bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–12–25
eightteen papers selected by
Connor Rogerson, University of Cambridge
  1. EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release.
  2. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.
  3. Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.
  4. Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.
  5. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.
  6. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
  7. HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin.
  8. A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling.
  9. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
  10. Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.
  11. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.
  12. Systematic identification and characterization of repressive domains in Drosophila transcription factors.
  13. Dynamic phase separation of the androgen receptor and its coactivators key to regulate gene expression.
  14. The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra.
  15. DNA-TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families.
  16. BRD8 maintains glioblastoma by epigenetic reprogramming of the p53 network.
  17. STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.
  18. Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae.
  1. Cell Rep. 2022 Dec 20. pii: S2211-1247(22)01722-3. [Epub ahead of print]41(12): 111830
    EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release.
    Kaustav Mukherjee, James J Bieker.
      EKLF/Klf1 is a zinc-finger transcription activator essential for erythroid lineage commitment and terminal differentiation. Using ChIP-seq, we investigate EKLF DNA binding and transcription activation mechanisms during mouse embryonic erythropoiesis. We utilize the Nan/+ mouse that expresses the EKLF-E339D (Nan) variant mutated in its conserved zinc-finger region and address the mechanism of hypomorphic and neomorphic changes in downstream gene expression. First, we show that Nan-EKLF limits normal EKLF binding to a subset of its sites. Second, we find that ectopic binding of Nan-EKLF occurs largely at enhancers and activates transcription through pioneering activity. Third, we find that for a subset of ectopic targets, gene activation is achieved in Nan/+ only by Nan-EKLF binding to distal enhancers, leading to RNA polymerase II pause-release. These results have general applicability to understanding how a DNA binding variant factor confers dominant disruptive effects on downstream gene expression even in the presence of its normal counterpart.
    Keywords:  CBP; CP: Molecular biology; ChIP-seq; EKLF/Klf1; H3K27ac; Nan; RNA polymerase; elongation; erythropoiesis; pausing; pioneering; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2022.111830
  2. Nat Biotechnol. 2022 Dec 19.
    Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.
    Marek Bartosovic, Gonçalo Castelo-Branco.
      Probing histone modifications at a single-cell level in thousands of cells has been enabled by technologies such as single-cell CUT&Tag. Here we describe nano-CUT&Tag (nano-CT), which allows simultaneous mapping of up to three epigenomic modalities at single-cell resolution using nanobody-Tn5 fusion proteins. Multimodal nano-CT is compatible with starting materials as low as 25,000-200,000 cells and has significantly higher sensitivity and number of fragments per cell than single-cell CUT&Tag. We use nano-CT to simultaneously profile chromatin accessibility, H3K27ac, and H3K27me3 in juvenile mouse brain, allowing for discrimination of more cell types and states than unimodal single-cell CUT&Tag. We also infer chromatin velocity between assay for transposase-accessible chromatin (ATAC) and H3K27ac in the oligodendrocyte lineage and deconvolute H3K27me3 repressive states, finding two sequential waves of H3K27me3 repression at distinct gene modules during oligodendrocyte lineage progression. Given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in complex biological systems at the single-cell level.
    DOI:  https://doi.org/10.1038/s41587-022-01535-4
  3. Brief Bioinform. 2022 Dec 22. pii: bbac541. [Epub ahead of print]
    Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.
    Risa Karakida Kawaguchi, Ziqi Tang, Stephan Fischer, Chandana Rajesh, Rohit Tripathy, Peter K Koo, Jesse Gillis.
       MOTIVATION: Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, cell-type identification of scATAC-seq data is known to be challenging due to the heterogeneity derived from different protocols and the high dropout rate.
    RESULTS: In this study, we perform a systematic comparison of seven scATAC-seq datasets of mouse brain to benchmark the efficacy of neuronal cell-type annotation from gene sets. We find that redundant marker genes give a dramatic improvement for a sparse scATAC-seq annotation across the data collected from different studies. Interestingly, simple aggregation of such marker genes achieves performance comparable or higher than that of machine-learning classifiers, suggesting its potential for downstream applications. Based on our results, we reannotated all scATAC-seq data for detailed cell types using robust marker genes. Their meta scATAC-seq profiles are publicly available at https://gillisweb.cshl.edu/Meta_scATAC. Furthermore, we trained a deep neural network to predict chromatin accessibility from only DNA sequence and identified key motifs enriched for each neuronal subtype. Those predicted profiles are visualized together in our database as a valuable resource to explore cell-type specific epigenetic regulation in a sequence-dependent and -independent manner.
    Keywords:  benchmark; cell typing; deep learning; marker genes; meta analysis; motif analysis; scATAC-seq
    DOI:  https://doi.org/10.1093/bib/bbac541
  4. Nat Biotechnol. 2022 Dec 19.
    Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.
    Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi.
      Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single experiment at single-cell resolution. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), an assay capable of measuring the genome-wide presence of up to three histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq uses recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk-cell and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in human immune cells. We also extend NTT-seq to enable simultaneous profiling of cell surface protein expression and multimodal chromatin states to study cells of the immune system.
    DOI:  https://doi.org/10.1038/s41587-022-01588-5
  5. Nat Genet. 2022 Dec 20.
    Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.
    Peter Zeller, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden.
      Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.
    DOI:  https://doi.org/10.1038/s41588-022-01260-3
  6. Cell. 2022 Dec 22. pii: S0092-8674(22)01503-3. [Epub ahead of print]185(26): 4937-4953.e23
    Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
    Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C Wu, Jesse M Engreitz, Kyle Farh, Ioannis Karakikes, Kevin C Wang, Thomas Quertermous, William J Greenleaf, Anshul Kundaje.
      To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human fetal heart tissues. We identified eight major differentiation trajectories involving primary cardiac cell types, each associated with dynamic transcription factor (TF) activity signatures. We contrasted regulatory landscapes of iPSC-derived cardiac cell types and their in vivo counterparts, which enabled optimization of in vitro differentiation of epicardial cells. Further, we interpreted sequence based deep learning models of cell-type-resolved chromatin accessibility profiles to decipher underlying TF motif lexicons. De novo mutations predicted to affect chromatin accessibility in arterial endothelium were enriched in congenital heart disease (CHD) cases vs. controls. In vitro studies in iPSCs validated the functional impact of identified variation on the predicted developmental cell types. This work thus defines the cell-type-resolved cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements in CHD.
    DOI:  https://doi.org/10.1016/j.cell.2022.11.028
  7. Nucleic Acids Res. 2022 Dec 19. pii: gkac1159. [Epub ahead of print]
    HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin.
    Daniel Ballmer, Mathieu Tardat, Raphael Ortiz, Alexandra Graff-Meyer, Evgeniy A Ozonov, Christel Genoud, Antoine H F M Peters, Grigorios Fanourgakis.
      Nucleoli are nuclear compartments regulating ribosome biogenesis and cell growth. In embryonic stem cells (ESCs), nucleoli containing transcriptionally active ribosomal genes are spatially separated from pericentromeric satellite repeat sequences packaged in largely repressed constitutive heterochromatin (PCH). To date, mechanisms underlying such nuclear partitioning and the physiological relevance thereof are unknown. Here we show that repressive chromatin at PCH ensures structural integrity and function of nucleoli during cell cycle progression. Loss of heterochromatin proteins HP1α and HP1β causes deformation of PCH, with reduced H3K9 trimethylation (H3K9me3) and HP1γ levels, absence of H4K20me3 and upregulated major satellites expression. Spatially, derepressed PCH aberrantly associates with nucleoli accumulating severe morphological defects during S/G2 cell cycle progression. Hp1α/β deficiency reduces cell proliferation, ribosomal RNA biosynthesis and mobility of Nucleophosmin, a major nucleolar component. Nucleolar integrity and function require HP1α/β proteins to be recruited to H3K9me3-marked PCH and their ability to dimerize. Correspondingly, ESCs deficient for both Suv39h1/2 H3K9 HMTs display similar nucleolar defects. In contrast, Suv4-20h1/2 mutant ESCs lacking H4K20me3 at PCH do not. Suv39h1/2 and Hp1α/β deficiency-induced nucleolar defects are reminiscent of those defining human ribosomopathy disorders. Our results reveal a novel role for SUV39H/HP1-marked repressive constitutive heterochromatin in regulating integrity, function and physiology of nucleoli.
    DOI:  https://doi.org/10.1093/nar/gkac1159
  8. Nat Struct Mol Biol. 2022 Dec 19.
    A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling.
    Megan A Frederick, Kaylyn E Williamson, Meilin Fernandez Garcia, Max B Ferretti, Ryan L McCarthy, Greg Donahue, Edgar Luzete Monteiro, Naomi Takenaka, Janice Reynaga, Cigall Kadoch, Kenneth S Zaret.
      To determine how different pioneer transcription factors form a targeted, accessible nucleosome within compacted chromatin and collaborate with an ATP-dependent chromatin remodeler, we generated nucleosome arrays in vitro with a central nucleosome containing binding sites for the hematopoietic E-Twenty Six (ETS) factor PU.1 and Basic Leucine Zipper (bZIP) factors C/EBPα and C/EBPβ. Our long-read sequencing reveals that each factor can expose a targeted nucleosome on linker histone-compacted arrays, but with different nuclease sensitivity patterns. The DNA binding domain of PU.1 binds mononucleosomes, but requires an additional intrinsically disordered domain to bind and open compacted chromatin. The canonical mammalian SWI/SNF (cBAF) remodeler was unable to act upon two forms of locally open chromatin unless cBAF was enabled by a separate transactivation domain of PU.1. cBAF potentiates the PU.1 DNA binding domain to weakly open chromatin in the absence of the PU.1 disordered domain. Our findings reveal a hierarchy by which chromatin is opened and show that pioneer factors can provide specificity for action by nucleosome remodelers.
    DOI:  https://doi.org/10.1038/s41594-022-00886-5
  9. Nat Struct Mol Biol. 2022 Dec 22.
    Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
    George Spracklin, Nezar Abdennur, Maxim Imakaev, Neil Chowdhury, Sriharsa Pradhan, Leonid A Mirny, Job Dekker.
      The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-dimensional interaction preferences and which, to our knowledge, has not previously been characterized. We find that heterochromatin marked by H3K9me3, HP1α and HP1β correlates with strong compartmentalization. We demonstrate that disruption of DNA methyltransferase activity greatly remodels genome compartmentalization whereby domains lose H3K9me3-HP1α/β binding and acquire the neutrally interacting state while retaining late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the silent portion of the genome and establishes connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.
    DOI:  https://doi.org/10.1038/s41594-022-00892-7
  10. Genome Biol. 2022 Dec 20. 23(1): 263
    Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.
    Thanvi Srikant, Wei Yuan, Kenneth Wayne Berendzen, Adrián Contreras-Garrido, Hajk-Georg Drost, Rebecca Schwab, Detlef Weigel.
       BACKGROUND: Despite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially between wild Arabidopsis thaliana accessions.
    RESULTS: To test our hypothesis that global reduction of CG methylation would reduce epigenomic, transcriptomic, and phenotypic diversity in A. thaliana accessions, we knock out MET1, which is required for CG methylation, in 18 early-flowering accessions. Homozygous met1 mutants in all accessions suffer from common developmental defects such as dwarfism and delayed flowering, in addition to accession-specific abnormalities in rosette leaf architecture, silique morphology, and fertility. Integrated analysis of genome-wide methylation, chromatin accessibility, and transcriptomes confirms that MET1 inactivation greatly reduces CG methylation and alters chromatin accessibility at thousands of loci. While the effects on TE activation are similarly drastic in all accessions, the quantitative effects on non-TE genes vary greatly. The global expression profiles of accessions become considerably more divergent from each other after genome-wide removal of CG methylation, although a few genes with diverse expression profiles across wild-type accessions tend to become more similar in mutants. Most differentially expressed genes do not exhibit altered chromatin accessibility or CG methylation in cis, suggesting that absence of MET1 can have profound indirect effects on gene expression and that these effects vary substantially between accessions.
    CONCLUSIONS: Systematic analysis of MET1 requirement in different A. thaliana accessions reveals a dual role for CG methylation: for many genes, CG methylation appears to canalize expression levels, with methylation masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.
    Keywords:  Arabidopsis; DNA methylation; Epigenetics; Methyltransferase; Natural variation
    DOI:  https://doi.org/10.1186/s13059-022-02833-5
  11. Nucleic Acids Res. 2022 Dec 20. pii: gkac1188. [Epub ahead of print]
    The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.
    Lisa Marie Weber, Yulin Jia, Bastian Stielow, Stephen S Gisselbrecht, Yinghua Cao, Yanpeng Ren, Iris Rohner, Jessica King, Elisabeth Rothman, Sabrina Fischer, Clara Simon, Ignasi Forné, Andrea Nist, Thorsten Stiewe, Martha L Bulyk, Zhanxin Wang, Robert Liefke.
      The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
    DOI:  https://doi.org/10.1093/nar/gkac1188
  12. EMBO J. 2022 Dec 22. e112100
    Systematic identification and characterization of repressive domains in Drosophila transcription factors.
    Loni Klaus, Bernardo P de Almeida, Anna Vlasova, Filip Nemčko, Alexander Schleiffer, Katharina Bergauer, Lorena Hofbauer, Martina Rath, Alexander Stark.
      All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities and properties of their repressive domains (RDs) are typically unknown and the specific co-repressors (CoRs) they recruit have not been determined. Here, we develop a high-throughput, next-generation sequencing-based screening method, repressive-domain (RD)-seq, to systematically identify RDs in complex DNA-fragment libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs, which are conserved between fly and human and are required for RD function, as demonstrated by motif mutagenesis. Moreover, we show that RDs that contain one of five distinct repressive motifs interact with and depend on different CoRs, such as Groucho, CtBP, Sin3A, or Smrter. These findings advance our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations and should provide a valuable resource for further studies.
    Keywords:  co-repressors; high-throughput screening; repressive domains; short linear motifs; transcription
    DOI:  https://doi.org/10.15252/embj.2022112100
  13. Nucleic Acids Res. 2022 Dec 20. pii: gkac1158. [Epub ahead of print]
    Dynamic phase separation of the androgen receptor and its coactivators key to regulate gene expression.
    Fan Zhang, Maitree Biswas, Shabnam Massah, Joseph Lee, Shreyas Lingadahalli, Samantha Wong, Christopher Wells, Jane Foo, Nabeel Khan, Helene Morin, Neetu Saxena, Sonia H Y Kung, Bei Sun, Ana Karla Parra Nuñez, Christophe Sanchez, Novia Chan, Lauren Ung, Umut Berkay Altıntaş, Jennifer M Bui, Yuzhuo Wang, Ladan Fazli, Htoo Zarni Oo, Paul S Rennie, Nathan A Lack, Artem Cherkasov, Martin E Gleave, Jörg Gsponer, Nada Lallous.
      Numerous cancers, including prostate cancer (PCa), are addicted to transcription programs driven by specific genomic regions known as super-enhancers (SEs). The robust transcription of genes at such SEs is enabled by the formation of phase-separated condensates by transcription factors and coactivators with intrinsically disordered regions. The androgen receptor (AR), the main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the transcriptional coactivator mediator complex subunit 1 (MED1) to SEs in androgen-dependent PCa cells, thereby promoting oncogenic transcriptional programs. In this work, we reveal that full-length AR forms foci with liquid-like properties in different PCa models. We demonstrate that foci formation correlates with AR transcriptional activity, as this activity can be modulated by changing cellular foci content chemically or by silencing MED1. AR ability to phase separate was also validated in vitro by using recombinant full-length AR protein. We also demonstrate that AR antagonists, which suppress transcriptional activity by targeting key regions for homotypic or heterotypic interactions of this receptor, hinder foci formation in PCa cells and phase separation in vitro. Our results suggest that enhanced compartmentalization of AR and coactivators may play an important role in the activation of oncogenic transcription programs in androgen-dependent PCa.
    DOI:  https://doi.org/10.1093/nar/gkac1158
  14. Sci Adv. 2022 Dec 23. 8(51): eabo0694
    The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra.
    Matthias Christian Vogg, Jaroslav Ferenc, Wanda Christa Buzgariu, Chrystelle Perruchoud, Paul Gerald Layague Sanchez, Leonardo Beccari, Clara Nuninger, Youn Le Cras, Céline Delucinge-Vivier, Panagiotis Papasaikas, Stéphane Vincent, Brigitte Galliot, Charisios D Tsiairis.
      The molecular mechanisms that maintain cellular identities and prevent dedifferentiation or transdifferentiation remain mysterious. However, both processes are transiently used during animal regeneration. Therefore, organisms that regenerate their organs, appendages, or even their whole body offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4, whose expression is controlled by Wnt3/β-catenin signaling and the Sp5 transcription factor, plays a key role in tentacle formation and tentacle maintenance. Reducing Zic4 expression suffices to induce transdifferentiation of tentacle epithelial cells into foot epithelial cells. This switch requires the reentry of tentacle battery cells into the cell cycle without cell division and is accompanied by degeneration of nematocytes embedded in these cells. These results indicate that maintenance of cell fate by a Wnt-controlled mechanism is a key process both during homeostasis and during regeneration.
    DOI:  https://doi.org/10.1126/sciadv.abo0694
  15. Nucleic Acids Res. 2022 Dec 22. pii: gkac1171. [Epub ahead of print]
    DNA-TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families.
    Yi Zhang, Yong-Ping Xu, Ju-Kui Nie, Hong Chen, Genji Qin, Bo Wang, Xiao-Dong Su.
      Plant-specific TCP transcription factors are key regulators of diverse plant functions. TCP transcription factors have long been annotated as basic helix-loop-helix (bHLH) transcription factors according to remote sequence homology without experimental validation, and their consensus DNA-binding sequences and protein-DNA recognition mechanisms have remained elusive. Here, we report the crystal structures of the class I TCP domain from AtTCP15 and the class II TCP domain from AtTCP10 in complex with different double-stranded DNA (dsDNA). The complex structures reveal that the TCP domain is a distinct DNA-binding motif and the homodimeric TCP domains adopt a unique three-site recognition mode, binding to dsDNA mainly through a central pair of β-strands formed by the dimer interface and two basic flexible loops from each monomer. The consensus DNA-binding sequence for class I TCPs is a perfectly palindromic 11 bp (GTGGGNCCCAC), whereas that for class II TCPs is a near-palindromic 11 bp (GTGGTCCCCAC). The unique DNA binding mode allows the TCP domains to display broad specificity for a range of DNA sequences even shorter than 11 bp, adding further complexity to the regulatory network of plant TCP transcription factors.
    DOI:  https://doi.org/10.1093/nar/gkac1171
  16. Nature. 2022 Dec 21.
    BRD8 maintains glioblastoma by epigenetic reprogramming of the p53 network.
    Xueqin Sun, Olaf Klingbeil, Bin Lu, Caizhi Wu, Carlos Ballon, Meng Ouyang, Xiaoli S Wu, Ying Jin, Yon Hwangbo, Yu-Han Huang, Tim D D Somerville, Kenneth Chang, Jung Park, Taemoon Chung, Scott K Lyons, Junwei Shi, Hannes Vogel, Michael Schulder, Christopher R Vakoc, Alea A Mills.
      Inhibition of the tumour suppressive function of p53 (encoded by TP53) is paramount for cancer development in humans. However, p53 remains unmutated in the majority of cases of glioblastoma (GBM)-the most common and deadly adult brain malignancy1,2. Thus, how p53-mediated tumour suppression is countered in TP53 wild-type (TP53WT) GBM is unknown. Here we describe a GBM-specific epigenetic mechanism in which the chromatin regulator bromodomain-containing protein 8 (BRD8) maintains H2AZ occupancy at p53 target loci through the EP400 histone acetyltransferase complex. This mechanism causes a repressive chromatin state that prevents transactivation by p53 and sustains proliferation. Notably, targeting the bromodomain of BRD8 displaces H2AZ, enhances chromatin accessibility and engages p53 transactivation. This in turn enforces cell cycle arrest and tumour suppression in TP53WT GBM. In line with these findings, BRD8 is highly expressed with H2AZ in proliferating single cells of patient-derived GBM, and is inversely correlated with CDKN1A, a canonical p53 target that encodes p21 (refs. 3,4). This work identifies BRD8 as a selective epigenetic vulnerability for a malignancy for which treatment has not improved for decades. Moreover, targeting the bromodomain of BRD8 may be a promising therapeutic strategy for patients with TP53WT GBM.
    DOI:  https://doi.org/10.1038/s41586-022-05551-x
  17. Nat Commun. 2022 Dec 20. 13(1): 7672
    STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.
    Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Jieru Li, Yuko Sato, Manabu Shintani, Hitoshi Owada, Yasuyuki Ohkawa, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura, Hiroshi Ochiai.
      Transcription is a dynamic process. To detect the dynamic relationship among protein clusters of RNA polymerase II and coactivators, gene loci, and transcriptional activity, we insert an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site. By optimizing the individual elements, we develop the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNA polymerase II and BRD4 are observed proximal to the transcription start site of Nanog when the gene is transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 tend to be located near the transcription start site, even without transcription activity. Thus, the STREAMING-tag system reveals the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding transcriptional regulation in living cells.
    DOI:  https://doi.org/10.1038/s41467-022-35286-2
  18. PLoS Genet. 2022 Dec 21. 18(12): e1010559
    Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae.
    Thomas B Bailey, Phaedra A Whitty, Eric U Selker, Jeffrey N McKnight, Laura E McKnight.
      Upon glucose starvation, S. cerevisiae shows a dramatic alteration in transcription, resulting in wide-scale repression of most genes and activation of some others. This coincides with an arrest of cellular proliferation. A subset of such cells enters quiescence, a reversible non-dividing state. Here, we demonstrate that the conserved transcriptional corepressor Tup1 is critical for transcriptional repression after glucose depletion. We show that Tup1-Ssn6 binds new targets upon glucose depletion, where it remains as the cells enter the G0 phase of the cell cycle. In addition, we show that Tup1 represses a variety of glucose metabolism and transport genes. We explored how Tup1 mediated repression is accomplished and demonstrated that Tup1 coordinates with the Rpd3L complex to deacetylate H3K23. We found that Tup1 coordinates with Isw2 to affect nucleosome positions at glucose transporter HXT family genes during G0. Finally, microscopy revealed that a quarter of cells with a Tup1 deletion contain multiple DAPI puncta. Taken together, these findings demonstrate the role of Tup1 in transcriptional reprogramming in response to environmental cues leading to the quiescent state.
    DOI:  https://doi.org/10.1371/journal.pgen.1010559
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