/10.1126/sciadv.ade3876
Nat Commun. 2023 Mar 03. 14(1): 1221

ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.

Oliver J Mainwaring, Holger Weishaupt, Miao Zhao, Gabriela Rosén, Anna Borgenvik, Laura Breinschmid, Annemieke D Verbaan, Stacey Richardson, Dean Thompson, Steven C Clifford, Rebecca M Hill, Karl Annusver, Anders Sundström, Karl O Holmberg, Maria Kasper, Sonja Hutter, Fredrik J Swartling.

Medulloblastoma, the most common malignant pediatric brain tumor, often harbors MYC amplifications. Compared to high-grade gliomas, MYC-amplified medulloblastomas often show increased photoreceptor activity and arise in the presence of a functional ARF/p53 suppressor pathway. Here, we generate an immunocompetent transgenic mouse model with regulatable MYC that develop clonal tumors that molecularly resemble photoreceptor-positive Group 3 medulloblastoma. Compared to MYCN-expressing brain tumors driven from the same promoter, pronounced ARF silencing is present in our MYC-expressing model and in human medulloblastoma. While partial Arf suppression causes increased malignancy in MYCN-expressing tumors, complete Arf depletion promotes photoreceptor-negative high-grade glioma formation. Computational models and clinical data further identify drugs targeting MYC-driven tumors with a suppressed but functional ARF pathway. We show that the HSP90 inhibitor, Onalespib, significantly targets MYC-driven but not MYCN-driven tumors in an ARF-dependent manner. The treatment increases cell death in synergy with cisplatin and demonstrates potential for targeting MYC-driven medulloblastoma.

DOI: https://doi.org/10.1038/s41467-023-36847-9
Cell. 2023 Mar 02. pii: S0092-8674(23)00109-5. [Epub ahead of print]186(5): 1066-1085.e36

Linking chromatin acylation mark-defined proteome and genome in living cells.

Fangfei Qin, Boyuan Li, Hui Wang, Sihui Ma, Jiaofeng Li, Shanglin Liu, Linghao Kong, Huangtao Zheng, Rongfeng Zhu, Yu Han, Mingdong Yang, Kai Li, Xiong Ji, Peng R Chen.

  A generalizable strategy with programmable site specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and β-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation and established linkages for chromatin acylation mark-defined proteome, genome, and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the "metabolites-modification-regulation" axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.

Keywords:  chromatin; crotonylation; gene regulation; genetic code expansion; histone mark; metabolites; multi-omics; post-translational modification; super-enhancer; β-hydroxybutyrylation

DOI:  https://doi.org/10.1016/j.cell.2023.02.007
Nucleic Acids Res. 2023 Mar 02. pii: gkad105. [Epub ahead of print]

HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.

Rui Tian, Zheying Huang, Lifang Li, Jingping Yuan, Qinghua Zhang, Lirong Meng, Bin Lang, Yongfeng Hong, Chaoyue Zhong, Xun Tian, Zifeng Cui, Zhuang Jin, Jiashuo Liu, Zhaoyue Huang, Yuyan Wang, Ye Chen, Zheng Hu.

Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at the genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV integration detection, super-enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified seven high-ranking cellular SEs generated by HPV integration in total (the HPV breakpoint-induced cellular SEs, BP-cSEs), leading to intra-chromosomal and inter-chromosomal regulation of chromosomal genes. The pathway analysis revealed that the dysregulated chromosomal genes were correlated to cancer-related pathways. Importantly, we demonstrated that BP-cSEs existed in the HPV-human hybrid ecDNAs, explaining the above transcriptional alterations. Our results suggest that HPV integration generates cellular SEs that function as ecDNA to regulate unconstrained transcription, expanding the tumorigenic mechanism of HPV integration and providing insights for developing new diagnostic and therapeutic strategies.

DOI: https://doi.org/10.1093/nar/gkad105
Development. 2023 Feb 27. pii: dev.201163. [Epub ahead of print]

Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury.

Daniel A Zuppo, Maria A Missinato, Lucas Santana-Santos, Guang Li, Panayiotis V Benos, Michael Tsang.

  The regenerative capacity of the mammalian heart is poor with one potential reason being that adult cardiomyocytes cannot proliferate at sufficient levels to replace lost tissue. During development and neonatal stages, cardiomyocytes can successfully divide under injury conditions; however, as these cells mature their ability to proliferate is lost. Therefore, understanding regulatory programs that can induce post-mitotic cardiomyocytes into a proliferative state is essential to enhance cardiac regeneration. Here we report the forkhead transcription factor, foxm1, is required for cardiomyocyte proliferation after injury through transcriptional regulation of cell cycle genes. Transcriptomic analysis of injured zebrafish hearts revealed that foxm1 expression is increased in border zone cardiomyocytes. Decreased cardiomyocyte proliferation and expression of cell cycle genes in foxm1 mutant hearts was observed, suggesting it is required for cell cycle checkpoints. Subsequent analysis of a candidate Foxm1 target gene, cenpf, revealed this microtubule and kinetochore binding protein is also required for cardiac regeneration. Moreover, cenpf mutants show increased cardiomyocyte binucleation. Thus, foxm1 and cenpf are required for cardiomyocytes to complete mitosis during zebrafish cardiac regeneration.

Keywords:  Binucleation; Cardiomyocyte proliferation; Cenpf; Foxm1; Heart regeneration; Zebrafish

DOI:  https://doi.org/10.1242/dev.201163