bims-crepig 2023-07-23 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–07–23
twenty papers selected by
Connor Rogerson, University of Cambridge

Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells.
H3K36 methylation maintains cell identity by regulating opposing lineage programmes.
UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability.
RNA polymerase II associates with active genes during DNA replication.
Histone variants shape chromatin states in Arabidopsis.
Mediator 1 ablation induces enamel-to-hair lineage conversion in mice through enhancer dynamics.
Separation of transcriptional repressor and activator functions in Drosophila HDAC3.
DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias.
High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer.
Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression.
OBOX regulates murine zygotic genome activation and early development.
Baf155 regulates skeletal muscle metabolism via HIF-1a signaling.
SIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma.
Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis.
Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance.
Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.
Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer.
TET1 facilitates specification of early human lineages including germ cells.
The human placenta exhibits a unique transcriptomic void.

iScience. 2023 Jul 21. 26(7): 107170

Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells.

Julio C Flores, Simone Sidoli, Meelad M Dawlaty.

  Tet2 is a member of the Ten-eleven translocation (Tet1/2/3) family of enzymes and is expressed in embryonic stem cells (ESCs). It demethylates DNA (catalytic functions) and partners with chromatin modifiers (noncatalytic functions) to regulate genes. However, the significance of these functions in ESCs is less defined. Using Tet2 catalytic mutant (Tet2m/m) and knockout (Tet2-/-) ESCs, we identified Tet2 target genes regulated by its catalytic dependent versus independent roles. Tet2 was enriched at their active enhancers and promoters to demethylate them. We also identified the histone deacetylase component Sin3a as a Tet2 partner, co-localizing at promoters and active enhancers. Tet2 deficiency diminished Sin3a at these regions. Tet2 and Sin3a co-occupancy overlapped with Tet1. Combined loss of Tet1/2, but not of their catalytic activities, reduced Sin3a at active enhancers. These findings establish Tet2 catalytic and noncatalytic functions as regulators of DNA demethylation and Sin3a recruitment at active enhancers in ESCs.

Keywords:  Biological sciences; Genetics; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.107170
Nat Cell Biol. 2023 Jul 17.

H3K36 methylation maintains cell identity by regulating opposing lineage programmes.

Michael S Hoetker, Masaki Yagi, Bruno Di Stefano, Justin Langerman, Simona Cristea, Lai Ping Wong, Aaron J Huebner, Jocelyn Charlton, Weixian Deng, Chuck Haggerty, Ruslan I Sadreyev, Alexander Meissner, Franziska Michor, Kathrin Plath, Konrad Hochedlinger.

The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.

DOI: https://doi.org/10.1038/s41556-023-01191-z
Mol Cell. 2023 Jul 12. pii: S1097-2765(23)00475-6. [Epub ahead of print]

UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability.

Jonathan M Tsai, Jacob D Aguirre, Yen-Der Li, Jared Brown, Vivian Focht, Lukas Kater, Georg Kempf, Brittany Sandoval, Stefan Schmitt, Justine C Rutter, Pius Galli, Colby R Sandate, Jevon A Cutler, Charles Zou, Katherine A Donovan, Ryan J Lumpkin, Simone Cavadini, Paul M C Park, Quinlan Sievers, Charlie Hatton, Elizabeth Ener, Brandon D Regalado, Micah T Sperling, Mikołaj Słabicki, Jeonghyeon Kim, Rebecca Zon, Zinan Zhang, Peter G Miller, Roger Belizaire, Adam S Sperling, Eric S Fischer, Rafael Irizarry, Scott A Armstrong, Nicolas H Thomä, Benjamin L Ebert.

  Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.

Keywords:  HECT-E3 ligases; nuclear receptors; protein degradation; structural biology; ubiquitin ligases

DOI:  https://doi.org/10.1016/j.molcel.2023.06.028
Nature. 2023 Jul 19.

RNA polymerase II associates with active genes during DNA replication.

Tyler K Fenstermaker, Svetlana Petruk, Sina K Kovermann, Hugh W Brock, Alexander Mazo.

The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.

DOI: https://doi.org/10.1038/s41586-023-06341-9
Elife. 2023 07 19. pii: RP87714. [Epub ahead of print]12

Histone variants shape chromatin states in Arabidopsis.

Bhagyshree Jamge, Zdravko J Lorković, Elin Axelsson, Akihisa Osakabe, Vikas Shukla, Ramesh Yelagandula, Svetlana Akimcheva, Annika Luisa Kuehn, Frédéric Berger.

  How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.

Keywords:  A. thaliana; Arabidopsis; DDM1; Histone variant; chromatin remodeler; chromatin state; genetics; genomics; transcription

DOI:  https://doi.org/10.7554/eLife.87714
Commun Biol. 2023 Jul 21. 6(1): 766

Mediator 1 ablation induces enamel-to-hair lineage conversion in mice through enhancer dynamics.

Roman Thaler, Keigo Yoshizaki, Thai Nguyen, Satoshi Fukumoto, Pamela Den Besten, Daniel D Bikle, Yuko Oda.

Postnatal cell fate is postulated to be primarily determined by the local tissue microenvironment. Here, we find that Mediator 1 (Med1) dependent epigenetic mechanisms dictate tissue-specific lineage commitment and progression of dental epithelia. Deletion of Med1, a key component of the Mediator complex linking enhancer activities to gene transcription, provokes a tissue extrinsic lineage shift, causing hair generation in incisors. Med1 deficiency gives rise to unusual hair growth via primitive cellular aggregates. Mechanistically, we find that MED1 establishes super-enhancers that control enamel lineage transcription factors in dental stem cells and their progenies. However, Med1 deficiency reshapes the enhancer landscape and causes a switch from the dental transcriptional program towards hair and epidermis on incisors in vivo, and in dental epithelial stem cells in vitro. Med1 loss also provokes an increase in the number and size of enhancers. Interestingly, control dental epithelia already exhibit enhancers for hair and epidermal key transcription factors; these transform into super-enhancers upon Med1 loss suggesting that these epigenetic mechanisms cause the shift towards epidermal and hair lineages. Thus, we propose a role for Med1 in safeguarding lineage specific enhancers, highlight the central role of enhancer accessibility in lineage reprogramming and provide insights into ectodermal regeneration.

DOI: https://doi.org/10.1038/s42003-023-05105-5
Development. 2023 Jul 17. pii: dev.201548. [Epub ahead of print]

Separation of transcriptional repressor and activator functions in Drosophila HDAC3.

Min Tang, Isabel Regadas, Sergey Belikov, Olga Shilkova, Lei Xu, Erik Wernersson, Xuewen Liu, Hongmei Wu, Magda Bienko, Mattias Mannervik.

  The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex and its canonical function is in transcriptional repression, but it can also activate transcription. Here we show that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N-terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhance repressor activity beyond wild-type in the early embryo. We conclude that the critical functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery.

Keywords:  Chromatin; Embryo development; HDAC3; Histone deacetylase; Transcription

DOI:  https://doi.org/10.1242/dev.201548
Nucleic Acids Res. 2023 Jul 18. pii: gkad581. [Epub ahead of print]

DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias.

Mathias Boulanger, Mays Aqrouq, Denis Tempé, Chamseddine Kifagi, Marko Ristic, Dana Akl, Rawan Hallal, Aude Carusi, Ludovic Gabellier, Marion de Toledo, Jon-Otti Sigurdsson, Tony Kaoma, Charlotte Andrieu-Soler, Thierry Forné, Eric Soler, Yosr Hicheri, Elise Gueret, Laurent Vallar, Jesper V Olsen, Guillaume Cartron, Marc Piechaczyk, Guillaume Bossis.

Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR), one of the main drugs used to treat Acute Myeloid Leukemia (AML), induces rapid (3 h) and broad transcriptional changes in AML cells. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, in particular at active promoters and enhancers. Surprisingly, inhibition of SUMOylation with ML-792 (SUMO E1 inhibitor), dampens DNR-induced transcriptional reprogramming. Quantitative proteomics shows that the proteins deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. DNR leads to a reconfiguration of chromatin loops engaging CTCF- and SUMO-bound NFKB2 promoter with a distal cis-regulatory region and inhibition of SUMOylation with ML-792 prevents these changes.

DOI: https://doi.org/10.1093/nar/gkad581
Cell Rep. 2023 Jul 18. pii: S2211-1247(23)00832-X. [Epub ahead of print]42(8): 112821

High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer.

Xiaoyong Fu, Resel Pereira, Chia-Chia Liu, Carmine De Angelis, Martin J Shea, Sarmistha Nanda, Lanfang Qin, Tamika Mitchell, Maria L Cataldo, Jamunarani Veeraraghavan, Vidyalakshmi Sethunath, Mario Giuliano, Carolina Gutierrez, Balázs Győrffy, Meghana V Trivedi, Ofir Cohen, Nikhil Wagle, Agostina Nardone, Rinath Jeselsohn, Mothaffar F Rimawi, C Kent Osborne, Rachel Schiff.

  Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) enriched in ER+ endocrine-resistant (EndoR) cells. We identify Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, as a strong predictor for poor outcomes of ER+ BC. It is elevated in ER+ metastases vs. primary tumors, irrespective of ESR1 mutations. Genomic ER binding near Secretome14 genes is also increased in mutant ER-expressing or mitogen-treated ER+ BC cells and in ER+ metastatic vs. primary tumors, suggesting a convergent pathway including high growth factor receptor signaling in activating pro-metastatic secretome genes. Our findings uncover H-FOXA1-induced ER reprogramming that drives EndoR and metastasis partly via an H-FOXA1/ER-dependent secretome.

Keywords:  CP: Cancer; breast cancer; cistrome; endocrine resistance; enhancer; epigenetic; estrogen receptor; forkhead box protein A1; metastasis; secretome; transcription factor

DOI:  https://doi.org/10.1016/j.celrep.2023.112821
Dev Cell. 2023 Jul 17. pii: S1534-5807(23)00324-6. [Epub ahead of print]

Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression.

Marissa M Gaskill, Isabella V Soluri, Annemarie E Branks, Alan P Boka, Michael R Stadler, Katherine Vietor, Hao-Yu S Huang, Tyler J Gibson, Apratim Mukherjee, Mustafa Mir, Shelby A Blythe, Melissa M Harrison.

  The eukaryotic genome is organized to enable the precise regulation of gene expression. This organization is established as the embryo transitions from a fertilized gamete to a totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. This non-uniform distribution is driven by binding to highly abundant GA repeats. At GA repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains essential for the robust regulation of gene expression.

Keywords:  Drosophila; MZT; ZGA; gene expression; heterochromatin; maternal-to-zygotic transition; subnuclear domains; zygotic genome acivation

DOI:  https://doi.org/10.1016/j.devcel.2023.06.010
Nature. 2023 Jul 17.

OBOX regulates murine zygotic genome activation and early development.

Shuyan Ji, Fengling Chen, Paula Stein, Jiacheng Wang, Ziming Zhou, Lijuan Wang, Qing Zhao, Zili Lin, Bofeng Liu, Kai Xu, Fangnong Lai, Zhuqing Xiong, Xiaoyu Hu, Tianxiang Kong, Feng Kong, Bo Huang, Qiujun Wang, Qianhua Xu, Qiang Fan, Ling Liu, Carmen J Williams, Richard M Schultz, Wei Xie.

Zygotic genome activation (ZGA) activates the quiescent genome to enable the maternal-to-zygotic transition1,2. However, the identity of transcription factors (TFs) that underlie mammalian ZGA in vivo remains elusive. Here, we showed that OBOX, a PRD-like homeobox domain TF family (OBOX1-8)3-5, are key regulators of mouse ZGA. Mice deficient for maternally transcribed Obox1/2/5/7 and zygotically expressed Obox3/4 had a 2-4 cell arrest accompanied by impaired ZGA. Maternal and zygotic OBOX redundantly supported embryonic development as Obox KO defects could be rescued by restoring either of them. Chromatin binding analysis revealed Obox knockout preferentially affected OBOX-binding targets. Mechanistically, OBOX facilitated RNA Pol II "pre-configuration", as Pol II relocated from the initial 1-cell binding targets to ZGA gene promoters and distal enhancers. The impaired Pol II pre-configuration in Obox mutants was accompanied by defective ZGA and chromatin accessibility transition, as well as aberrant activation of 1-cell Pol II targets. Finally, ectopic expression of OBOX activated ZGA genes and MERVL repeats in mESCs. Hence, these data demonstrate that OBOX regulates murine ZGA and early embryogenesis.

DOI: https://doi.org/10.1038/s41586-023-06428-3
PLoS Biol. 2023 Jul 21. 21(7): e3002192

Baf155 regulates skeletal muscle metabolism via HIF-1a signaling.

Jong-Seol Kang, Dongha Kim, Joonwoo Rhee, Ji-Yun Seo, Inkuk Park, Ji-Hoon Kim, Daewon Lee, WonUk Lee, Ye Lynne Kim, Kyusang Yoo, Sunghwan Bae, Jongkyeong Chung, Rho Hyun Seong, Young-Yun Kong.

During exercise, skeletal muscle is exposed to a low oxygen condition, hypoxia. Under hypoxia, the transcription factor hypoxia-inducible factor-1α (HIF-1α) is stabilized and induces expressions of its target genes regulating glycolytic metabolism. Here, using a skeletal muscle-specific gene ablation mouse model, we show that Brg1/Brm-associated factor 155 (Baf155), a core subunit of the switch/sucrose non-fermentable (SWI/SNF) complex, is essential for HIF-1α signaling in skeletal muscle. Muscle-specific ablation of Baf155 increases oxidative metabolism by reducing HIF-1α function, which accompanies the decreased lactate production during exercise. Furthermore, the augmented oxidation leads to high intramuscular adenosine triphosphate (ATP) level and results in the enhancement of endurance exercise capacity. Mechanistically, our chromatin immunoprecipitation (ChIP) analysis reveals that Baf155 modulates DNA-binding activity of HIF-1α to the promoters of its target genes. In addition, for this regulatory function, Baf155 requires a phospho-signal transducer and activator of transcription 3 (pSTAT3), which forms a coactivator complex with HIF-1α, to activate HIF-1α signaling. Our findings reveal the crucial role of Baf155 in energy metabolism of skeletal muscle and the interaction between Baf155 and hypoxia signaling.

DOI: https://doi.org/10.1371/journal.pbio.3002192
Nat Commun. 2023 07 19. 14(1): 4357

SIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma.

Connor J Hughes, Kaiah M Fields, Etienne P Danis, Jessica Y Hsu, Deepika Neelakantan, Melanie Y Vincent, Annika L Gustafson, Michael J Oliphant, Varsha Sreekanth, Vadym Zaberezhnyy, James C Costello, Paul Jedlicka, Heide L Ford.

Ewing sarcoma (ES), which is characterized by the presence of oncogenic fusion proteins such as EWS/FLI1, is an aggressive pediatric malignancy with a high rate of early dissemination and poor outcome after distant spread. Here we demonstrate that the SIX1 homeoprotein, which enhances metastasis in most tumor types, suppresses ES metastasis by co-regulating EWS/FLI1 target genes. Like EWS/FLI1, SIX1 promotes cell growth/transformation, yet dramatically inhibits migration and invasion, as well as metastasis in vivo. We show that EWS/FLI1 promotes SIX1 protein expression, and that the two proteins share genome-wide binding profiles and transcriptional regulatory targets, including many metastasis-associated genes such as integrins, which they co-regulate. We further show that SIX1 downregulation of integrins is critical to its ability to inhibit invasion, a key characteristic of metastatic cells. These data demonstrate an unexpected anti-metastatic function for SIX1, through coordinate gene regulation with the key oncoprotein in ES, EWS/FLI1.

DOI: https://doi.org/10.1038/s41467-023-39945-w
Nat Commun. 2023 07 17. 14(1): 4103

Epigenetic mechanisms to propagate histone acetylation by p300/CBP.

Masaki Kikuchi, Satoshi Morita, Masatoshi Wakamori, Shin Sato, Tomomi Uchikubo-Kamo, Takehiro Suzuki, Naoshi Dohmae, Mikako Shirouzu, Takashi Umehara.

Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone N-terminal tail acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization.

DOI: https://doi.org/10.1038/s41467-023-39735-4
Nucleic Acids Res. 2023 Jul 20. pii: gkad593. [Epub ahead of print]

Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis.

Anastasios Liakos, Anna-Chloe Synacheri, Dimitris Konstantopoulos, Georgios C Stefos, Matthieu D Lavigne, Maria Fousteri.

In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.

DOI: https://doi.org/10.1093/nar/gkad593
Commun Biol. 2023 Jul 21. 6(1): 765

Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance.

Huihui Fan, Feng Wang, Andy Zeng, Alex Murison, Katarzyna Tomczak, Dapeng Hao, Fatima Zahra Jelloul, Bofei Wang, Praveen Barrodia, Shaoheng Liang, Ken Chen, Linghua Wang, Zhongming Zhao, Kunal Rai, Abhinav K Jain, John Dick, Naval Daver, Andy Futreal, Hussein A Abbas.

Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.

DOI: https://doi.org/10.1038/s42003-023-05120-6
Nature. 2023 Jul 19.

Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.

Haipeng Guan, Pei Wang, Pei Zhang, Chun Ruan, Yutian Ou, Bo Peng, Xiangdong Zheng, Jianlin Lei, Bing Li, Chuangye Yan, Haitao Li.

Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation1-4. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions5-7. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.

DOI: https://doi.org/10.1038/s41586-023-06349-1
Cell Rep. 2023 Jul 13. pii: S2211-1247(23)00789-1. [Epub ahead of print]42(7): 112778

Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer.

Kyukwang Kim, Mooyoung Kim, Andrew J Lee, Sang-Hyun Song, Jun-Kyu Kang, Junghyun Eom, Gyeong Hoon Kang, Jeong Mo Bae, Sunwoo Min, Yeonsoo Kim, Yoojoo Lim, Han Sang Kim, Young-Joon Kim, Tae-You Kim, Inkyung Jung.

  The regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation remains unclear. This study investigated SV-mediated gene dysregulation by profiling 3D cancer genome maps from 40 patients with colorectal cancer (CRC). We developed a machine learning-based method for spatial characterization of the altered 3D cancer genome. This revealed a frequent establishment of "de novo chromatin contacts" that can span multiple topologically associating domains (TADs) in addition to the canonical TAD fusion/shuffle model. Using this information, we precisely identified super-enhancer (SE)-hijacking and its clonal characteristics. Clonal SE-hijacking genes, such as TOP2B, are recurrently associated with cell-cycle/DNA-processing functions, which can potentially be used as CRC prognostic markers. Oncogene activation and increased drug resistance due to SE-hijacking were validated by reconstructing the patient's SV using CRISPR-Cas9. Collectively, the spatial and clonality-resolved analysis of the 3D cancer genome reveals regulatory principles of large-scale SVs in oncogene activation and their clinical implications.

Keywords:  3D cancer genome; CP: Cancer; CP: Genomics; clonality; colorectal cancer; enhancer-hijacking; in situ Hi-C; prognostic marker; structural variations

DOI:  https://doi.org/10.1016/j.celrep.2023.112778
iScience. 2023 Jul 21. 26(7): 107191

TET1 facilitates specification of early human lineages including germ cells.

Fei-Man Hsu, Qiu Ya Wu, Emily B Fabyanic, Alex Wei, Hao Wu, Amander T Clark.

  Ten Eleven Translocation 1 (TET1) is a regulator of localized DNA demethylation through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). To examine DNA demethylation in human primordial germ cell-like cells (hPGCLCs) induced from human embryonic stem cells (hESCs), we performed bisulfite-assisted APOBEC coupled epigenetic sequencing (bACEseq) followed by integrated genomics analysis. Our data indicates that 5hmC enriches at hPGCLC-specific NANOG, SOX17 or TFAP2C binding sites on hPGCLC induction, and this is accompanied by localized DNA demethylation. Using CRISPR-Cas9, we show that deleting the catalytic domain of TET1 reduces hPGCLC competency when starting with hESC cultured on mouse embryonic fibroblasts, and this phenotype can be rescued after transitioning hESCs to defined media and a recombinant substrate. Taken together, our study demonstrates the importance of 5hmC in facilitating hPGCLC competency, and the role of hESC culture conditions in modulating this effect.

Keywords:  Developmental biology; Embryology; Epigenetics

DOI:  https://doi.org/10.1016/j.isci.2023.107191
Cell Rep. 2023 Jul 13. pii: S2211-1247(23)00811-2. [Epub ahead of print]42(7): 112800

The human placenta exhibits a unique transcriptomic void.

Sungsam Gong, Francesca Gaccioli, Irving L M H Aye, Giulia Avellino, Emma Cook, Andrew R J Lawson, Luke M R Harvey, Gordon C S Smith, D Stephen Charnock-Jones.

  The human placenta exhibits a unique genomic architecture with an unexpectedly high mutation burden and many uniquely expressed genes. The aim of this study is to identify transcripts that are uniquely absent or depleted in the placenta. Here, we show that 40 of 46 of the other organs have no selectively depleted transcripts and that, of the remaining six, the liver has the largest number, with 26. In contrast, the term placenta has 762 depleted transcripts. Gene Ontology analysis of this depleted set highlighted multiple pathways reflecting known unique elements of placental physiology. For example, transcripts associated with neuronal function are in the depleted set-as expected given the lack of placental innervation. However, this demonstrated overrepresentation of genes involved in mitochondrial function (p = 5.8 × 10-10), including PGC-1α, the master regulator of mitochondrial biogenesis, and genes involved in polyamine metabolism (p = 2.1 × 10-4).

Keywords:  CP: Developmental biology; CP: Molecular biology

DOI:  https://doi.org/10.1016/j.celrep.2023.112800