bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–11–26
eightteen papers selected by
Connor Rogerson, University of Cambridge
  1. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.
  2. Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification.
  3. Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids.
  4. CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.
  5. Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF.
  6. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS.
  7. TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.
  8. ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster.
  9. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions.
  10. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing.
  11. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.
  12. BRWD1 orchestrates small pre-B cell chromatin topology by converting static to dynamic cohesin.
  13. Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
  14. IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events.
  15. A single fiber view of the nucleosome organization in eukaryotic chromatin.
  16. Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.
  17. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome.
  18. A modular dCas9-based recruitment platform for combinatorial epigenome editing.
  1. Life Sci Alliance. 2024 Feb;pii: e202302154. [Epub ahead of print]7(2):
    Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.
    Silvia Kocanova, Flavien Raynal, Isabelle Goiffon, Betul Akgol Oksuz, Davide Baú, Alain Kamgoué, Sylvain Cantaloube, Ye Zhan, Bryan Lajoie, Marc A Marti-Renom, Job Dekker, Kerstin Bystricky.
      The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
    DOI:  https://doi.org/10.26508/lsa.202302154
  2. Life Sci Alliance. 2024 Feb;pii: e202302363. [Epub ahead of print]7(2):
    Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification.
    Alexander Maytum, Benjamin Edginton-White, Peter Keane, Peter N Cockerill, Jean-Baptiste Cazier, Constanze Bonifer.
      Tissue-specific gene regulation during development involves the interplay between transcription factors and epigenetic regulators binding to enhancer and promoter elements. The pattern of active enhancers defines the cellular differentiation state. However, developmental gene activation involves a previous step called chromatin priming which is not fully understood. We recently developed a genome-wide functional assay that allowed us to functionally identify enhancer elements integrated in chromatin regulating five stages spanning the in vitro differentiation of embryonic stem cells to blood. We also measured global chromatin accessibility, histone modifications, and transcription factor binding. The integration of these data identified and characterised cis-regulatory elements which become activated before the onset of gene expression, some of which are primed in a signalling-dependent fashion. Deletion of such a priming element leads to a delay in the up-regulation of its associated gene in development. Our work uncovers the details of a complex network of regulatory interactions with the dynamics of early chromatin opening being at the heart of dynamic tissue-specific gene expression control.
    DOI:  https://doi.org/10.26508/lsa.202302363
  3. Nat Cell Biol. 2023 Nov 23.
    Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids.
    Florian Noack, Silvia Vangelisti, Nora Ditzer, Faye Chong, Mareike Albert, Boyan Bonev.
      Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomics methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a method-3D genome, RNA, accessibility and methylation sequencing (3DRAM-seq)-that simultaneously interrogates spatial genome organization, chromatin accessibility and DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA sequencing in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay to profile cell-type-specific enhancer activity in organoids and to functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues.
    DOI:  https://doi.org/10.1038/s41556-023-01296-5
  4. Bioinformatics. 2023 Nov 01. pii: btad687. [Epub ahead of print]39(11):
    CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.
    Trisevgeni Rapakoulia, Sara Lopez Ruiz De Vargas, Persia Akbari Omgba, Verena Laupert, Igor Ulitsky, Martin Vingron.
       MOTIVATION: Identifying target promoters of active enhancers is a crucial step for realizing gene regulation and deciphering phenotypes and diseases. Up to now, several computational methods were developed to predict enhancer gene interactions, but they require either many epigenomic and transcriptomic experimental assays to generate cell-type (CT)-specific predictions or a single experiment applied to a large cohort of CTs to extract correlations between activities of regulatory elements. Thus, inferring CT-specific enhancer gene interactions in unstudied or poorly annotated CTs becomes a laborious and costly task.
    RESULTS: Here, we aim to infer CT-specific enhancer target interactions, using minimal experimental input. We introduce Cell-specific ENhancer Target pREdiction (CENTRE), a machine learning framework that predicts enhancer target interactions in a CT-specific manner, using only gene expression and ChIP-seq data for three histone modifications for the CT of interest. CENTRE exploits the wealth of available datasets and extracts cell-type agnostic statistics to complement the CT-specific information. CENTRE is thoroughly tested across many datasets and CTs and achieves equivalent or superior performance than existing algorithms that require massive experimental data.
    AVAILABILITY AND IMPLEMENTATION: CENTRE's open-source code is available at GitHub via https://github.com/slrvv/CENTRE.
    DOI:  https://doi.org/10.1093/bioinformatics/btad687
  5. Nucleic Acids Res. 2023 Nov 23. pii: gkad1081. [Epub ahead of print]
    Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF.
    Katerina Cermakova, Ling Tao, Milan Dejmek, Michal Sala, Matthew D Montierth, Yuen San Chan, Ivanshi Patel, Courtney Chambers, Mario Loeza Cabrera, Dane Hoffman, Ronald J Parchem, Wenyi Wang, Radim Nencka, Eveline Barbieri, H Courtney Hodges.
      Several cancer core regulatory circuitries (CRCs) depend on the sustained generation of DNA accessibility by SWI/SNF chromatin remodelers. However, the window when SWI/SNF is acutely essential in these settings has not been identified. Here we used neuroblastoma (NB) cells to model and dissect the relationship between cell-cycle progression and SWI/SNF ATPase activity. We find that SWI/SNF inactivation impairs coordinated occupancy of non-pioneer CRC members at enhancers within 1 hour, rapidly breaking their autoregulation. By precisely timing inhibitor treatment following synchronization, we show that SWI/SNF is dispensable for survival in S and G2/M, but becomes acutely essential only during G1 phase. We furthermore developed a new approach to analyze the oscillating patterns of genome-wide DNA accessibility across the cell cycle, which revealed that SWI/SNF-dependent CRC binding sites are enriched at enhancers with peak accessibility during G1 phase, where they activate genes involved in cell-cycle progression. SWI/SNF inhibition strongly impairs G1-S transition and potentiates the ability of retinoids used clinically to induce cell-cycle exit. Similar cell-cycle effects in diverse SWI/SNF-addicted settings highlight G1-S transition as a common cause of SWI/SNF dependency. Our results illustrate that deeper knowledge of the temporal patterns of enhancer-related dependencies may aid the rational targeting of addicted cancers.
    DOI:  https://doi.org/10.1093/nar/gkad1081
  6. Cell. 2023 Nov 22. pii: S0092-8674(23)01174-1. [Epub ahead of print]186(24): 5269-5289.e22
    Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS.
    Yeguang Hu, Daniela Salgado Figueroa, Zhihong Zhang, Margaret Veselits, Sourya Bhattacharyya, Mariko Kashiwagi, Marcus R Clark, Bruce A Morgan, Ferhat Ay, Katia Georgopoulos.
      A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.
    Keywords:  3D genome organization; Hi-C; HiChIP; IKAROS; Igκ locus contraction; enhancer loops; inter-compartmental loops; lineage-specific genome organization; lymphocyte development; superTADs
    DOI:  https://doi.org/10.1016/j.cell.2023.10.023
  7. Nucleic Acids Res. 2023 Nov 22. pii: gkad1030. [Epub ahead of print]
    TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.
    Marcio L Acencio, Miguel Vazquez, Konika Chawla, Astrid Lægreid, Martin Kuiper.
      Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins. Here, we describe TFCheckpoint 2.0 (https://www.tfcheckpoint.org/index.php), comprising 13 collections of dbTFs, coTFs and GTFs. TFCheckpoint 2.0 provides an easy and versatile cross-referencing system for users to view and download collections that may otherwise be cumbersome to find, compare and retrieve.
    DOI:  https://doi.org/10.1093/nar/gkad1030
  8. Sci Adv. 2023 11 24. 9(47): eadj1261
    ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster.
    Marc A J Morgan, Saeid Mohammad Parast, Marta Iwanaszko, Yuki Aoi, DongAhn Yoo, Zachary J Dumar, Benjamin C Howard, Kathryn A Helmin, Qianli Liu, William R Thakur, Jacob M Zeidner, Benjamin D Singer, Evan E Eichler, Ali Shilatifard.
      The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.
    DOI:  https://doi.org/10.1126/sciadv.adj1261
  9. EMBO J. 2023 Nov 21. e114221
    An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions.
    Aliaksandra Radzisheuskaya, Isabel Peña-Rømer, Eugenia Lorenzini, Richard Koche, Yingqian Zhan, Pavel V Shliaha, Alexandra J Cooper, Zheng Fan, Daria Shlyueva, Jens V Johansen, Ronald C Hendrickson, Kristian Helin.
      Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
    Keywords:  BPTF; SMARCA5; acute myeloid leukemia; chromatin remodeling; insulator regions
    DOI:  https://doi.org/10.15252/embj.2023114221
  10. Cell Rep. 2023 Nov 17. pii: S2211-1247(23)01458-4. [Epub ahead of print]42(11): 113446
    Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing.
    Amanda J Craig, Maruhen A Datsch Silveira, Lichun Ma, Mahler Revsine, Limin Wang, Sophia Heinrich, Zachary Rae, Allison Ruchinskas, Kimia Dadkhah, Whitney Do, Shay Behrens, Farid R Mehrabadi, Dana A Dominguez, Marshonna Forgues, Anuradha Budhu, Jittiporn Chaisaingmongkol, Jonathan M Hernandez, Jeremy L Davis, Bao Tran, Jens U Marquardt, Mathuros Ruchirawat, Michael Kelly, Tim F Greten, Xin W Wang.
      Primary liver cancer (PLC) consists of two main histological subtypes; hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). The role of transcription factors (TFs) in malignant hepatobiliary lineage commitment between HCC and iCCA remains underexplored. Here, we present genome-wide profiling of transcription regulatory elements of 16 PLC patients using single-cell assay for transposase accessible chromatin sequencing. Single-cell open chromatin profiles reflect the compositional diversity of liver cancer, identifying both malignant and microenvironment component cells. TF motif enrichment levels of 31 TFs strongly discriminate HCC from iCCA tumors. These TFs are members of the nuclear/retinoid receptor, POU, or ETS motif families. POU factors are associated with prognostic features in iCCA. Overall, nuclear receptors, ETS and POU TF motif families delineate transcription regulation between HCC and iCCA tumors, which may be relevant to development and selection of PLC subtype-specific therapeutics.
    Keywords:  CP: Cancer; ETS; POU; hepatocellular carcinoma; intrahepatic cholangiocarcinoma; nuclear receptors; primary liver cancer; retinoid receptors; scATAC-seq; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2023.113446
  11. Nat Commun. 2023 11 18. 14(1): 7482
    scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.
    Guanao Yan, Dongyuan Song, Jingyi Jessica Li.
      Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling.
    DOI:  https://doi.org/10.1038/s41467-023-43162-w
  12. Nat Immunol. 2023 Nov 20.
    BRWD1 orchestrates small pre-B cell chromatin topology by converting static to dynamic cohesin.
    Malay Mandal, Mark Maienschein-Cline, Yeguang Hu, Azam Mohsin, Margaret L Veselits, Nathaniel E Wright, Michael K Okoreeh, Young Me Yoon, Jacob Veselits, Katia Georgopoulos, Marcus R Clark.
      Lymphocyte development consists of sequential and mutually exclusive cell states of proliferative selection and antigen receptor gene recombination. Transitions between each state require large, coordinated changes in epigenetic landscapes and transcriptional programs. How this occurs remains unclear. Here we demonstrate that in small pre-B cells, the lineage and stage-specific epigenetic reader bromodomain and WD repeat-containing protein 1 (BRWD1) reorders three-dimensional chromatin topology to affect the transition between proliferative and gene recombination molecular programs. BRWD1 regulated the switch between poised and active enhancers interacting with promoters, and coordinated this switch with Igk locus contraction. BRWD1 did so by converting chromatin-bound static to dynamic cohesin competent to mediate long-range looping. ATP-depletion revealed cohesin conversion to be the main energetic mechanism dictating dynamic chromatin looping. Our findings provide a new mechanism of cohesin regulation and reveal how cohesin function can be dictated by lineage contextual mechanisms to facilitate specific cell fate transitions.
    DOI:  https://doi.org/10.1038/s41590-023-01666-z
  13. J Biol Chem. 2023 Nov 17. pii: S0021-9258(23)02505-X. [Epub ahead of print] 105477
    Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
    Munetaka Akatsu, Haruhiko Ehara, Tomoya Kujirai, Risa Fujita, Tomoko Ito, Ken Osumi, Mitsuo Ogasawara, Yoshimasa Takizawa, Shun-Ichi Sekine, Hitoshi Kurumizaka.
      RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 (SHL(-5) and SHL(-1), respectively). In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.
    Keywords:  DNA looping; RNA polymerase; chromatin; cryo-electron microscopy; nucleosome; transcription
    DOI:  https://doi.org/10.1016/j.jbc.2023.105477
  14. Mol Cell. 2023 Nov 14. pii: S1097-2765(23)00902-4. [Epub ahead of print]
    IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events.
    Rina Fujiwara, Si-Nan Zhai, Dongming Liang, Aayushi P Shah, Matthew Tracey, Xu-Kai Ma, Christopher J Fields, María Saraí Mendoza-Figueroa, Michele C Meline, Deirdre C Tatomer, Li Yang, Jeremy E Wilusz.
      The metazoan-specific Integrator complex catalyzes 3' end processing of small nuclear RNAs (snRNAs) and premature termination that attenuates the transcription of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are required for complex function. Here, we show IntS6 (Integrator subunit 6) over-expression blocks Integrator function at a subset of Drosophila protein-coding genes, although having no effect on snRNAs or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits, thereby only affecting gene loci where phosphatase activity is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not bind Integrator, is also sufficient to inhibit Integrator activity. These results show that the phosphatase module is critical at only a subset of Integrator-regulated genes and point to PP2A recruitment as a tunable step that modulates transcription termination efficiency.
    Keywords:  3′ end processing; INTAC; Integrator complex; Integrator subunit 6; PP2A; RNA polymerase II; promoter-proximal termination; protein phosphatase 2A; snRNA; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2023.10.035
  15. Nucleic Acids Res. 2023 Nov 22. pii: gkad1098. [Epub ahead of print]
    A single fiber view of the nucleosome organization in eukaryotic chromatin.
    Mark Boltengagen, Daan Verhagen, Michael Roland Wolff, Elisa Oberbeckmann, Matthias Hanke, Ulrich Gerland, Philipp Korber, Felix Mueller-Planitz.
      Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this stereotypic organization describes the nucleosome organization in Saccharomyces cerevisiae using Fiber-Seq, a long-read sequencing technique that maps entire nucleosome arrays on individual chromatin fibers in a high throughput manner. With each fiber coming from a different cell, Fiber-Seq uncovers cell-to-cell heterogeneity. The long reads reveal the nucleosome architecture even over repetitive DNA such as the ribosomal DNA repeats. The absolute nucleosome occupancy, a parameter that is difficult to obtain with conventional sequencing approaches, is a direct readout of Fiber-Seq. We document substantial deviations from the stereotypical nucleosome organization with unexpectedly long linker DNAs between nucleosomes, gene bodies missing entire nucleosomes, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays and irregular nucleosome spacing. Nucleosome array structures are indistinguishable throughout the gene body and with respect to the direction of transcription arguing against transcription promoting array formation. Acute nucleosome depletion destroyed most of the array organization indicating that nucleosome remodelers cannot efficiently pack nucleosomes under those conditions. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity uncovered by Fiber-Seq provides much needed information to understand chromatin structure and function.
    DOI:  https://doi.org/10.1093/nar/gkad1098
  16. PLoS Comput Biol. 2023 Nov 20. 19(11): e1011491
    Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.
    Sarvesh Nikumbh, Boris Lenhard.
      Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complexes. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their motifs at near-fixed distances from a reference point, such as TSS. When combined with experimental data from CAGE, seqArchR can efficiently identify TSS-directing motifs, including known ones like TATA, DPE, and nucleosome positioning signal, as well as novel lineage-specific motifs and the function of genes associated with them. By using seqArchR on developmental time courses, we reveal how relative use of promoter architectures changes over time with stage-specific expression. seqArchR is a powerful tool for initial genome-wide classification and functional characterization of promoters. Its use cases are more general: it can also be used to discover any motifs at near-fixed distances from a reference point, even if they are present in only a small subset of sequences.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011491
  17. Nat Commun. 2023 11 18. 14(1): 7484
    H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome.
    Zhen Wang, Claudia M Castillo-González, Changjiang Zhao, Chun-Yip Tong, Changhao Li, Songxiao Zhong, Zhiyang Liu, Kaili Xie, Jiaying Zhu, Zhongshou Wu, Xu Peng, Yannick Jacob, Scott D Michaels, Steven E Jacobsen, Xiuren Zhang.
      The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
    DOI:  https://doi.org/10.1038/s41467-023-43311-1
  18. Nucleic Acids Res. 2023 Nov 24. pii: gkad1108. [Epub ahead of print]
    A modular dCas9-based recruitment platform for combinatorial epigenome editing.
    Tessa Swain, Christian Pflueger, Saskia Freytag, Daniel Poppe, Jahnvi Pflueger, Trung Viet Nguyen, Ji Kevin Li, Ryan Lister.
      Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct 'effector' chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and, by testing it against existing multi-effector targeting systems, demonstrate its comparable efficacy. Furthermore, we demonstrate the importance of the spatial ordering of the recruited effectors for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.
    DOI:  https://doi.org/10.1093/nar/gkad1108
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