bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023‒06‒11
eighteen papers selected by
Connor Rogerson
University of Cambridge
  1. A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.
  2. Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells.
  3. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.
  4. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression.
  5. The histone methyltransferase NSD3 contributes to sister chromatid cohesion and to cohesin loading at mitotic exit.
  6. Heritable transcriptional defects from aberrations of nuclear architecture.
  7. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition.
  8. Co-option of endogenous retroviruses through genetic escape from TRIM28 repression.
  9. CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression.
  10. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing.
  11. Pluripotency-independent induction of human trophoblast stem cells from fibroblasts.
  12. Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.
  13. Epigenetic dysregulation from chromosomal transit in micronuclei.
  14. STAT1 is required to establish but not maintain interferon-γ-induced transcriptional memory.
  15. RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization.
  16. A chromatin remodelling SWI/SNF subunit Snr1 regulates neural stem cell determination and differentiation.
  17. Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs.
  18. Deficiency of the Polycomb protein RYBP and TET methylcytosine oxidases promotes extensive CpG island hypermethylation and malignant transformation.
  1. Nat Commun. 2023 Jun 05. 14(1): 3242
    A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.
    Sandra Kessler, Maryline Minoux, Onkar Joshi, Yousra Ben Zouari, Sebastien Ducret, Fiona Ross, Nathalie Vilain, Adwait Salvi, Joachim Wolff, Hubertus Kohler, Michael B Stadler, Filippo M Rijli.
      Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
    DOI:  https://doi.org/10.1038/s41467-023-38953-0
  2. iScience. 2023 Jun 16. 26(6): 106908
    Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells.
    Jiankang Wang, Ryuichiro Nakato.
      Chromatin organization, whose malfunction causes various diseases including cancer, is fundamentally controlled by cohesin. While cancer cells have been found with mutated or misexpressed cohesin genes, there is no comprehensive survey about the presence and role of abnormal cohesin binding in cancer cells. Here, we systematically identified ∼1% of cohesin-binding sites (701-2,633) as cancer-aberrant binding sites of cohesin (CASs). We integrated CASs with large-scale transcriptomics, epigenomics, 3D genomics, and clinical information. CASs represent tissue-specific epigenomic signatures enriched for cancer-dysregulated genes with functional and clinical significance. CASs exhibited alterations in chromatin compartments, loops within topologically associated domains, and cis-regulatory elements, indicating that CASs induce dysregulated genes through misguided chromatin structure. Cohesin depletion data suggested that cohesin binding at CASs actively regulates cancer-dysregulated genes. Overall, our comprehensive investigation suggests that aberrant cohesin binding is an essential epigenomic signature responsible for dysregulated chromatin structure and transcription in cancer cells.
    Keywords:  Cancer systems biology; Epigenetics; Omics
    DOI:  https://doi.org/10.1016/j.isci.2023.106908
  3. Nat Commun. 2023 Jun 06. 14(1): 3303
    Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.
    Hannah L Harris, Huiya Gu, Moshe Olshansky, Ailun Wang, Irene Farabella, Yossi Eliaz, Achyuth Kalluchi, Akshay Krishna, Mozes Jacobs, Gesine Cauer, Melanie Pham, Suhas S P Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae Kim, Michael H Nichols, Eric S Davis, Dimos Gkountaroulis, Devika Udupa, Aviva Presser Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble, Guy Nir, Michele Di Pierro, Jeong-Sun Seo, Michael E Talkowski, Erez Lieberman Aiden, M Jordan Rowley.
      Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
    DOI:  https://doi.org/10.1038/s41467-023-38429-1
  4. Cell Rep. 2023 Jun 08. pii: S2211-1247(23)00598-3. [Epub ahead of print]42(6): 112587
    Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression.
    Mohd Saleem Dar, Isaiah K Mensah, Ming He, Sarah McGovern, Ikjot Singh Sohal, Hannah Christian Whitlock, Nina Elise Bippus, Madison Ceminsky, Martin L Emerson, Hern J Tan, Mark C Hall, Humaira Gowher.
      Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
    Keywords:  CP: Molecular biology; DNA methylation; Dnmt3bas; PRC2 complex; alternative splicing; chromatin modifications; dnmt3b; enhancers; hnRNPL; lncRNA; promoters
    DOI:  https://doi.org/10.1016/j.celrep.2023.112587
  5. J Cell Sci. 2023 Jun 01. pii: jcs261014. [Epub ahead of print]136(11):
    The histone methyltransferase NSD3 contributes to sister chromatid cohesion and to cohesin loading at mitotic exit.
    Grégory Eot-Houllier, Laura Magnaghi-Jaulin, Gaëlle Bourgine, Fatima Smagulova, Régis Giet, Erwan Watrin, Christian Jaulin.
      Sister chromatid cohesion is a multi-step process implemented throughout the cell cycle to ensure the correct transmission of chromosomes to daughter cells. Although cohesion establishment and mitotic cohesion dissolution have been extensively explored, the regulation of cohesin loading is still poorly understood. Here, we report that the methyltransferase NSD3 is essential for mitotic sister chromatid cohesion before mitosis entry. NSD3 interacts with the cohesin loader complex kollerin (composed of NIPBL and MAU2) and promotes the chromatin recruitment of MAU2 and cohesin at mitotic exit. We also show that NSD3 associates with chromatin in early anaphase, prior to the recruitment of MAU2 and RAD21, and dissociates from chromatin when prophase begins. Among the two NSD3 isoforms present in somatic cells, the long isoform is responsible for regulating kollerin and cohesin chromatin-loading, and its methyltransferase activity is required for efficient sister chromatid cohesion. Based on these observations, we propose that NSD3-dependent methylation contributes to sister chromatid cohesion by ensuring proper kollerin recruitment and thus cohesin loading.
    Keywords:  Cohesin; MAU2; Methylation; Mitosis; NIPBL; NSD3
    DOI:  https://doi.org/10.1242/jcs.261014
  6. Nature. 2023 Jun 07.
    Heritable transcriptional defects from aberrations of nuclear architecture.
    Stamatis Papathanasiou, Nikos A Mynhier, Shiwei Liu, Gregory Brunette, Ema Stokasimov, Etai Jacob, Lanting Li, Caroline Comenho, Bas van Steensel, Jason D Buenrostro, Cheng-Zhong Zhang, David Pellman.
      Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance1-3. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer4,5, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture.
    DOI:  https://doi.org/10.1038/s41586-023-06157-7
  7. Nat Commun. 2023 Jun 03. 14(1): 3212
    Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition.
    Mattia Zaghi, Federica Banfi, Luca Massimino, Monica Volpin, Edoardo Bellini, Simone Brusco, Ivan Merelli, Cristiana Barone, Michela Bruni, Linda Bossini, Luigi Antonio Lamparelli, Laura Pintado, Deborah D'Aliberti, Silvia Spinelli, Luca Mologni, Gaia Colasante, Federica Ungaro, Jean-Michel Cioni, Emanuele Azzoni, Rocco Piazza, Eugenio Montini, Vania Broccoli, Alessandro Sessa.
      Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.
    DOI:  https://doi.org/10.1038/s41467-023-39043-x
  8. Cell Rep. 2023 Jun 07. pii: S2211-1247(23)00636-8. [Epub ahead of print]42(6): 112625
    Co-option of endogenous retroviruses through genetic escape from TRIM28 repression.
    Rocio Enriquez-Gasca, Poppy A Gould, Hale Tunbak, Lucia Conde, Javier Herrero, Alexandra Chittka, Christine R Beck, Robert Gifford, Helen M Rowe.
      Endogenous retroviruses (ERVs) have rewired host gene networks. To explore the origins of co-option, we employed an active murine ERV, IAPEz, and an embryonic stem cell (ESC) to neural progenitor cell (NPC) differentiation model. Transcriptional silencing via TRIM28 maps to a 190 bp sequence encoding the intracisternal A-type particle (IAP) signal peptide, which confers retrotransposition activity. A subset of "escapee" IAPs (∼15%) exhibits significant genetic divergence from this sequence. Canonical repressed IAPs succumb to a previously undocumented demarcation by H3K9me3 and H3K27me3 in NPCs. Escapee IAPs, in contrast, evade repression in both cell types, resulting in their transcriptional derepression, particularly in NPCs. We validate the enhancer function of a 47 bp sequence within the U3 region of the long terminal repeat (LTR) and show that escapee IAPs convey an activating effect on nearby neural genes. In sum, co-opted ERVs stem from genetic escapees that have lost vital sequences required for both TRIM28 restriction and autonomous retrotransposition.
    Keywords:  CP: Developmental biology; CP: Stem cell research; ERVs; IAPs; KRAB-zinc finger proteins; TRIM28; cancer; co-option; endogenous retroviruses; enhancers; epigenetic silencing; exaptation; intracisternal A-type particles; retrotransposition; retrotransposon
    DOI:  https://doi.org/10.1016/j.celrep.2023.112625
  9. Nat Commun. 2023 Jun 03. 14(1): 3225
    CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression.
    Gemma Noviello, Rutger A F Gjaltema, Edda G Schulz.
      Certain cellular processes are dose-dependent, requiring specific quantities or stoichiometries of gene products, as exemplified by haploinsufficiency and sex-chromosome dosage compensation. Understanding dosage-sensitive processes requires tools to quantitatively modulate protein abundance. Here we present CasTuner, a CRISPR-based toolkit for analog tuning of endogenous gene expression. The system exploits Cas-derived repressors that are quantitatively tuned by ligand titration through a FKBP12F36V degron domain. CasTuner can be applied at the transcriptional or post-transcriptional level using a histone deacetylase (hHDAC4) fused to dCas9, or the RNA-targeting CasRx, respectively. We demonstrate analog tuning of gene expression homogeneously across cells in mouse and human cells, as opposed to KRAB-dependent CRISPR-interference systems, which exhibit digital repression. Finally, we quantify the system's dynamics and use it to measure dose-response relationships of NANOG and OCT4 with their target genes and with the cellular phenotype. CasTuner thus provides an easy-to-implement tool to study dose-responsive processes in their physiological context.
    DOI:  https://doi.org/10.1038/s41467-023-38909-4
  10. Nat Commun. 2023 Jun 06. 14(1): 3275
    PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing.
    Xiangbin Ruan, Kaining Hu, Xiaochang Zhang.
      RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
    DOI:  https://doi.org/10.1038/s41467-023-39054-8
  11. Nat Commun. 2023 Jun 08. 14(1): 3359
    Pluripotency-independent induction of human trophoblast stem cells from fibroblasts.
    Moriyah Naama, Moran Rahamim, Valery Zayat, Shulamit Sebban, Ahmed Radwan, Dana Orzech, Rachel Lasry, Annael Ifrah, Mohammad Jaber, Ofra Sabag, Hazar Yassen, Areej Khatib, Silvina Epsztejn-Litman, Michal Novoselsky-Persky, Kirill Makedonski, Noy Deri, Debra Goldman-Wohl, Howard Cedar, Simcha Yagel, Rachel Eiges, Yosef Buganim.
      Human trophoblast stem cells (hTSCs) can be derived from embryonic stem cells (hESCs) or be induced from somatic cells by OCT4, SOX2, KLF4 and MYC (OSKM). Here we explore whether the hTSC state can be induced independently of pluripotency, and what are the mechanisms underlying its acquisition. We identify GATA3, OCT4, KLF4 and MYC (GOKM) as a combination of factors that can generate functional hiTSCs from fibroblasts. Transcriptomic analysis of stable GOKM- and OSKM-hiTSCs reveals 94 hTSC-specific genes that are aberrant specifically in OSKM-derived hiTSCs. Through time-course-RNA-seq analysis, H3K4me2 deposition and chromatin accessibility, we demonstrate that GOKM exert greater chromatin opening activity than OSKM. While GOKM primarily target hTSC-specific loci, OSKM mainly induce the hTSC state via targeting hESC and hTSC shared loci. Finally, we show that GOKM efficiently generate hiTSCs from fibroblasts that harbor knockout for pluripotency genes, further emphasizing that pluripotency is dispensable for hTSC state acquisition.
    DOI:  https://doi.org/10.1038/s41467-023-39104-1
  12. Genome Res. 2023 Jun 05.
    Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.
    Vivek Hari Sundar G, Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Steffi Raju, Tania Chakraborty, Rebecca A Mosher, P V Shivaprasad.
      Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared with Arabidopsis Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.
    DOI:  https://doi.org/10.1101/gr.277353.122
  13. Nature. 2023 Jun 07.
    Epigenetic dysregulation from chromosomal transit in micronuclei.
    Albert S Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S C L Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguole Norkunaite, Robert M Myers, Mercedes Duran, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eléonore Toufektchan, Kristina Keuper, Paul S Mischel, Vivek Mittal, Sohrab P Shah, John Maciejowski, Zuzana Storchova, Enrico Gratton, Peter Ly, Dan Landau, Mathieu F Bakhoum, Richard P Koche, Simone Sidoli, Vineet Bafna, Yael David, Samuel F Bakhoum.
      Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
    DOI:  https://doi.org/10.1038/s41586-023-06084-7
  14. EMBO J. 2023 Jun 05. e112259
    STAT1 is required to establish but not maintain interferon-γ-induced transcriptional memory.
    Sahar Sh Tehrani, Pawel Mikulski, Izma Abdul-Zani, João F Mata, Wojciech Siwek, Lars Et Jansen.
      Exposure of human cells to interferon-γ (IFNγ) results in a mitotically heritable yet reversible state called long-term transcriptional memory. We previously identified the clustered GBP genes as strongly primed by IFNγ. Here, we discovered that in primed cells, both interferon-responsive transcription factors STAT1 and IRF1 target chromatin with accelerated kinetics upon re-exposure to IFNγ, specifically at promotors of primed genes. Priming does not alter the degree of IFNγ-induced STAT1 activation or nuclear import, indicating that memory does not alter upstream JAK-STAT signaling. We found STAT1 to be critical to establish transcriptional memory but in a manner that is independent of mere transcription activation. Interestingly, while Serine 727 phosphorylation of STAT1 was maintained during the primed state, STAT1 is not required for the heritability of GBP gene memory. Our results suggest that the memory of interferon exposure constitutes a STAT1-mediated, heritable state that is established during priming. This renders GBP genes poised for subsequent STAT1 and IRF1 binding and accelerated gene activation upon a secondary interferon exposure.
    Keywords:  GBPs; IRF1; STAT1; epigenetic memory; epigenetics; trained immunity
    DOI:  https://doi.org/10.15252/embj.2022112259
  15. Nat Struct Mol Biol. 2023 Jun 08.
    RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization.
    Samuel Collombet, Isabell Rall, Claire Dugast-Darzacq, Alec Heckert, Aliaksandr Halavatyi, Agnes Le Saux, Gina Dailey, Xavier Darzacq, Edith Heard.
      Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in XCI, and might explain the exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single-particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during the initiation of XCI. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin stably bound fraction. These findings indicate that initial exclusion of RNAPII from the inactive X reflects the absence of actively transcribing RNAPII, rather than a consequence of putative physical compartmentalization of the inactive X heterochromatin domain.
    DOI:  https://doi.org/10.1038/s41594-023-01008-5
  16. Development. 2023 Jun 09. pii: dev.201484. [Epub ahead of print]
    A chromatin remodelling SWI/SNF subunit Snr1 regulates neural stem cell determination and differentiation.
    Sophie E Keegan, Julie Haskins, Andrew J Simmonds, Sarah C Hughes.
      Coordinated spatio-temporal regulation of the determination and differentiation of neural stem cells is essential for brain development. Failure to integrate multiple factors leads to defective brain structures or tumor formation. Previous studies suggest changes of chromatin state are needed to direct neural stem cell differentiation, but the mechanisms are unclear. Analysis of Snr1, the Drosophila orthologue of SMARCB1, an ATP-dependent chromatin remodelling protein, identified a key role in regulating the transition of neuroepithelial cells into neural stem cells and subsequent differentiation of neural stem cells into cells needed to build the brain. Loss of Snr1 in neuroepithelial cells leads to premature neural stem cell formation. Additionally, loss of Snr1 in neural stem cells results in inappropriate perdurance of neural stem cells into adulthood. Snr1 reduction in neuroepithelial or neural stem cells leads to the differential expression of target genes. We find that Snr1 is associated with the actively transcribed chromatin region of these target genes. Thus, Snr1 likely regulates the chromatin state in neuroepithelial cells and maintains chromatin state in neural stem cells for proper brain development.
    Keywords:   Drosophila ; Differentiation; Neural stem cell; Neuroblast; Neuroepithelial cells; Optic lobe; SMARCB1; SWI/SNF complex; Snr1
    DOI:  https://doi.org/10.1242/dev.201484
  17. NAR Cancer. 2023 Jun;5(2): zcad027
    Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs.
    Spencer Arnesen, Jacob T Polaski, Zannel Blanchard, Kyle S Osborne, Alana L Welm, Ryan M O'Connell, Jason Gertz.
      Estrogen receptor α (ER) mutations occur in up to 30% of metastatic ER-positive breast cancers. Recent data has shown that ER mutations impact the expression of thousands of genes not typically regulated by wildtype ER. While the majority of these altered genes can be explained by constant activity of mutant ER or genomic changes such as altered ER binding and chromatin accessibility, as much as 33% remain unexplained, indicating the potential for post-transcriptional effects. Here, we explored the role of microRNAs in mutant ER-driven gene regulation and identified several microRNAs that are dysregulated in ER mutant cells. These differentially regulated microRNAs target a significant portion of mutant-specific genes involved in key cellular processes. When the activity of microRNAs is altered using mimics or inhibitors, significant changes are observed in gene expression and cellular proliferation related to mutant ER. An in-depth evaluation of miR-301b led us to discover an important role for PRKD3 in the proliferation of ER mutant cells. Our findings show that microRNAs contribute to mutant ER gene regulation and cellular effects in breast cancer cells.
    DOI:  https://doi.org/10.1093/narcan/zcad027
  18. Cancer Res. 2023 Jun 06. pii: CAN-23-0269. [Epub ahead of print]
    Deficiency of the Polycomb protein RYBP and TET methylcytosine oxidases promotes extensive CpG island hypermethylation and malignant transformation.
    Wei Cui, Zhijun Huang, Seung-Gi Jin, Jennifer Johnson, Kin H Lau, Galen Hostetter, Gerd P Pfeifer.
      Hypermethylation of CpG islands is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine oxidases in protecting CpG islands from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5-methylcytosine oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CpG islands affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CpG islands and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CpG islands in tumors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-0269
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