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RNAseq analysis of mutants in coding and non-coding transcription of phosphate genes in the yeast Saccharomyces cerevisiae

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GENOMICS 2023年第5期115卷 110672页

作者： van Heusden, G. Paul H. Leiden Univ Inst Biol Leiden Netherlands Sylviusweg 72 NL-2333 AL Leiden Netherlands

In the yeast Saccharomyces cerevisiae phosphate starvation induces the expression of PHO genes, including PHO84, encoding an high-affinity phosphate transporter, and SPL2, encoding a regulatory protein. PHO84 is down-regulated by antisense transcription. Here, using strand-specific RNAseq the effect is studied of mutations related to sense and antisense transcription of phosphate genes. Replacement of the transcriptional terminator of PHO84 by that of CYC1 resulted, unexpectedly, in an increased antisense transcription and a strongly reduced sense transcription of PHO84 and a strongly reduced SPL2 expression. The expression of unrelated genes was altered as well. The data suggest that antisense transcription of PHO84 and not the Pho84 transporter affects the expression of SPL2. Deletion of the two putative binding sites for Ume6 in the SPL2 promoter or deletion of UME6 differently affected SPL2 expression, suggesting that Ume6 regulates SPL2 by a mechanism different from a simple binding to the putative Ume6 binding sites.

关键词： Saccharomyces cerevisiae Phosphate uptake non-coding transcription Strand-specific RNAseq

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Regulation of Gene Expression and Replication Initiation by non-coding transcription: A Model Based on Reshaping Nucleosome-Depleted Regions

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BIOESSAYS 2019年第11期41卷 1900043-1900043页

作者： Soudet, Julien Stutz, Francoise Univ Geneva Dept Cell Biol CH-1211 Geneva Switzerland

RNA polymerase II (RNAP II) non-coding transcription is now known to cover almost the entire eukaryotic genome, a phenomenon referred to as pervasive transcription. As a consequence, regions previously thought to be non-transcribed are subject to the passage of RNAP II and its associated proteins for histone modification. This is the case for the nucleosome-depleted regions (NDRs), which provide key sites of entry into the chromatin for proteins required for the initiation of coding gene transcription and DNA replication. In this review, recent data on the effects of pervasive transcription through NDRs are summarized and a model is proposed to explain how RNAP II-driven transcription is able to modify the nucleosomes flanking the NDRs, leading to nucleosome repositioning and NDR closure. Even though much of the mechanistic detail underlying these events remains to be elucidated, such a model provides a basis to explain how non-coding transcription through NDRs can regulate the initiation of coding gene expression and DNA replication.

关键词： chromatin remodeler HDAC histone modifications NDR non-coding transcription nucleosome replication initiation

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non-coding transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

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CELL 2017年第1期171卷 103-+页

作者： Isoda, Takeshi Moore, Amanda J. He, Zhaoren Chandra, Vivek Aida, Masatoshi Denholtz, Matthew van Hamburg, Jan Piet Fisch, Kathleen M. Chang, Aaron N. Fahl, Shawn P. Wiest, David L. Murre, Cornelis Univ Calif San Diego Dept Mol Biol La Jolla CA 92093 USA Univ Calif San Diego Dept Med Ctr Computat Biol & Bioinformat Inst Genom Med La Jolla CA 92093 USA Fox Chase Canc Ctr Blood Cell Dev & Funct 333 Cottman Ave Philadelphia PA 19111 USA

It is now established that Bcl11b specifies T cell fate. Here, we show that in developing T cells, the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (thymocyte differentiation factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single-loop domain. These large-scale changes in nuclear architecture were associated with the deposition of activating epigenetic marks across the loop domain, plausibly facilitating phase separation. These data indicate how, during developmental progression and tumor suppression, noncoding transcription orchestrates chromatin folding and compartmentalization to direct with high precision enhancer-promoter communication.

关键词： CTCF non-coding transcription T cell development cohesin compartmentalization leukemia loop extrusion lymphoma phase separation single-loop domain

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Centromere inactivation during aging can be rescued in human cells

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MOLECULAR CELL 2025年第2期85卷 692-707.e7页

作者： Sikder, Sweta Baek, Songjoon Mcneil, Truman Dalal, Yamini NCI Ctr Canc Res NIH Bethesda MD 20892 USA St Olaf Coll 1520 St Olaf Ave Northfield MN 55057 USA

Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres in aged human fibroblasts and tissues and in various cellular senescent models. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to the mitotic rejuvenation of these cells. These results offer insights into a unique mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.

关键词： centromere non-coding transcription histone demethylase aging p53 CENP-A senescence chromatin genome instability cancer

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The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures

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Plant Communications 2023年第4期4卷 77-87页

作者： Vasiliki Zacharaki Shiv Kumar Meena Peter Kindgren UmeåPlant Science Centre Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural Sciences90187 Umea°Sweden

non-coding transcription is present in all eukaryotic genomes,but we lack fundamental knowledge about its importance for an organism’s ability to develop *** plants,emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding ***,we have few molecular insights into this ***,we show that a long isoform of the long noncoding RNA SVALKA-L(SVK-L)forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis ***,we show detailed evidence for the specific mode of action of *** pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA ***,the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal *** study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene’s mRNA.

关键词： SVALKA cis-natural antisense transcript non-coding transcription CBF1 Arabidopsis

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Sen1 is a key regulator of transcription-driven conflicts

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MOLECULAR CELL 2022年第16期82卷 2952-+页

作者： Aiello, Umberto Challal, Drice Wentzinger, Griselda Lengronne, Armelle Appanah, Rowin Pasero, Philippe Palancade, Benoit Libri, Domenico Univ Paris Cite Inst Jacques Monod CNRS F-75013 Paris France Univ Montpellier Inst Genet Humaine CNRS Montpellier France Univ Sussex Genome Damage & Stabil Ctr Sch Life Sci Brighton BN1 9RQ E Sussex England Univ Paris Saclay CNRS Inst Biol Integrat Cellule UMR9198 CEA F-91198 Gif Sur Yvette France Univ Montpellier Inst Genet Mol Montpellier CNRS Montpellier France

Cellular homeostasis requires the coordination of several machineries concurrently engaged in the DNA. Wide-spread transcription can interfere with other processes, and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase not only terminates non-coding transcription but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability, but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that, under physiological conditions, Sen1 removes RNA polymerase II at TRCs within genes and the rDNA and at sites of transcription-transcription conflicts, thus qualifying as a "key regulator of conflicts." We demonstrate that genomic stability is affected by Sen1 mutation only when in addition to its role at the replisome, the termination of non-coding transcription or R-loop removal are additionally compromised.

关键词： transcription replication transcription-replication conflicts TRCs Sen1 RNase H R-loops genome stability non-coding transcription H-CRAC

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Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues

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CELL GENOMICS 2023年第10期3卷 100411-100411页

作者： de Langen, Pierre Hammal, Fayrouz Gueret, Elise Mouren, Jean-Christophe Spinelli, Lionel Ballester, Benoit Aix Marseille Univ INSERM TAGC Marseille France

Intergenic transcription in normal and cancerous tissues is pervasive but incompletely understood. To inves-tigate this, we constructed an atlas of over 180,000 consensus RNA polymerase II (RNAPII)-bound intergenic regions from 900 RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments in normal and cancer samples. Through unsupervised analysis, we identified 51 RNAPII consensus clusters, many of which mapped to specific biotypes and revealed tissue-specific regulatory signatures. We developed a meta -clus-tering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Ency-clopedia of DNA Elements (ENCODE). This analysis revealed strong tissue-and disease-specific intercon-nections between RNAPII occupancy and transcriptional activity. We demonstrate that intergenic transcrip-tion at RNAPII-bound regions is a novel per-cancer and pan-cancer biomarker. This biomarker displays genomic and clinically relevant characteristics, distinguishing cancer subtypes and linking to overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover intergenic transcriptional activity in normal and cancer tissues.

关键词： enhancers non-coding DNA regulatory genomics intergenic RNA Polymerase II gene regulation cancer genomics non-coding transcription

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Epigenetic regulation of centromere function

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CELLULAR AND MOLECULAR LIFE SCIENCES 2020年第15期77卷 2899-2917页

作者： Wong, Charmaine Yan Yu Lee, Bernard Chi Hang Yuen, Karen Wing Yee Univ Hong Kong Sch Biol Sci Kadoorie Biol Sci BldgPokfulam Rd Hong Kong Peoples R China

The centromere is a specialized region on the chromosome that directs equal chromosome segregation. Centromeres are usually not defined by DNA sequences alone. How centromere formation and function are determined by epigenetics is still not fully understood. Active centromeres are often marked by the presence of centromeric-specific histone H3 variant, centromere protein A (CENP-A). How CENP-A is assembled into the centromeric chromatin during the cell cycle and propagated to the next cell cycle or the next generation to maintain the centromere function has been intensively investigated. In this review, we summarize current understanding of how post-translational modifications of CENP-A and other centromere proteins, centromeric and pericentric histone modifications, non-coding transcription and transcripts contribute to centromere function, and discuss their intricate relationships and potential feedback mechanisms.

关键词： Centromere Post-translational modifications Histone modifications non-coding transcription Centromeric transcript Pericentric heterochromatin

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Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2

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BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021年第6-7期1864卷 194714-194714页

作者： Crooijmans, Marjolein E. Delzenne, Tijn O. Hensen, Tim Darehei, Mina de Winde, Johannes H. van Heusden, G. Paul H. Leiden Univ Inst Biol Leiden Netherlands

Dependent on phosphate availability the yeast Saccharomyces cerevisiae expresses either low or high affinity phosphate transporters. In the presence of phosphate yeast cells still express low levels of the high affinity phosphate transporter Pho84. The regulator Spl2 is expressed in approximately 90% of the cells, and is not expressed in the remaining cells. Here we report that deletion of RRP6, encoding an exonuclease degrading non-coding RNA, or BMH1, encoding the major 14-3-3 isoform, resulted in less cells expressing SPL2 and in increased levels of RNA transcribed from sequences upstream of the SPL2 coding region. SPL2 stimulates its own expression and that of PHO84 ensuing a positive feedback. Upon deletion of the region responsible for upstream SPL2 transcription almost all cells express SPL2. These results indicate that the cell-to-cell variation in PHO84 and SPL2 expression is dependent on a specific part of the SPL2 promoter and is controlled by Bmh1 and Spl2.

关键词： Phosphate metabolism Saccharomyces cerevisiae non-coding transcription Bimodal gene expression transcription start site

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Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin

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EMBO JOURNAL 2012年第23期31卷 4375-4387页

作者： Shim, Young Sam Choi, Yoonjung Kang, Keunsoo Cho, Kun Oh, Seunghee Lee, Junwoo Grewal, Shiv I. S. Lee, Daeyoup Korea Adv Inst Sci & Technol Dept Biol Sci Taejon 305701 South Korea Korea Basic Sci Inst Div Mass Spectrometry Res Chungbuk South Korea NCI Biochem & Mol Biol Lab NIH Bethesda MD 20892 USA

The positioning of the nucleosome by ATP-dependent remodellers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Recently, genome-wide nucleosome mapping has revealed more detailed information on the chromatin-remodelling factors. Here, we report that the Schizosaccharomyces pombe CHD remodeller, Hrp3, is a global regulator that drives proper nucleosome positioning and nucleosome stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3 Delta cells emphasized the importance of nucleosome architecture for proper transcription. Notably, perturbation of the nucleosome in hrp3 deletion mutant was also associated with destabilization of the DNA-histone interaction and cell cycle-dependent alleviation of heterochromatin silencing. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome by Hrp3 is important for the spatial-temporal control of transcription-associated processes. The EMBO Journal (2012) 31, 4375-4387. doi:10.1038/emboj. 2012.267;Published online 18 September 2012

关键词： chromatin remodeller heterochromatin silencing Hrp3 non-coding transcription nucleosome positioning

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