1
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Morse K, Bishop AL, Swerdlow S, Leslie JM, Ünal E. Swi/Snf chromatin remodeling regulates transcriptional interference and gene repression. Mol Cell 2024; 84:3080-3097.e9. [PMID: 39043178 PMCID: PMC11419397 DOI: 10.1016/j.molcel.2024.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 03/11/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. Although transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by functional genomics, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. This study provides clear evidence for Swi/Snf playing a direct role in gene repression via a cis transcriptional interference mechanism.
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Affiliation(s)
- Kaitlin Morse
- Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall, Berkeley, CA 94720, USA
| | - Alena L Bishop
- Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall, Berkeley, CA 94720, USA
| | - Sarah Swerdlow
- Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall, Berkeley, CA 94720, USA
| | - Jessica M Leslie
- Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall, Berkeley, CA 94720, USA.
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2
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Giannakakis A, Tsifintaris M, Gouzouasis V, Ow GS, Aau MY, Papp C, Ivshina AV, Kuznetsov VA. KDM7A-DT induces genotoxic stress, tumorigenesis, and progression of p53 missense mutation-associated invasive breast cancer. Front Oncol 2024; 14:1227151. [PMID: 38756663 PMCID: PMC11097164 DOI: 10.3389/fonc.2024.1227151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
Stress-induced promoter-associated and antisense lncRNAs (si-paancRNAs) originate from a reservoir of oxidative stress (OS)-specific promoters via RNAPII pausing-mediated divergent antisense transcription. Several studies have shown that the KDM7A divergent transcript gene (KDM7A-DT), which encodes a si-paancRNA, is overexpressed in some cancer types. However, the mechanisms of this overexpression and its corresponding roles in oncogenesis and cancer progression are poorly understood. We found that KDM7A-DT expression is correlated with highly aggressive cancer types and specific inherently determined subtypes (such as ductal invasive breast carcinoma (BRCA) basal subtype). Its regulation is determined by missense TP53 mutations in a subtype-specific context. KDM7A-DT transcribes several intermediate-sized ncRNAs and a full-length transcript, exhibiting distinct expression and localization patterns. Overexpression of KDM7A-DT upregulates TP53 protein expression and H2AX phosphorylation in nonmalignant fibroblasts, while in semi-transformed fibroblasts, OS superinduces KDM7A-DT expression in a TP53-dependent manner. KDM7A-DT knockdown and gene expression profiling in TP53-missense mutated luminal A BRCA variant, where it is abundantly expressed, indicate its significant role in cancer pathways. Endogenous over-expression of KDM7A-DT inhibits DNA damage response/repair (DDR/R) via the TP53BP1-mediated pathway, reducing apoptosis and promoting G2/M checkpoint arrest. Higher KDM7A-DT expression in BRCA is associated with KDM7A-DT locus gain/amplification, higher histologic grade, aneuploidy, hypoxia, immune modulation scores, and activation of the c-myc pathway. Higher KDM7A-DT expression is associated with relatively poor survival outcomes in patients with luminal A or Basal subtypes. In contrast, it is associated with favorable outcomes in patients with HER2+ER- or luminal B subtypes. KDM7A-DT levels are coregulated with critical transcripts and proteins aberrantly expressed in BRCA, including those involved in DNA repair via non-homologous end joining and epithelial-to-mesenchymal transition pathway. In summary, KDM7A-DT and its si-lncRNA exhibit several intrinsic biological and clinical characteristics that suggest important roles in invasive BRCA and its subtypes. KDM7A-DT-defined mRNA and protein subnetworks offer resources for identifying clinically relevant RNA-based signatures and prospective targets for therapeutic intervention.
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Affiliation(s)
- Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- University Research Institute for the Study of Genetic & Malignant Disorders in Childhood, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Tsifintaris
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vasileios Gouzouasis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ghim Siong Ow
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei Yee Aau
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Csaba Papp
- Department of Urology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Anna V. Ivshina
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Vladimir A. Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Urology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
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3
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Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. eLife 2024; 12:RP90425. [PMID: 38411169 PMCID: PMC10939502 DOI: 10.7554/elife.90425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a functional homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
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Affiliation(s)
- Amanda J Su
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Siri C Yendluri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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4
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Zhang F, Sen ND, Hinnebusch AG. Repression of MRP51 in cis does not contribute to the synthetic growth defect conferred by an hphMX4-marked deletion of DBP1 in a ded1-ts mutant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578007. [PMID: 38410469 PMCID: PMC10896344 DOI: 10.1101/2024.01.30.578007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Powers et al. recently demonstrated that the hphMX6 cassette used to delete DPB1 in dbp1Δ::hphMX6 yeast mutants leads to reduced expression in cis of the adjacent gene MRP51, encoding the mitochondrial small subunit (SSU) ribosomal protein Mrp51. Here we provide evidence that elimination of Dbp1, not reduced MRP51 expression, underlies the synthetic growth defect of a dbp1Δ::hphMX6 ded1-ts mutant on glucose-containing medium, where respiration is dispensable, consistent with our previous conclusion that Dbp1 and Ded1 perform overlapping functions in stimulating translation initiation on mRNAs burdened with long or structured 5'UTRs in cells cultured with glucose.
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Affiliation(s)
- Fan Zhang
- Division of Molecular and Cellular Biology, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Neelam Dabas Sen
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Alan G. Hinnebusch
- Division of Molecular and Cellular Biology, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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5
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Zhu P, Schon M, Questa J, Nodine M, Dean C. Causal role of a promoter polymorphism in natural variation of the Arabidopsis floral repressor gene FLC. Curr Biol 2023; 33:4381-4391.e3. [PMID: 37729909 DOI: 10.1016/j.cub.2023.08.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/06/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Noncoding polymorphism frequently associates with phenotypic variation, but causation and mechanism are rarely established. Noncoding single-nucleotide polymorphisms (SNPs) characterize the major haplotypes of the Arabidopsis thaliana floral repressor gene FLOWERING LOCUS C (FLC). This noncoding polymorphism generates a range of FLC expression levels, determining the requirement for and the response to winter cold. The major adaptive determinant of these FLC haplotypes was shown to be the autumnal levels of FLC expression. Here, we investigate how noncoding SNPs influence FLC transcriptional output. We identify an upstream transcription start site (uTSS) cluster at FLC, whose usage is increased by an A variant at the promoter SNP-230. This variant is present in relatively few Arabidopsis accessions, with the majority containing G at this site. We demonstrate a causal role for the A variant at -230 in reduced FLC transcriptional output. The G variant upregulates FLC expression redundantly with the major transcriptional activator FRIGIDA (FRI). We demonstrate an additive interaction of SNP-230 with an intronic SNP+259, which also differentially influences uTSS usage. Combinatorial interactions between noncoding SNPs and transcriptional activators thus generate quantitative variation in FLC transcription that has facilitated the adaptation of Arabidopsis accessions to distinct climates.
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Affiliation(s)
- Pan Zhu
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michael Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands; Gregor Mendel Institute, Vienna Biocenter, Vienna 1030, Austria
| | - Julia Questa
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michael Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands; Gregor Mendel Institute, Vienna Biocenter, Vienna 1030, Austria
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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6
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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7
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Harris A, Ünal E. The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis. Genetics 2023; 225:iyad123. [PMID: 37431893 PMCID: PMC10550318 DOI: 10.1093/genetics/iyad123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
The process of gametogenesis is orchestrated by a dynamic gene expression program, where a vital subset constitutes the early meiotic genes. In budding yeast, the transcription factor Ume6 represses early meiotic gene expression during mitotic growth. However, during the transition from mitotic to meiotic cell fate, early meiotic genes are activated in response to the transcriptional regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes early meiotic gene expression, the mechanism of early meiotic gene activation remains elusive. Two competing models have been proposed whereby Ime1 either forms an activator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy. First, we identify the set of genes that are directly regulated by Ume6, including UME6 itself. While Ume6 protein levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to early meiotic gene activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger early meiotic gene expression and produce viable gametes in the absence of Ime1. We conclude that Ime1 and Ume6 form an activator complex. While Ume6 is indispensable for early meiotic gene expression, Ime1 primarily serves as a transactivator for Ume6.
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Affiliation(s)
- Anthony Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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8
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Shah S, Mittal P, Kumar D, Mittal A, Ghosh SK. Evidence of kinesin motors involved in stable kinetochore assembly during early meiosis. Mol Biol Cell 2023; 34:ar107. [PMID: 37556230 PMCID: PMC10559306 DOI: 10.1091/mbc.e22-12-0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
During mitosis, the budding yeast, kinetochores remain attached to microtubules, except for a brief period during S phase. Sister-kinetochores separate into two clusters (bilobed organization) upon stable end-on attachment to microtubules emanating from opposite spindle poles. However, in meiosis, the outer kinetochore protein (Ndc80) reassembles at the centromeres much later after prophase I, establishing new kinetochore-microtubule attachments. Perhaps due to this, despite homolog bi-orientation, we observed that the Ndc80 are linearly dispersed between spindle poles during metaphase I of meiosis. The presence of end-on attachment marker Dam1 as a cluster near each pole suggests one of the other possibilities that the pole-proximal and pole-distal kinetochores are attached end-on and laterally to the microtubules, respectively. Colocalization studies of kinetochores and kinesin motors suggest that budding yeast kinesin 5, Cin8, and Kip1 perhaps localize to the end-on attached kinetochores while kinesin 8 and Kip3 resides at all the kinetochores. Our findings, including kinesin 5 and Ndc80 coappearance after prophase I and reduced Ndc80 levels in cin8 null mutant, suggest that kinesin motors are crucial for kinetochore reassembly and stability during early meiosis. Thus, this work reports yet another meiosis specific function of kinesin motors.
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Affiliation(s)
- Seema Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Priyanka Mittal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Deepanshu Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Anjani Mittal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Santanu K. Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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9
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Ensinck I, Maman A, Albihlal WS, Lassandro M, Salzano G, Sideri T, Howell SA, Calvani E, Patel H, Bushkin G, Ralser M, Snijders AP, Skehel M, Casañal A, Schwartz S, van Werven FJ. The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles. eLife 2023; 12:RP87860. [PMID: 37490041 PMCID: PMC10393049 DOI: 10.7554/elife.87860] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/insects/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis and was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian MTC orthologues. Unlike the mammalian bipartite MTC, the yeast MTC is unipartite, yet multifunctional. The mRNA interacting module, comprising Ime4, Mum2, Vir1, and Kar4, exerts the MTC's m6A-independent function, while Slz1 enables the MTC catalytic function in m6A deposition. Both functions are critical for meiotic progression. Kar4 also has a mechanistically separate role from the MTC during mating. The yeast MTC constituents play distinguishable m6A-dependent, MTC-dependent, and MTC-independent functions, highlighting their complexity and paving the path towards dissecting multi-layered MTC functions in mammals.
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Affiliation(s)
| | - Alexander Maman
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | | | | | | | | | | | | | | | - Guy Bushkin
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Markus Ralser
- The Francis Crick InstituteLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Department of BiochemistryBerlinGermany
| | | | - Mark Skehel
- The Francis Crick InstituteLondonUnited Kingdom
| | | | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
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10
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Morse K, Swerdlow S, Ünal E. Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538572. [PMID: 37162931 PMCID: PMC10168381 DOI: 10.1101/2023.04.27.538572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by integrated genomic analysis, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. To our knowledge, this study is the first to observe Swi/Snf's direct involvement in gene repression via a cis transcriptional interference mechanism.
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Affiliation(s)
- Kaitlin Morse
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Sarah Swerdlow
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
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11
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:2976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Affiliation(s)
| | | | - Izabela Makałowska
- Institute of Human Biology and Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Ponańskiego 6, 61-614 Poznań, Poland
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12
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Weber R, Ghoshdastider U, Spies D, Duré C, Valdivia-Francia F, Forny M, Ormiston M, Renz PF, Taborsky D, Yigit M, Bernasconi M, Yamahachi H, Sendoel A. Monitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer. Oncogene 2023; 42:638-650. [PMID: 36550360 PMCID: PMC9957725 DOI: 10.1038/s41388-022-02578-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5' and 3' untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5'UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identical coding sequences and demonstrate that the underlying transcription start site heterogeneity frequently results in 5' terminal oligopyrimidine (TOP) and pyrimidine-rich translational element (PRTE) motif switches to drive mTORC1-dependent translation of the mRNA. Genome-wide, we show that highly translated squamous cell carcinoma transcripts switch towards increased use of 5'TOP and PRTE motifs, have generally shorter 5'UTRs and expose decreased RNA secondary structures. Notably, we found that the two 5'TOP motif-containing, but not the TOP-less, RPL21 transcript isoforms strongly correlated with overall survival in human head and neck squamous cell carcinoma patients. Our findings warrant isoform-specific analyses in human cancer datasets and suggest that switching between 5'UTR isoforms is an elegant and simple way to alter protein synthesis rates, set their sensitivity to the mTORC1-dependent nutrient-sensing pathway and direct the translational potential of an mRNA by the precise 5'UTR sequence.
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Affiliation(s)
- Ramona Weber
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Umesh Ghoshdastider
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Daniel Spies
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Clara Duré
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Merima Forny
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Mark Ormiston
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - David Taborsky
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Merve Yigit
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Martino Bernasconi
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Homare Yamahachi
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland.
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13
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Vander Wende HM, Gopi M, Onyundo M, Medrano C, Adanlawo T, Brar GA. Meiotic resetting of the cellular Sod1 pool is driven by protein aggregation, degradation, and transient LUTI-mediated repression. J Biophys Biochem Cytol 2023; 222:213795. [PMID: 36622328 PMCID: PMC9836244 DOI: 10.1083/jcb.202206058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/28/2022] [Accepted: 12/13/2022] [Indexed: 01/10/2023] Open
Abstract
Gametogenesis requires packaging of the cellular components needed for the next generation. In budding yeast, this process includes degradation of many mitotically stable proteins, followed by their resynthesis. Here, we show that one such case-Superoxide dismutase 1 (Sod1), a protein that commonly aggregates in human ALS patients-is regulated by an integrated set of events, beginning with the formation of pre-meiotic Sod1 aggregates. This is followed by degradation of a subset of the prior Sod1 pool and clearance of Sod1 aggregates. As degradation progresses, Sod1 protein production is transiently blocked during mid-meiotic stages by transcription of an extended and poorly translated SOD1 mRNA isoform, SOD1LUTI. Expression of SOD1LUTI is induced by the Unfolded Protein Response, and it acts to repress canonical SOD1 mRNA expression. SOD1LUTI is no longer expressed following the meiotic divisions, enabling a resurgence of canonical mRNA and synthesis of new Sod1 protein such that gametes inherit a full complement of Sod1 protein. Failure to aggregate and degrade Sod1 results in reduced gamete fitness in the presence of oxidants, highlighting the importance of this regulation. Investigation of Sod1 during yeast gametogenesis, an unusual cellular context in which Sod1 levels are tightly regulated, could shed light on conserved aspects of its aggregation and degradation, with relevance to understanding Sod1's role in human disease.
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Affiliation(s)
- Helen M. Vander Wende
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Mounika Gopi
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Megan Onyundo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Medrano
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA,Correspondence to Gloria A. Brar:
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14
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Powers EN, Chan C, Doron-Mandel E, Llacsahuanga Allcca L, Kim Kim J, Jovanovic M, Brar GA. Bidirectional promoter activity from expression cassettes can drive off-target repression of neighboring gene translation. eLife 2022; 11:e81086. [PMID: 36503721 PMCID: PMC9754628 DOI: 10.7554/elife.81086] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Targeted selection-based genome-editing approaches have enabled many fundamental discoveries and are used routinely with high precision. We found, however, that replacement of DBP1 with a common selection cassette in budding yeast led to reduced expression and function for the adjacent gene, MRP51, despite all MRP51 coding and regulatory sequences remaining intact. Cassette-induced repression of MRP51 drove all mutant phenotypes detected in cells deleted for DBP1. This behavior resembled the 'neighboring gene effect' (NGE), a phenomenon of unknown mechanism whereby cassette insertion at one locus reduces the expression of a neighboring gene. Here, we leveraged strong off-target mutant phenotypes resulting from cassette replacement of DBP1 to provide mechanistic insight into the NGE. We found that the inherent bidirectionality of promoters, including those in expression cassettes, drives a divergent transcript that represses MRP51 through combined transcriptional interference and translational repression mediated by production of a long undecoded transcript isoform (LUTI). Divergent transcript production driving this off-target effect is general to yeast expression cassettes and occurs ubiquitously with insertion. Despite this, off-target effects are often naturally prevented by local sequence features, such as those that terminate divergent transcripts between the site of cassette insertion and the neighboring gene. Thus, cassette-induced off-target effects can be eliminated by the insertion of transcription terminator sequences into the cassette, flanking the promoter. Because the driving features of this off-target effect are broadly conserved, our study suggests it should be considered in the design and interpretation of experiments using integrated expression cassettes in other eukaryotic systems, including human cells.
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Affiliation(s)
- Emily Nicole Powers
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Charlene Chan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ella Doron-Mandel
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | | | - Jenny Kim Kim
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkleyBerkleyUnited States
- Center for Computational Biology, University of California, BerkeleyBerkeleyUnited States
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15
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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16
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Varier RA, Sideri T, Capitanchik C, Manova Z, Calvani E, Rossi A, Edupuganti RR, Ensinck I, Chan VWC, Patel H, Kirkpatrick J, Faull P, Snijders AP, Vermeulen M, Ralser M, Ule J, Luscombe NM, van Werven FJ. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. eLife 2022; 11:e84034. [PMID: 36422864 PMCID: PMC9731578 DOI: 10.7554/elife.84034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022] Open
Abstract
N6- methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3'end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.
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Affiliation(s)
| | | | | | | | | | - Alice Rossi
- The Francis Crick InstituteLondonUnited Kingdom
| | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Biomedical Research BuildingMiamiUnited States
| | | | | | | | | | - Peter Faull
- The Francis Crick InstituteLondonUnited Kingdom
- Biological Mass Spectrometry Facility, The University of Texas at AustinAustinUnited States
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
| | - Markus Ralser
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Biochemistry, Charité Universitätsmedizin BerlinBerlinGermany
| | - Jernej Ule
- The Francis Crick InstituteLondonUnited Kingdom
- Dementia Research Institute, King's College LondonLondonUnited Kingdom
| | - Nicholas M Luscombe
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Genetics, Evolution and Environment, UCL Genetics InstituteLondonUnited Kingdom
- Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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17
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Dang TTV, Colin J, Janbon G. Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi. J Fungi (Basel) 2022; 8:1044. [PMID: 36294609 PMCID: PMC9604717 DOI: 10.3390/jof8101044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/20/2022] Open
Abstract
Pathogenic fungi require delicate gene regulation mechanisms to adapt to diverse living environments and escape host immune systems. Recent advances in sequencing technology have exposed the complexity of the fungal genome, thus allowing the gradual disentanglement of multiple layers of gene expression control. Alternative transcription start site (aTSS) usage, previously reported to be prominent in mammals and to play important roles in physiopathology, is also present in fungi to fine-tune gene expression. Depending on the alteration in their sequences, RNA isoforms arising from aTSSs acquire different characteristics that significantly alter their stability and translational capacity as well as the properties and biologic functions of the resulting proteins. Disrupted control of aTSS usage has been reported to severely impair growth, virulence, and the infectious capacity of pathogenic fungi. Here, we discuss principle concepts, mechanisms, and the functional implication of aTSS usage in fungi.
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Affiliation(s)
- Thi Tuong Vi Dang
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
| | - Jessie Colin
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
- Ecole Pratique des Hautes Etudes, PSL Research University, F-75014 Paris, France
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Université de Paris Cité, F-75015 Paris, France
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18
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Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
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Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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19
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Sing TL, Conlon K, Lu SH, Madrazo N, Morse K, Barker JC, Hollerer I, Brar GA, Sudmant PH, Ünal E. Meiotic cDNA libraries reveal gene truncations and mitochondrial proteins important for competitive fitness in Saccharomyces cerevisiae. Genetics 2022; 221:iyac066. [PMID: 35471663 PMCID: PMC9157139 DOI: 10.1093/genetics/iyac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/13/2022] [Indexed: 01/16/2023] Open
Abstract
Gametogenesis is an evolutionarily conserved developmental program whereby a diploid progenitor cell undergoes meiosis and cellular remodeling to differentiate into haploid gametes, the precursors for sexual reproduction. Even in the simple eukaryotic organism Saccharomyces cerevisiae, the meiotic transcriptome is very rich and complex, thereby necessitating new tools for functional studies. Here, we report the construction of 5 stage-specific, inducible complementary DNA libraries from meiotic cells that represent over 84% of the genes found in the budding yeast genome. We employed computational strategies to detect endogenous meiotic transcript isoforms as well as library-specific gene truncations. Furthermore, we developed a robust screening pipeline to test the effect of each complementary DNA on competitive fitness. Our multiday proof-of-principle time course revealed 877 complementary DNAs that were detrimental for competitive fitness when overexpressed. The list included mitochondrial proteins that cause dose-dependent disruption of cellular respiration as well as library-specific gene truncations that expose a dominant negative effect on competitive growth. Together, these high-quality complementary DNA libraries provide an important tool for systematically identifying meiotic genes, transcript isoforms, and protein domains that are important for a specific biological function.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Katie Conlon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie H Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicole Madrazo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaitlin Morse
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Juliet C Barker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ina Hollerer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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20
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Tresenrider A, Chia M, van Werven FJ, Ünal E. Long undecoded transcript isoform (LUTI) detection in meiotic budding yeast by direct RNA and transcript leader sequencing. STAR Protoc 2022; 3:101145. [PMID: 35169715 PMCID: PMC8829799 DOI: 10.1016/j.xpro.2022.101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
LUTIs (Long Undecoded Transcript Isoforms) are 5'-extended and poorly translated mRNAs that can downregulate transcription from promoters more proximal to a gene's coding sequence (CDS). In this protocol, polyA RNA is extracted from budding yeast cells undergoing highly synchronized meiosis. Using a combination of long-read direct RNA sequencing and transcript leader sequencing (TL-seq), meiosis-specific LUTIs are systematically identified. Following identification, TL-seq is used to quantify the abundance of both LUTI and the more canonical gene-proximal (PROX) transcripts. For complete details on the use and execution of this protocol, please refer to Tresenrider et al. (2021).
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Affiliation(s)
- Amy Tresenrider
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Genome Sciences, Foege Hall, University of Washington, Seattle, WA 98105, USA
| | - Minghao Chia
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
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21
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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22
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Crooijmans ME, Delzenne TO, Hensen T, Darehei M, de Winde JH, van Heusden GPH. Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194714. [PMID: 33971368 DOI: 10.1016/j.bbagrm.2021.194714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022]
Abstract
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.
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Affiliation(s)
| | - Tijn O Delzenne
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Tim Hensen
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mina Darehei
- Institute of Biology, Leiden University, Leiden, the Netherlands
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23
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Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. Mol Cell 2021; 81:2231-2245.e11. [PMID: 33826921 PMCID: PMC8153250 DOI: 10.1016/j.molcel.2021.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/05/2021] [Accepted: 03/09/2021] [Indexed: 12/31/2022]
Abstract
Long undecoded transcript isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed important aspects of LUTI-based repression, how these features affect gene regulation on a global scale is unknown. Using transcript leader and direct RNA sequencing, here, we identify 74 LUTI candidates that are specifically induced in meiotic prophase. Translational repression of these candidates appears to be ubiquitous and is dependent on upstream open reading frames. However, LUTI-based transcriptional repression is variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.
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24
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Chen J, Ünal E. Meiotic regulation of the Ndc80 complex composition and function. Curr Genet 2021; 67:511-518. [PMID: 33745061 PMCID: PMC8254699 DOI: 10.1007/s00294-021-01174-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/30/2022]
Abstract
This review describes the current models for how the subunit abundance of the Ndc80 complex, a key kinetochore component, is regulated in budding yeast and metazoan meiosis. The past decades of kinetochore research have established the Ndc80 complex to be a key microtubule interactor and a central hub for regulating chromosome segregation. Recent studies further demonstrate that Ndc80 is the limiting kinetochore subunit that dictates the timing of kinetochore activation in budding yeast meiosis. Here, we discuss the molecular circuits that regulate Ndc80 protein synthesis and degradation in budding yeast meiosis and compare the findings with those from metazoans. We envision the regulatory principles discovered in budding yeast to be conserved in metazoans, thereby providing guidance into future investigations on kinetochore regulation in human health and disease.
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Affiliation(s)
- Jingxun Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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25
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Comparative Genomics of the BDNF Gene, Non-Canonical Modes of Transcriptional Regulation, and Neurological Disease. Mol Neurobiol 2021; 58:2851-2861. [PMID: 33517560 DOI: 10.1007/s12035-021-02306-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Alternative splicing of genes in the central nervous system is ubiquitous and utilizes many different mechanisms. Splicing generates unique transcript or protein isoforms of the primary gene that result in shortened, lengthened, or reorganized products that may have distinct functions from the parent gene. Learning and memory genes respond selectively to a variety of environmental stimuli and have evolved a number of complex mechanisms for transcriptional regulation to act rapidly and flexibly to environmental demands. Their patterns of expression, however, are incompletely understood. Many activity-inducible genes generate transcripts by alternative splicing that have an unknown physiological or behavioral function. One such gene codes for the protein brain-derived neurotrophic factor (BDNF). BDNF is a neurotrophin whose expression is essential for cellular growth, synaptogenesis, and synaptic plasticity. It is an important model gene because of its complex structure and the variety of transcriptional mechanisms it displays for expression in response to external stimuli. Some of these are unexpected, or non-canonical, transcriptional control mechanisms that require further exploration in an activity-dependent context. In this review, a comparative genomics approach is taken to highlight the different forms of BDNF gene transcription including potential autoregulatory mechanisms. Modes of BDNF control have general implications for understanding the origins of several neurological disorders that are associated with reduced BDNF function.
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26
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Moretto F, Wood NE, Chia M, Li C, Luscombe NM, van Werven FJ. Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell Rep 2021; 34:108643. [PMID: 33472063 PMCID: PMC7816125 DOI: 10.1016/j.celrep.2020.108643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription through noncoding regions of the genome is pervasive. How these transcription events regulate gene expression remains poorly understood. Here, we report that, in S. cerevisiae, the levels of transcription through a noncoding region, IRT2, located upstream in the promoter of the inducer of meiosis, IME1, regulate opposing chromatin and transcription states. At low levels, the act of IRT2 transcription promotes histone exchange, delivering acetylated histone H3 lysine 56 to chromatin locally. The subsequent open chromatin state directs transcription factor recruitment and induces downstream transcription to repress the IME1 promoter and meiotic entry. Conversely, increasing transcription turns IRT2 into a repressor by promoting transcription-coupled chromatin assembly. The two opposing functions of IRT2 transcription shape a regulatory circuit, which ensures a robust cell-type-specific control of IME1 expression and yeast meiosis. Our data illustrate how intergenic transcription levels are key to controlling local chromatin state, gene expression, and cell fate outcomes.
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Affiliation(s)
- Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Cai Li
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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27
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Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
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Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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28
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Gowthaman U, García-Pichardo D, Jin Y, Schwarz I, Marquardt S. DNA Processing in the Context of Noncoding Transcription. Trends Biochem Sci 2020; 45:1009-1021. [DOI: 10.1016/j.tibs.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
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29
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Higdon AL, Brar GA. Rules are made to be broken: a "simple" model organism reveals the complexity of gene regulation. Curr Genet 2020; 67:49-56. [PMID: 33130938 DOI: 10.1007/s00294-020-01121-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 11/27/2022]
Abstract
Global methods for assaying translation have greatly improved our understanding of the protein-coding capacity of the genome. In particular, it is now possible to perform genome-wide and condition-specific identification of translation initiation sites through modified ribosome profiling methods that selectively capture initiating ribosomes. Here we discuss our recent study applying such an approach to meiotic and mitotic timepoints in the simple eukaryote, budding yeast, as an example of the surprising diversity of protein products-many of which are non-canonical-that can be revealed by such methods. We also highlight several key challenges in studying non-canonical protein isoforms that have precluded their prior systematic discovery. A growing body of work supports expanded use of empirical protein-coding region identification, which can help relieve some of the limitations and biases inherent to traditional genome annotation approaches. Our study also argues for the adoption of less static views of gene identity and a broader framework for considering the translational capacity of the genome.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
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30
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Learning-Dependent Transcriptional Regulation of BDNF by its Truncated Protein Isoform in Turtle. J Mol Neurosci 2020; 71:999-1014. [DOI: 10.1007/s12031-020-01722-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/25/2020] [Indexed: 10/23/2022]
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31
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Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2020; 10:1575-1583. [PMID: 32213532 PMCID: PMC7202008 DOI: 10.1534/g3.119.400937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neighboring sequences of a gene can influence its expression. In the phenomenon known as transcriptional interference, transcription at one region in the genome can repress transcription at a nearby region in cis. Transcriptional interference occurs at a number of eukaryotic loci, including the alcohol dehydrogenase (Adh) gene in Drosophila melanogaster. Adh is regulated by two promoters, which are distinct in their developmental timing of activation. It has been shown using transgene insertion that when the promoter distal from the Adh start codon is deleted, transcription from the proximal promoter becomes de-regulated. As a result, the Adh proximal promoter, which is normally active only during the early larval stages, becomes abnormally activated in adults. Whether this type of regulation occurs in the endogenous Adh context, however, remains unclear. Here, we employed the CRISPR/Cas9 system to edit the endogenous Adh locus and found that removal of the distal promoter also resulted in the untimely expression of the proximal promoter-driven mRNA isoform in adults, albeit at lower levels than previously reported. Importantly, transcription from the distal promoter was sufficient to repress proximal transcription in larvae, and the degree of this repression was dependent on the degree of distal promoter activity. Finally, upregulation of the distal Adh transcript led to the enrichment of histone 3 lysine 36 trimethylation over the Adh proximal promoter. We conclude that the endogenous Adh locus is developmentally regulated by transcriptional interference in a tunable manner.
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32
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Chen J, Liao A, Powers EN, Liao H, Kohlstaedt LA, Evans R, Holly RM, Kim JK, Jovanovic M, Ünal E. Aurora B-dependent Ndc80 degradation regulates kinetochore composition in meiosis. Genes Dev 2020; 34:209-225. [PMID: 31919192 PMCID: PMC7000919 DOI: 10.1101/gad.333997.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/12/2019] [Indexed: 12/24/2022]
Abstract
The kinetochore complex is a conserved machinery that connects chromosomes to spindle microtubules. During meiosis, the kinetochore is restructured to accommodate a specialized chromosome segregation pattern. In budding yeast, meiotic kinetochore remodeling is mediated by the temporal changes in the abundance of a single subunit called Ndc80. We previously described the regulatory events that control the timely synthesis of Ndc80. Here, we report that Ndc80 turnover is also tightly regulated in meiosis: Ndc80 degradation is active in meiotic prophase, but not in metaphase I. Ndc80 degradation depends on the ubiquitin ligase APCAma1 and is mediated by the proteasome. Importantly, Aurora B-dependent Ndc80 phosphorylation, a mark that has been previously implicated in correcting erroneous microtubule-kinetochore attachments, is essential for Ndc80 degradation in a microtubule-independent manner. The N terminus of Ndc80, including a 27-residue sequence and Aurora B phosphorylation sites, is both necessary and sufficient for kinetochore protein degradation. Finally, defects in Ndc80 turnover predispose meiotic cells to chromosome mis-segregation. Our study elucidates the mechanism by which meiotic cells modulate their kinetochore composition through regulated Ndc80 degradation, and demonstrates that Aurora B-dependent regulation of kinetochores extends beyond altering microtubule attachments.
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Affiliation(s)
- Jingxun Chen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Andrew Liao
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Emily N Powers
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Hanna Liao
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Lori A Kohlstaedt
- UC Berkeley QB3 Proteomics Facility, University of California at Berkeley, Berkeley, California 94720, USA
| | - Rena Evans
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ryan M Holly
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Jenny Kim Kim
- Department of Biology, Columbia University, New York City, New York 10027, USA
| | - Marko Jovanovic
- Department of Biology, Columbia University, New York City, New York 10027, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
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33
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Santos DA, Shi L, Tu BP, Weissman JS. Cycloheximide can distort measurements of mRNA levels and translation efficiency. Nucleic Acids Res 2019; 47:4974-4985. [PMID: 30916348 PMCID: PMC6547433 DOI: 10.1093/nar/gkz205] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/01/2019] [Accepted: 03/16/2019] [Indexed: 01/26/2023] Open
Abstract
Regulation of the efficiency with which an mRNA is translated into proteins represents a key mechanism for controlling gene expression. Such regulation impacts the number of actively translating ribosomes per mRNA molecule, referred to as translation efficiency (TE), which can be monitored using ribosome profiling and RNA-seq, or by evaluating the position of an mRNA in a polysome gradient. Here we show that in budding yeast, under nutrient limiting conditions, the commonly used translation inhibitor cycloheximide induces rapid transcriptional upregulation of hundreds of genes involved in ribosome biogenesis. Cycloheximide also prevents translation of these newly transcribed messages, leading to an apparent drop in TE of these genes under conditions that include key transitions during the yeast metabolic cycle, meiosis, and amino acid starvation; however, this effect is abolished when cycloheximide pretreatment is omitted. This response requires TORC1 signaling, and is modulated by the genetic background as well as the vehicle used to deliver the drug. The present work highlights an important caveat to the use of translation inhibitors when measuring TE or mRNA levels, and will hopefully aid in future experimental design as well as interpretation of prior results.
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Affiliation(s)
- Daniel A Santos
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lei Shi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
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34
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Wei W, Hennig BP, Wang J, Zhang Y, Piazza I, Pareja Sanchez Y, Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V. Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast. Genome Res 2019; 29:1974-1984. [PMID: 31740578 PMCID: PMC6886497 DOI: 10.1101/gr.243378.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/07/2019] [Indexed: 02/06/2023]
Abstract
Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptional consequences in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chromatin accessibility. We define the 5' and 3' boundaries of cryptic transcripts and show that, contrary to RNA degradation-sensitive ones, they often overlap with the end of the gene, thereby using the canonical polyadenylation site, and associate to polyribosomes. We show that chromatin-sensitive cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Finally, we confirm the presence of the predicted polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding the functional consequences of cryptic transcription and proteome complexity.
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Affiliation(s)
- Wu Wei
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Bianca P Hennig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Ilaria Piazza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yerma Pareja Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christophe D Chabbert
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.,Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
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35
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Tatip S, Taggart J, Wang Y, MacDiarmid CW, Eide DJ. Changes in transcription start sites of Zap1-regulated genes during zinc deficiency: Implications for HNT1 gene regulation. Mol Microbiol 2019; 113:285-296. [PMID: 31692084 DOI: 10.1111/mmi.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2019] [Indexed: 12/01/2022]
Abstract
Changes in RNA are often poor predictors of protein accumulation. One factor disrupting this relationship are changes in transcription start sites (TSSs). Therefore, we explored how alterations in TSS affected expression of genes regulated by the Zap1 transcriptional activator of Saccharomyces cerevisiae. Zap1 controls their response to zinc deficiency. Among over 80 known Zap1-regulated genes, several produced long leader transcripts (LLTs) in one zinc status condition and short leader transcripts (SLTs) in the other. Fusing LLT and SLT transcript leaders to green fluorescent protein indicated that for five genes, the start site shift likely has little effect on protein synthesis. For four genes, however, the different transcript leaders greatly affected translation. We focused on the HNT1 gene. Zap1 caused a shift from SLT HNT1 RNA in zinc-replete cells to LLT HNT1 RNA in deficient cells. This shift correlated with decreased protein production despite increased RNA. The LLT RNA contains multiple upstream open reading frames that can inhibit translation. Expression of the LLT HNT1 RNA was dependent on Zap1. However, expression of the long transcript was not required to decrease SLT HNT1 mRNA. Our results suggest that the Zap1-activated LLT RNA is a "fail-safe" mechanism to ensure decreased Hnt1 protein in zinc deficiency.
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Affiliation(s)
- Supinda Tatip
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin W MacDiarmid
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
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36
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Yu X, Martin PGP, Michaels SD. BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants. Nat Commun 2019; 10:4359. [PMID: 31554790 PMCID: PMC6761125 DOI: 10.1038/s41467-019-12328-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/30/2019] [Indexed: 12/18/2022] Open
Abstract
Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here we show that BORDER proteins are enriched in intergenic regions and prevent interference between closely spaced genes on the same strand by promoting the 3' pausing of RNA polymerase II at the upstream gene. In the absence of BORDER proteins, 3' pausing associated with the upstream gene is reduced and shifts into the promoter region of the downstream gene. This is consistent with a model in which BORDER proteins inhibit transcriptional interference by preventing RNA polymerase from intruding into the promoters of downstream genes.
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Affiliation(s)
- Xuhong Yu
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA
| | - Pascal G P Martin
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA.,Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA.
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37
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Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nat Commun 2019; 10:3072. [PMID: 31296853 PMCID: PMC6624317 DOI: 10.1038/s41467-019-10905-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/27/2019] [Indexed: 12/22/2022] Open
Abstract
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation. The mechanisms underlying specific TSS selection in mammals remain unclear. Here the authors show that the ubiquitously expressed transcription factor NF-Y regulate fidelity of transcription initiation at gene promoters, maintaining the region upstream of TSSs in a nucleosome-depleted state, while protecting this region from ectopic transcription initiation.
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Affiliation(s)
- Andrew J Oldfield
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA. .,Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, 34396, France.
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Dhirendra Kumar
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Senthilkumar Cinghu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Damien Paulet
- Department of Computer Science, LIRMM, CNRS et Université de Montpellier, Montpellier, 34095, France.,Institut de Biologie Computationnelle (IBC), Université de Montpellier, Montpellier, 34095, France
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Pengyi Yang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA.,Charles Perkins Centre and School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Eric Rivals
- Department of Computer Science, LIRMM, CNRS et Université de Montpellier, Montpellier, 34095, France.,Institut de Biologie Computationnelle (IBC), Université de Montpellier, Montpellier, 34095, France
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Raja Jothi
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA.
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38
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Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA. Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. G3 (BETHESDA, MD.) 2019; 9:1045-1053. [PMID: 30723103 PMCID: PMC6469420 DOI: 10.1534/g3.118.200802] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/25/2019] [Indexed: 11/18/2022]
Abstract
We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that prevented translation of the main ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown. Here we find that, indeed, a similar type of regulation occurs at the locus for the human oncogene MDM2 We observe evidence of transcriptional interference between the two MDM2 promoters, which produce a poorly translated distal promoter-derived uORF-containing mRNA isoform and a well-translated proximal promoter-derived transcript. Down-regulation of distal promoter activity markedly up-regulates proximal promoter-driven expression and results in local reduction of histone H3K36 trimethylation. Moreover, we observe that this transcript toggling between the two MDM2 isoforms naturally occurs during human embryonic stem cell differentiation programs.
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Affiliation(s)
- Ina Hollerer
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Juliet C Barker
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Amy Tresenrider
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Leon Y Chan
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Gloria A Brar
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
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39
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Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. Cell 2019; 172:910-923.e16. [PMID: 29474919 DOI: 10.1016/j.cell.2018.01.035] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous genome-wide measurements of mRNA, translation, and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases, or over 8% of all measured genes, involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether or not an mRNA is induced but rather on the type of transcript produced.
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40
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Eisenberg AR, Higdon A, Keskin A, Hodapp S, Jovanovic M, Brar GA. Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis. Cell Rep 2018; 25:3603-3617.e2. [PMID: 30590036 PMCID: PMC6328264 DOI: 10.1016/j.celrep.2018.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Protein degradation is known to be a key component of expression regulation for individual genes, but its global impact on gene expression has been difficult to determine. We analyzed a parallel gene expression dataset of yeast meiotic differentiation, identifying instances of coordinated protein-level decreases to identify new cases of regulated meiotic protein degradation, including of ribosomes and targets of the meiosis-specific anaphase-promoting complex adaptor Ama1. Comparison of protein and translation measurements over time also revealed that, although meiotic cells are capable of synthesizing protein complex members at precisely matched levels, they typically do not. Instead, the members of most protein complexes are synthesized imprecisely, but their protein levels are matched, indicating that wild-type eukaryotic cells routinely use post-translational adjustment of protein complex partner levels to achieve proper stoichiometry. Outlier cases, in which specific complex components show divergent protein-level trends, suggest timed regulation of these complexes.
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Affiliation(s)
- Amy Rose Eisenberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrea Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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41
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Wu ACK, Patel H, Chia M, Moretto F, Frith D, Snijders AP, van Werven FJ. Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor. Mol Cell 2018; 72:942-954.e7. [PMID: 30576656 PMCID: PMC6310685 DOI: 10.1016/j.molcel.2018.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/06/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022]
Abstract
Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here, we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1-regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of previously described chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeler. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality toward productive transcription.
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Affiliation(s)
- Andrew C K Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Frith
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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42
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Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, Pogson BJ. RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling. PLANT PHYSIOLOGY 2018; 178:1614-1630. [PMID: 30301775 PMCID: PMC6288732 DOI: 10.1104/pp.18.00758] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/25/2018] [Indexed: 05/07/2023]
Abstract
In plants, the molecular function(s) of the nucleus-localized 5'-3' EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3' read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8 Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
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Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Anthony A Millar
- Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
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43
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Van Dalfsen KM, Hodapp S, Keskin A, Otto GM, Berdan CA, Higdon A, Cheunkarndee T, Nomura DK, Jovanovic M, Brar GA. Global Proteome Remodeling during ER Stress Involves Hac1-Driven Expression of Long Undecoded Transcript Isoforms. Dev Cell 2018; 46:219-235.e8. [PMID: 30016623 PMCID: PMC6140797 DOI: 10.1016/j.devcel.2018.06.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 11/30/2022]
Abstract
Cellular stress responses often require transcription-based activation of gene expression to promote cellular adaptation. Whether general mechanisms exist for stress-responsive gene downregulation is less clear. A recently defined mechanism enables both up- and downregulation of protein levels for distinct gene sets by the same transcription factor via coordinated induction of canonical mRNAs and long undecoded transcript isoforms (LUTIs). We analyzed parallel gene expression datasets to determine whether this mechanism contributes to the conserved Hac1-driven branch of the unfolded protein response (UPRER), indeed observing Hac1-dependent protein downregulation accompanying the upregulation of ER-related proteins that typifies UPRER activation. Proteins downregulated by Hac1-driven LUTIs include those with electron transport chain (ETC) function. Abrogated ETC function improves the fitness of UPRER-activated cells, suggesting functional importance to this regulation. We conclude that the UPRER drives large-scale proteome remodeling, including coordinated up- and downregulation of distinct protein classes, which is partly mediated by Hac1-induced LUTIs.
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Affiliation(s)
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - George Maxwell Otto
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Charles Andrew Berdan
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Andrea Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Tia Cheunkarndee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel Koji Nomura
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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44
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Watts BR, Wittmann S, Wery M, Gautier C, Kus K, Birot A, Heo DH, Kilchert C, Morillon A, Vasiljeva L. Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Nucleic Acids Res 2018; 46:5426-5440. [PMID: 29618061 PMCID: PMC6009587 DOI: 10.1093/nar/gky232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022] Open
Abstract
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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Affiliation(s)
- Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Institut für Biochemie, Heinrich-Buff-Ring 17, 35392 Gießen, Germany
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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45
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Otto GM, Brar GA. Seq-ing answers: uncovering the unexpected in global gene regulation. Curr Genet 2018; 64:1183-1188. [PMID: 29675618 PMCID: PMC6223828 DOI: 10.1007/s00294-018-0839-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 11/26/2022]
Abstract
The development of techniques for measuring gene expression globally has greatly expanded our understanding of gene regulatory mechanisms in depth and scale. We can now quantify every intermediate and transition in the canonical pathway of gene expression—from DNA to mRNA to protein—genome-wide. Employing such measurements in parallel can produce rich datasets, but extracting the most information requires careful experimental design and analysis. Here, we argue for the value of genome-wide studies that measure multiple outputs of gene expression over many timepoints during the course of a natural developmental process. We discuss our findings from a highly parallel gene expression dataset of meiotic differentiation, and those of others, to illustrate how leveraging these features can provide new and surprising insight into fundamental mechanisms of gene regulation.
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Affiliation(s)
- George Maxwell Otto
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA.
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46
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Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4950591. [PMID: 29765496 PMCID: PMC5889882 DOI: 10.1155/2018/4950591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/07/2018] [Indexed: 02/02/2023]
Abstract
We summarize current knowledge regarding regulatory functions of long noncoding RNAs (lncRNAs) in yeast, with emphasis on lncRNAs identified recently in yeast colonies and biofilms. Potential regulatory functions of these lncRNAs in differentiated cells of domesticated colonies adapted to plentiful conditions versus yeast colony biofilms are discussed. We show that specific cell types differ in their complements of lncRNA, that this complement changes over time in differentiating upper cells, and that these lncRNAs target diverse functional categories of genes in different cell subpopulations and specific colony types.
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47
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Krzyszton M, Zakrzewska-Placzek M, Kwasnik A, Dojer N, Karlowski W, Kufel J. Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1017-1031. [PMID: 29356198 DOI: 10.1111/tpj.13826] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.
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Affiliation(s)
- Michal Krzyszton
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Monika Zakrzewska-Placzek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Kwasnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Norbert Dojer
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
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48
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Moretto F, Wood NE, Kelly G, Doncic A, van Werven FJ. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nat Commun 2018; 9:780. [PMID: 29472539 PMCID: PMC5823921 DOI: 10.1038/s41467-018-03213-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/24/2018] [Indexed: 12/27/2022] Open
Abstract
Transcription of long noncoding RNAs (lncRNAs) regulates local gene expression in eukaryotes. Many examples of how a single lncRNA controls the expression of an adjacent or nearby protein-coding gene have been described. Here we examine the regulation of a locus consisting of two contiguous lncRNAs and the master regulator for entry into yeast meiosis, IME1. We find that the cluster of two lncRNAs together with several transcription factors form a regulatory circuit by which IME1 controls its own promoter and thereby promotes its own expression. Inhibition or stimulation of this unusual feedback circuit affects timing and rate of IME1 accumulation, and hence the ability for cells to enter meiosis. Our data demonstrate that orchestrated transcription through two contiguous lncRNAs promotes local gene expression and determines a critical cell fate decision.
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Affiliation(s)
- Fabien Moretto
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andreas Doncic
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX, 75390, USA
- Green Center for Systems Biology, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
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49
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One-two punch mechanism of gene repression: a fresh perspective on gene regulation. Curr Genet 2017; 64:581-588. [PMID: 29218463 PMCID: PMC5948300 DOI: 10.1007/s00294-017-0793-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 02/04/2023]
Abstract
Cellular differentiation depends on temporally controlled waves of gene activation and inactivation that ultimately transform one cell type into another. It is well established that transcription factor cascades coordinate the timely activation of gene expression clusters during development. In comparison, much less is understood about how gene repression events are coordinated with the transcription factor-driven waves of gene activation and how this repression is achieved at a mechanistic level. Using budding yeast as a model, we recently discovered a new gene regulatory event, whereby a central meiotic transcription factor induces the expression of an mRNA isoform to repress gene expression through an integrated transcriptional and translational mechanism. This new model could explain how gene activation and inactivation waves can be temporally coordinated. In this review, we discuss our findings and their potential implications.
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50
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Hildreth AE, Arndt KM. A transcriptional switch controls meiosis. eLife 2017; 6. [PMID: 29063829 PMCID: PMC5655149 DOI: 10.7554/elife.31911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 11/18/2022] Open
Abstract
A key protein involved in the segregation of meiotic chromosomes is produced 'just in time' by the regulated expression of two mRNA isoforms.
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Affiliation(s)
- A Elizabeth Hildreth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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