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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [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: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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2
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Giordano M, Infantino L, Biggiogera M, Montecucco A, Biamonti G. Heat Shock Affects Mitotic Segregation of Human Chromosomes Bound to Stress-Induced Satellite III RNAs. Int J Mol Sci 2020; 21:ijms21082812. [PMID: 32316575 PMCID: PMC7216065 DOI: 10.3390/ijms21082812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Heat shock activates the transcription of arrays of Satellite III (SatIII) DNA repeats in the pericentromeric heterochromatic domains of specific human chromosomes, the longest of which is on chromosome 9. Long non-coding SatIII RNAs remain associated with transcription sites where they form nuclear stress bodies or nSBs. The biology of SatIII RNAs is still poorly understood. Here, we show that SatIII RNAs and nSBs are detectable up to four days after thermal stress and are linked to defects in chromosome behavior during mitosis. Heat shock perturbs the execution of mitosis. Cells reaching mitosis during the first 3 h of recovery accumulate in pro-metaphase. During the ensuing 48 h, this block is no longer detectable; however, a significant fraction of mitoses shows chromosome segregation defects. Notably, most of lagging chromosomes and chromosomal bridges are bound to nSBs and contain arrays of SatIII DNA. Disappearance of mitotic defects at the end of day 2 coincides with the processing of long non-coding SatIII RNAs into a ladder of small RNAs associated with chromatin and ranging in size from 25 to 75 nt. The production of these molecules does not rely on DICER and Argonaute 2 components of the RNA interference apparatus. Thus, massive transcription of SatIII DNA may contribute to chromosomal instability.
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Affiliation(s)
- Manuela Giordano
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche via Abbiategrasso 207, 27100 Pavia, Italy; (M.G.); (L.I.); (A.M.)
| | - Lucia Infantino
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche via Abbiategrasso 207, 27100 Pavia, Italy; (M.G.); (L.I.); (A.M.)
| | - Marco Biggiogera
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy;
| | - Alessandra Montecucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche via Abbiategrasso 207, 27100 Pavia, Italy; (M.G.); (L.I.); (A.M.)
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche via Abbiategrasso 207, 27100 Pavia, Italy; (M.G.); (L.I.); (A.M.)
- Correspondence: ; Tel.: +39-0382-546-334
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3
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Akoury E, Ma G, Demolin S, Brönner C, Zocco M, Cirilo A, Ivic N, Halic M. Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity. Nucleic Acids Res 2019; 47:6726-6736. [PMID: 31165882 PMCID: PMC6649693 DOI: 10.1093/nar/gkz480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
Heterochromatin is a distinctive chromatin structure that is essential for chromosome segregation, genome stability and regulation of gene expression. H3K9 methylation (H3K9me), a hallmark of heterochromatin, is deposited by the Su(var)3-9 family of proteins; however, the mechanism by which H3K9 methyltransferases bind and methylate the nucleosome is poorly understood. In this work we determined the interaction of Clr4, the fission yeast H3K9 methyltransferase, with nucleosomes using nuclear magnetic resonance, biochemical and genetic assays. Our study shows that the Clr4 chromodomain binds the H3K9me3 tail and that both, the chromodomain and the disordered region connecting the chromodomain and the SET domain, bind the nucleosome core. We show that interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Moreover, we show that those interactions with the nucleosome core are contributing to de novo deposition of H3K9me and to establishment of heterochromatin.
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Affiliation(s)
- Elias Akoury
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
- Department of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität LMU, Butenandtstrasse 5-13, 81377 Munich, Germany
- Department of Natural Sciences, Lebanese American University, Beirut 1102-2801, Lebanon
| | - Guoli Ma
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Segolene Demolin
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Cornelia Brönner
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Manuel Zocco
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
- Université Libre de Bruxelles, IRIBHM, Brussels B-1070, Belgium
| | - Alexandre Cirilo
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Nives Ivic
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
- Department of Physical Chemistry, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Mario Halic
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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4
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Zernov NV, Marakhonov AV, Vyakhireva JV, Guskova AA, Dadali EL, Skoblov MY. Clinical and genetic characteristics and diagnostic features of Landouzy–Dejerine facioscapulohumeral muscular dystrophy. RUSS J GENET+ 2017. [DOI: 10.1134/s102279541706014x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Jain R, Iglesias N, Moazed D. Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation. Mol Cell 2016; 63:191-205. [PMID: 27397687 PMCID: PMC5576859 DOI: 10.1016/j.molcel.2016.05.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/05/2016] [Accepted: 05/26/2016] [Indexed: 11/16/2022]
Abstract
Small-RNA (sRNA)-guided transcriptional gene silencing by Argonaute (Ago)-containing complexes is fundamental to genome integrity and epigenetic inheritance. The RNA cleavage ("Slicer") activity of Argonaute has been implicated in both sRNA maturation and target RNA cleavage. Typically, Argonaute slices and releases the passenger strand of duplex sRNA to generate active silencing complexes, but it remains unclear whether slicing of target nascent RNAs, or other RNAi components, also contributes to downstream transcriptional silencing. Here, we develop a strategy for loading the fission yeast Ago1 with a single-stranded sRNA guide, which bypasses the requirement for slicer activity in generation of active silencing complexes. We show that slicer-defective Ago1 can mediate secondary sRNA generation, H3K9 methylation, and silencing similar to or better than wild-type and associates with chromatin more efficiently. The results define an ancient and minimal sRNA-mediated chromatin silencing mechanism, which resembles the germline-specific sRNA-dependent transcriptional silencing pathways in Drosophila and mammals.
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Affiliation(s)
- Ruchi Jain
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nahid Iglesias
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Danesh Moazed
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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7
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Yang J, Li F. Are all repeats created equal? Understanding DNA repeats at an individual level. Curr Genet 2016; 63:57-63. [PMID: 27260214 DOI: 10.1007/s00294-016-0619-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/24/2023]
Abstract
Repetitive DNA sequences, comprising up to 50 % of the genome in all eukaryotes, play important roles in a wide range of cellular functions, such as transcriptional regulation, genome stability, and cellular differentiation. However, due to technical difficulties in differentiating their sequences, DNA repeats remain one of the most mysterious parts of eukaryotic genomes. Key questions, such as how repetitive entities behave at individual level and how the internal architecture of these repeats is organized, are still poorly understood. Recent advances from our group reveal unexpected position-dependent variation within tandem DNA repeats in fission yeast. Despite sharing identical DNA sequences, the peri-centromeric repeats are organized into diverse epigenetic states and chromatin structures. We demonstrate that this position-dependent variation requires key heterochromatin factors and condensin. Our works further suggest that the peri-centromeric repeats are organized into distinct higher order structures that ensure a proper positioning of CENP-A, the centromere-specific histone H3 variant, to centromeres. These most recent developments offer insights into the mechanisms underlying the position effect within tandem DNA arrays, and have broad implications in the field of epigenetics and chromatin biology.
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Affiliation(s)
- Jinpu Yang
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY, 10003, USA. .,1009 Silver Center, 100 Washington Square East, New York, NY, 10003-6688, USA.
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8
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Li Y, Li J, Fang C, Shi L, Tan J, Xiong Y, Bin Fan, Li C. Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages. Sci Rep 2016; 6:26852. [PMID: 27229484 PMCID: PMC4882596 DOI: 10.1038/srep26852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023] Open
Abstract
Some documented evidences proved small RNAs (sRNA) and targeted genes are involved in mammalian testicular development and spermatogenesis. However, the detailed molecular regulation mechanisms of them remain largely unknown so far. In this study, we obtained a total of 10,716 mRNAs, 67 miRNAs and 16,953 piRNAs which were differentially expressed between LC and LW pig breeds or between the two sexual maturity stages. Of which, we identified 16 miRNAs and 28 targeted genes possibly related to spermatogenesis; 14 miRNA and 18 targeted genes probably associated with cell adhesion related testis development. We also annotated 579 piRNAs which could potentially regulate cell death, nucleosome organization and other basic biology process, which implied that those piRNAs might be involved in sexual maturation difference. The integrated network analysis results suggested that some differentially expressed genes were involved in spermatogenesis through the ECM-receptor interaction, focal adhesion, Wnt and PI3K-Akt signaling pathways, some particular miRNAs have the negative regulation roles and some special piRNAs have the positive and negative regulation roles in testicular development. Our data provide novel insights into the molecular expression and regulation similarities and diversities of spermatogenesis and testicular development in different pig breeds at different stages of sexual maturity.
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Affiliation(s)
- Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jialian Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Liang Shi
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Jiajian Tan
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Yuanzhu Xiong
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Fan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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9
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Zocco M, Marasovic M, Pisacane P, Bilokapic S, Halic M. The Chp1 chromodomain binds the H3K9me tail and the nucleosome core to assemble heterochromatin. Cell Discov 2016; 2:16004. [PMID: 27462451 PMCID: PMC4849473 DOI: 10.1038/celldisc.2016.4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/31/2016] [Indexed: 01/16/2023] Open
Abstract
To maintain genome stability, cells pack large portions of their genome into silent chromatin or heterochromatin. Histone H3 lysine 9 methylation, a hallmark of heterochromatin, is recognized by conserved readers called chromodomains. But how chromodomains interact with their actual binding partner, the H3K9 methylated nucleosome, remains elusive. We have determined the structure of a nucleosome trimethylated at lysine 9 of histone H3 (H3K9me3 Nucleosome) in a complex with the chromodomain of Chp1, a protein required for RNA interference-dependent heterochromatin formation in fission yeast. The cryo-electron microscopy structure reveals that the chromodomain of Chp1 binds the histone H3 lysine 9 methylated tail and the core of the nucleosome, primarily histones H3 and H2B. Mutations in chromodomain of Chp1 loops, which interact with the nucleosome core, abolished this interaction in vitro. Moreover, fission yeast cells with Chp1 loop mutations have a defect in Chp1 recruitment and heterochromatin formation. This study reveals the structural basis for heterochromatic silencing and suggests that chromodomains could read histone code in the H3 tail and the nucleosome core, which would provide an additional layer of regulation.
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Affiliation(s)
- Manuel Zocco
- Department of Biochemistry, Gene Center, University of Munich , Munich, Germany
| | - Mirela Marasovic
- Department of Biochemistry, Gene Center, University of Munich , Munich, Germany
| | - Paola Pisacane
- Department of Biochemistry, Gene Center, University of Munich , Munich, Germany
| | - Silvija Bilokapic
- Department of Biochemistry, Gene Center, University of Munich , Munich, Germany
| | - Mario Halic
- Department of Biochemistry, Gene Center, University of Munich , Munich, Germany
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10
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Ozawa N, Furuhashi H, Masuko K, Numao E, Makino T, Yano T, Kurata S. Organ identity specification factor WGE localizes to the histone locus body and regulates histone expression to ensure genomic stability in Drosophila. Genes Cells 2016; 21:442-56. [PMID: 27145109 DOI: 10.1111/gtc.12354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/28/2016] [Indexed: 12/19/2022]
Abstract
Over-expression of Winged-Eye (WGE) in the Drosophila eye imaginal disc induces an eye-to-wing transformation. Endogenous WGE is required for organ development, and wge-deficient mutants exhibit growth arrest at the larval stage, suggesting that WGE is critical for normal growth. The function of WGE, however, remains unclear. Here, we analyzed the subcellular localization of WGE to gain insight into its endogenous function. Immunostaining showed that WGE localized to specific nuclear foci called the histone locus body (HLB), an evolutionarily conserved nuclear body required for S phase-specific histone mRNA production. Histone mRNA levels and protein levels in cytosolic fractions were aberrantly up-regulated in wge mutant larva, suggesting a role for WGE in regulating histone gene expression. Genetic analyses showed that wge suppresses position-effect variegation, and that WGE and a HLB component Mute appears to be synergistically involved in heterochromatin formation. Further supporting a role in chromatin regulation, wge-deficient mutants showed derepression of retrotransposons and increased γH2Av signals, a DNA damage marker. These findings suggest that WGE is a component of HLB in Drosophila with a role in heterochromatin formation and transposon silencing. We propose that WGE at HLB contributes to genomic stability and development by regulating heterochromatin structure via histone gene regulation.
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Affiliation(s)
- Nao Ozawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Keita Masuko
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Eriko Numao
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Tamaki Yano
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
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11
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Gal C, Murton HE, Subramanian L, Whale AJ, Moore KM, Paszkiewicz K, Codlin S, Bähler J, Creamer KM, Partridge JF, Allshire RC, Kent NA, Whitehall SK. Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organisation. EMBO Rep 2015; 17:79-93. [PMID: 26582768 PMCID: PMC4718406 DOI: 10.15252/embr.201540476] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/26/2015] [Indexed: 12/28/2022] Open
Abstract
Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA‐ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis‐positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re‐establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis‐segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome‐wide.
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Affiliation(s)
- Csenge Gal
- Institute for Cell & Molecular Biosciences, Newcastle University, Newcastle, UK
| | - Heather E Murton
- Institute for Cell & Molecular Biosciences, Newcastle University, Newcastle, UK
| | - Lakxmi Subramanian
- Wellcome Trust Centre for Cell Biology & Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Alex J Whale
- Institute for Cell & Molecular Biosciences, Newcastle University, Newcastle, UK
| | - Karen M Moore
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Konrad Paszkiewicz
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, UK
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, UK
| | - Kevin M Creamer
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology & Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kent
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Simon K Whitehall
- Institute for Cell & Molecular Biosciences, Newcastle University, Newcastle, UK
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12
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Esnault C, Levin HL. The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe. Microbiol Spectr 2015; 3:10.1128/microbiolspec.MDNA3-0040-2014. [PMID: 26350316 PMCID: PMC6388632 DOI: 10.1128/microbiolspec.mdna3-0040-2014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 12/15/2022] Open
Abstract
The long terminal repeat (LTR) retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe are active mobile elements of the Ty3/gypsy family. The mobilization of these retrotransposons depends on particle formation, reverse transcription and integration, processes typical of other LTR retrotransposons. However, Tf1 and Tf2 are distinct from other LTR elements in that they assemble virus-like particles from a single primary translation product, initiate reverse transcription with an unusual self-priming mechanism, and, in the case of Tf1, integrate with a pattern that favors specific promoters of RNA pol II-transcribed genes. To avoid the chromosome instability and genome damage that results from increased copy number, S. pombe applies a variety of defense mechanisms that restrict Tf1 and Tf2 activity. The mRNA of the Tf elements is eliminated by an exosome-based pathway when cells are in favorable conditions whereas nutrient deprivation triggers an RNA interference-dependent pathway that results in the heterochromatization of the elements. Interestingly, Tf1 integrates into the promoters of stress-induced genes and these insertions are capable of increasing the expression of adjacent genes. These properties of Tf1 transposition raise the possibility that Tf1 benefits cells with specific insertions by providing resistance to environmental stress.
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Affiliation(s)
- Caroline Esnault
- Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Henry L Levin
- Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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13
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Abstract
The chemical modification of DNA bases plays a key role in epigenetic gene regulation. While much attention has been focused on the classical epigenetic mark, 5-methylcytosine, the field garnered increased interest through the recent discovery of additional modifications. In this review, we focus on the epigenetic regulatory roles of DNA modifications in animals. We present the symmetric modification of 5-methylcytosine on CpG dinucleotide as a key feature, because it permits the inheritance of methylation patterns through DNA replication. However, the distribution patterns of cytosine methylation are not conserved in animals and independent molecular functions will likely be identified. Furthermore, the discovery of enzymes that catalyse the hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine not only identified an active demethylation pathway, but also a candidate for a new epigenetic mark associated with activated transcription. Most recently, N6-methyladenine was described as an additional eukaryotic DNA modification with epigenetic regulatory potential. Interestingly, this modification is also present in genomes that lack canonical cytosine methylation patterns, suggesting independent functions. This newfound diversity of DNA modifications and their potential for combinatorial interactions indicates that the epigenetic DNA code is substantially more complex than previously thought.
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Affiliation(s)
- Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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14
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Kobayashi N, Suzuki Y, Schoenfeld LW, Müller CA, Nieduszynski C, Wolfe KH, Tanaka TU. Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. Curr Biol 2015; 25:2026-33. [PMID: 26166782 PMCID: PMC4533239 DOI: 10.1016/j.cub.2015.06.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/26/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022]
Abstract
Centromeres are the chromosomal regions promoting kinetochore assembly for chromosome segregation. In many eukaryotes, the centromere consists of up to mega base pairs of DNA. On such “regional centromeres,” kinetochore assembly is mainly defined by epigenetic regulation [1]. By contrast, a clade of budding yeasts (Saccharomycetaceae) has a “point centromere” of 120–200 base pairs of DNA, on which kinetochore assembly is defined by the consensus DNA sequence [2, 3]. During evolution, budding yeasts acquired point centromeres, which replaced ancestral, regional centromeres [4]. All known point centromeres among different yeast species share common consensus DNA elements (CDEs) [5, 6], implying that they evolved only once and stayed essentially unchanged throughout evolution. Here, we identify a yeast centromere that challenges this view: that of the budding yeast Naumovozyma castellii is the first unconventional point centromere with unique CDEs. The N. castellii centromere CDEs are essential for centromere function but have different DNA sequences from CDEs in other point centromeres. Gene order analyses around N. castellii centromeres indicate their unique, and separate, evolutionary origin. Nevertheless, they are still bound by the ortholog of the CBF3 complex, which recognizes CDEs in other point centromeres. The new type of point centromere originated prior to the divergence between N. castellii and its close relative Naumovozyma dairenensis and disseminated to all N. castellii chromosomes through extensive genome rearrangement. Thus, contrary to the conventional view, point centromeres can undergo rapid evolutionary changes. These findings give new insights into the evolution of point centromeres. A new type of point centromere has been identified in budding yeast N. castellii Its DNA sequence and evolutionary origin are different from other point centromeres N. castellii centromeres are bound by CBF3 that recognizes other point centromeres Contrary to the conventional view, point centromeres can change rapidly in evolution
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Affiliation(s)
- Norihiko Kobayashi
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yutaka Suzuki
- Department of Computational Biology, School of Frontier Medicine, University of Tokyo, Chiba 277-8562, Japan
| | - Lori W Schoenfeld
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolin A Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Conrad Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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15
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Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
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Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
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16
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Gay S, Foiani M. Nuclear envelope and chromatin, lock and key of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 317:267-330. [PMID: 26008788 DOI: 10.1016/bs.ircmb.2015.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity.
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Affiliation(s)
- Sophie Gay
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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17
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Wang J, Reddy BD, Jia S. Rapid epigenetic adaptation to uncontrolled heterochromatin spreading. eLife 2015; 4. [PMID: 25774602 PMCID: PMC4395908 DOI: 10.7554/elife.06179] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
Heterochromatin, a highly compact chromatin state characterized by histone H3K9 methylation and HP1 protein binding, silences the underlying DNA and influences the expression of neighboring genes. However, the mechanisms that regulate heterochromatin spreading are not well understood. In this study, we show that the conserved Mst2 histone acetyltransferase complex in fission yeast regulates histone turnover at heterochromatin regions to control heterochromatin spreading and prevents ectopic heterochromatin assembly. The combined loss of Mst2 and the JmjC domain protein Epe1 results in uncontrolled heterochromatin spreading and massive ectopic heterochromatin, leading to severe growth defects due to the inactivation of essential genes. Interestingly, these cells quickly recover by accumulating heterochromatin at genes essential for heterochromatin assembly, leading to their reduced expression to restrain heterochromatin spreading. Our studies discover redundant pathways that control heterochromatin spreading and prevent ectopic heterochromatin assembly and reveal a fast epigenetic adaptation response to changes in heterochromatin landscape. DOI:http://dx.doi.org/10.7554/eLife.06179.001 The DNA in the nucleus of a cell is wrapped around histone proteins to form a compact structure known as chromatin. Chromatin's structure can control how the genes in DNA are expressed. Loosely packed chromatin contains active genes, whereas densely packed chromatin (also called ‘heterochromatin’) contains silenced genes that are not expressed. The assembly of DNA into heterochromatin needs to be carefully controlled. Otherwise, the DNA next to heterochromatin regions can become densely packed as well (via a process called ‘heterochromatin spreading’), and the genes within this DNA are incorrectly silenced. Incorrect gene silencing is often associated with diseases such as cancer. Cells add chemical groups onto the histone proteins to influence how chromatin is compacted. Densely packed chromatin contains histones with many methyl groups but few acetyl groups. A protein called Epe1, which potentially removes methyl groups, helps to prevent heterochromatin spreading in yeast cells. Wang et al. found that an enzyme called Mst2, which adds acetyl groups onto histones, also limits heterochromatin spreading and prevents extra heterochromatin from assembling at undesirable locations. Wang et al. then generated yeast cells that lacked both Epe1 and Mst2. At first, these cells were sickly and unable to grow, because several essential genes were incorrectly silenced due to rampant heterochromatin spreading. However, the cells quickly overcame this growth defect by gaining an additional mutation. Normally mutations occur through changes in DNA sequences. However, Wang et al. found that the cells acquired this mutation by packing a gene required for heterochromatin assembly into heterochromatin. This in turn stopped more chromatin from becoming packed too densely. Changes to chromatin can also be passed on to the yeast's offspring, and such a change could help the offspring to better cope with changes in heterochromatin levels. Future work could test how often inheritable changes to chromatin modification help organisms adapt to environmental stresses, or if similar changes allow cancer cells to become tolerant to anticancer drugs. DOI:http://dx.doi.org/10.7554/eLife.06179.002
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Bharat D Reddy
- Department of Biological Sciences, Columbia University, New York, United States
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, United States
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18
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Zimmermann C, Romero Y, Warnefors M, Bilican A, Borel C, Smith LB, Kotaja N, Kaessmann H, Nef S. Germ cell-specific targeting of DICER or DGCR8 reveals a novel role for endo-siRNAs in the progression of mammalian spermatogenesis and male fertility. PLoS One 2014; 9:e107023. [PMID: 25244517 PMCID: PMC4171096 DOI: 10.1371/journal.pone.0107023] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/05/2014] [Indexed: 11/19/2022] Open
Abstract
Small non-coding RNAs act as critical regulators of gene expression and are essential for male germ cell development and spermatogenesis. Previously, we showed that germ cell-specific inactivation of Dicer1, an endonuclease essential for the biogenesis of micro-RNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), led to complete male infertility due to alterations in meiotic progression, increased spermatocyte apoptosis and defects in the maturation of spermatozoa. To dissect the distinct physiological roles of miRNAs and endo-siRNAs in spermatogenesis, we compared the testicular phenotype of mice with Dicer1 or Dgcr8 depletion in male germ cells. Dgcr8 mutant mice, which have a defective miRNA pathway while retaining an intact endo-siRNA pathway, were also infertile and displayed similar defects, although less severe, to Dicer1 mutant mice. These included cumulative defects in meiotic and haploid phases of spermatogenesis, resulting in oligo-, terato-, and azoospermia. In addition, we found by RNA sequencing of purified spermatocytes that inactivation of Dicer1 and the resulting absence of miRNAs affected the fine tuning of protein-coding gene expression by increasing low level gene expression. Overall, these results emphasize the essential role of miRNAs in the progression of spermatogenesis, but also indicate a role for endo-siRNAs in this process.
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Affiliation(s)
- Céline Zimmermann
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Yannick Romero
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Maria Warnefors
- Center for Integrative Genomics, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adem Bilican
- Center for Integrative Genomics, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Lee B. Smith
- MRC Centre for Reproductive Health, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, United Kingdom
| | - Noora Kotaja
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
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19
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White SA, Buscaino A, Sanchez-Pulido L, Ponting CP, Nowicki MW, Allshire RC. The RFTS domain of Raf2 is required for Cul4 interaction and heterochromatin integrity in fission yeast. PLoS One 2014; 9:e104161. [PMID: 25090107 PMCID: PMC4121317 DOI: 10.1371/journal.pone.0104161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/11/2014] [Indexed: 11/18/2022] Open
Abstract
Centromeric heterochromatin assembly in fission yeast is critical for faithful chromosome segregation at mitosis. Its assembly requires a concerted pathway of events whereby the RNA interference (RNAi) pathway guides H3K9 methylation to target sequences. H3K9 methylation, a hallmark of heterochromatin structure, is mediated by the single histone methyltransferase Clr4 (equivalent to metazoan Suv3-9), a component of the CLRC complex. Loss of or defects in CLRC components disrupts heterochromatin formation due to loss of H3K9 methylation, thus an intact, fully functional CLRC complex is required for heterochromatin integrity. Despite its importance, little is known about the contribution of the CLRC component Raf2 to H3K9 methylation and heterochromatin assembly. We demonstrate that Raf2 is concentrated at centromeres and contrary to other analyses, we find that loss of Raf2 does not affect CENP-ACnp1 localisation or recruitment to centromeres. Our sequence alignments show that Raf2 contains a Replication Foci Targeting Sequence (RFTS) domain homologous to the RFTS domain of the human DNA methyltransferase DNMT1. We show that the Raf2 RFTS domain is required for centromeric heterochromatin formation as its mutation disrupts H3K9 methylation but not the processing of centromeric transcripts into small interfering RNAs (siRNAs) by the RNAi pathway. Analysis of biochemical interactions demonstrates that the RFTS domain mediates an interaction between Raf2 and the CLRC component Cul4. We conclude that the RFTS domain of Raf2 is a protein interaction module that plays an important role in heterochromatin formation at centromeres.
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Affiliation(s)
- Sharon A. White
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alessia Buscaino
- School of Biosciences, Kent Fungal Group, University of Kent, Canterbury, Kent, United Kingdom
| | - Luis Sanchez-Pulido
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Chris P. Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthew W. Nowicki
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Robin C. Allshire
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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20
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Cohen AL, Jia S. Noncoding RNAs and the borders of heterochromatin. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:835-47. [PMID: 25044367 DOI: 10.1002/wrna.1249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 04/30/2014] [Accepted: 05/21/2014] [Indexed: 11/08/2022]
Abstract
Eukaryotic genomes contain long stretches of repetitive DNA sequences, which are the preferred sites for the assembly of heterochromatin structures. The formation of heterochromatin results in highly condensed chromosomal domains that limit the accessibility of DNA to the transcription and recombination machinery to maintain genome stability. Heterochromatin has the tendency to spread, and the formation of boundaries that block heterochromatin spreading is required to maintain stable gene expression patterns. Recent work has suggested that noncoding RNAs (ncRNAs) are involved in regulating boundary formation in addition to their well-established roles in chromatin regulation. Here, we present a review of our current understanding of the involvement of ncRNA at the boundaries of heterochromatin, highlighting their mechanisms of action in different settings.
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Affiliation(s)
- Allison L Cohen
- Department of Biological Sciences, Columbia University, New York, NY, USA
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21
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Abstract
Germ cell differentiation, the cellular process by which a diploid progenitor cell produces by meiotic divisions haploid cells, is conserved from the unicellular yeasts to mammals. Over the recent years, yeast germ cell differentiation process has proven to be a powerful biological system to identify and study several long noncoding RNAs (lncRNAs) that play a central role in regulating cellular differentiation by acting directly on chromatin. Remarkably, in the well-studied budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, the lncRNA-based chromatin regulations of germ cell differentiation are quite different. In this review, we present an overview of these regulations by focusing on the mechanisms and their respective functions both in S. cerevisiae and in S. pombe. Part of these lncRNA-based chromatin regulations may be conserved in other eukaryotes and play critical roles either in the context of germ cell differentiation or, more generally, in the development of multicellular organisms.
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22
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Kallgren SP, Andrews S, Tadeo X, Hou H, Moresco JJ, Tu PG, Yates JR, Nagy PL, Jia S. The proper splicing of RNAi factors is critical for pericentric heterochromatin assembly in fission yeast. PLoS Genet 2014; 10:e1004334. [PMID: 24874881 PMCID: PMC4038458 DOI: 10.1371/journal.pgen.1004334] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin preferentially assembles at repetitive DNA elements, playing roles in transcriptional silencing, recombination suppression, and chromosome segregation. The RNAi machinery is required for heterochromatin assembly in a diverse range of organisms. In fission yeast, RNA splicing factors are also required for pericentric heterochromatin assembly, and a prevailing model is that splicing factors provide a platform for siRNA generation independently of their splicing activity. Here, by screening the fission yeast deletion library, we discovered four novel splicing factors that are required for pericentric heterochromatin assembly. Sequencing total cellular RNAs from the strongest of these mutants, cwf14Δ, showed intron retention in mRNAs of several RNAi factors. Moreover, introducing cDNA versions of RNAi factors significantly restored pericentric heterochromatin in splicing mutants. We also found that mutations of splicing factors resulted in defective telomeric heterochromatin assembly and mis-splicing the mRNA of shelterin component Tpz1, and that replacement of tpz1+ with its cDNA partially rescued heterochromatin defects at telomeres in splicing mutants. Thus, proper splicing of RNAi and shelterin factors contributes to heterochromatin assembly at pericentric regions and telomeres.
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Affiliation(s)
- Scott P. Kallgren
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Stuart Andrews
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Haitong Hou
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patricia G. Tu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Peter L. Nagy
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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23
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Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CRM, Miller CJ. A global non-coding RNA system modulates fission yeast protein levels in response to stress. Nat Commun 2014; 5:3947. [PMID: 24853205 PMCID: PMC4050258 DOI: 10.1038/ncomms4947] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/25/2014] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are frequent and prevalent across the taxa. Although individual non-coding loci have been assigned a function, most are uncharacterized. Their global biological significance is unproven and remains controversial. Here we investigate the role played by ncRNAs in the stress response of Schizosaccharomyces pombe. We integrate global proteomics and RNA sequencing data to identify a systematic programme in which elevated antisense RNA arising both from ncRNAs and from 3'-overlapping convergent gene pairs is directly associated with substantial reductions in protein levels throughout the genome. We describe an extensive array of ncRNAs with trans associations that have the potential to influence multiple pathways. Deletion of one such locus reduces levels of atf1, a transcription factor downstream of the stress-activated mitogen-activated protein kinase (MAPK) pathway, and alters sensitivity to oxidative stress. These non-coding transcripts therefore regulate specific stress responses, adding unanticipated information-processing capacity to the MAPK signalling system.
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Affiliation(s)
- Hui Sun Leong
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
- These authors contributed equally to this work
| | - Keren Dawson
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
- These authors contributed equally to this work
| | - Chris Wirth
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
| | - Yaoyong Li
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
| | - Yvonne Connolly
- Biological Mass Spectrometry Facility, Cancer Research UK
Manchester Institute, University of Manchester, Wilmslow
Road, Manchester
M20 4BX, UK
| | - Duncan L. Smith
- Biological Mass Spectrometry Facility, Cancer Research UK
Manchester Institute, University of Manchester, Wilmslow
Road, Manchester
M20 4BX, UK
| | - Caroline R. M. Wilkinson
- Cell Regulation Group, Cancer Research UK Manchester Institute,
University of Manchester, Wilmslow Road,
Manchester
M20 4BX, UK
| | - Crispin J. Miller
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
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24
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Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP, Legube G. Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat Struct Mol Biol 2014; 21:366-74. [PMID: 24658350 PMCID: PMC4300393 DOI: 10.1038/nsmb.2796] [Citation(s) in RCA: 468] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 02/24/2014] [Indexed: 12/17/2022]
Abstract
Although both homologous recombination (HR) and nonhomologous end joining can repair DNA double-strand breaks (DSBs), the mechanisms by which one of these pathways is chosen over the other remain unclear. Here we show that transcriptionally active chromatin is preferentially repaired by HR. Using chromatin immunoprecipitation-sequencing (ChIP-seq) to analyze repair of multiple DSBs induced throughout the human genome, we identify an HR-prone subset of DSBs that recruit the HR protein RAD51, undergo resection and rely on RAD51 for efficient repair. These DSBs are located in actively transcribed genes and are targeted to HR repair via the transcription elongation-associated mark trimethylated histone H3 K36. Concordantly, depletion of SETD2, the main H3 K36 trimethyltransferase, severely impedes HR at such DSBs. Our study thereby demonstrates a primary role in DSB repair of the chromatin context in which a break occurs.
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Affiliation(s)
- François Aymard
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Beatrix Bugler
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Christine K Schmidt
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2] Department of Biochemistry, University of Cambridge, Cambridge, UK. [3] Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Emmanuelle Guillou
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Pierre Caron
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Sébastien Briois
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM, University of Toulouse, Toulouse, France
| | - Virginie Daburon
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Kyle M Miller
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2]
| | - Stephen P Jackson
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2] Department of Biochemistry, University of Cambridge, Cambridge, UK. [3] Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Gaëlle Legube
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
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25
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Tadeo X, Wang J, Kallgren SP, Liu J, Reddy BD, Qiao F, Jia S. Elimination of shelterin components bypasses RNAi for pericentric heterochromatin assembly. Genes Dev 2014; 27:2489-99. [PMID: 24240238 PMCID: PMC3841737 DOI: 10.1101/gad.226118.113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The RNAi pathway is required for heterochromatin assembly, and loss of RNAi causes pericentric heterochromatin defects. Tadeo et al. show that deletion of telomere shelterin components in RNAi mutants restores pericentric heterochromatin. Shelterin component Poz1 mutant analysis reveals that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Furthermore, heterochromatin protein Swi6 is redistributed to pericentric regions in RNAi mutants. Heterochromatin domains thus use multiple pathways to restrain Swi6 and avoid promiscuous heterochromatin formation. The RNAi pathway is required for heterochromatin assembly at repetitive DNA elements in diverse organisms. In fission yeast, loss of RNAi causes pericentric heterochromatin defects, compromising gene silencing and chromosome segregation. Here we show that deletion of telomere shelterin components restores pericentric heterochromatin and its functions in RNAi mutants. We further isolated a separation-of-function mutant of Poz1 and revealed that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Further analyses demonstrated that compromising shelterin-mediated heterochromatin assembly in RNAi mutants releases heterochromatin protein Swi6, which is redistributed to pericentric regions through RNAi-independent heterochromatin assembly pathways. Given the high mobility of Swi6 protein and that increased levels of Swi6 facilitates heterochromatin spreading as well as ectopic heterochromatin assembly, our results suggest that constitutive heterochromatin domains use multiple pathways to form high-affinity platforms to restrain Swi6, thus limiting its availability and avoiding promiscuous heterochromatin formation.
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Affiliation(s)
- Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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26
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Abstract
RNA transcripts that do not code for proteins have been long known to lie at the heart of many biological processes, such as splicing and translation. Yet their full potential has only been appreciated recently and non-coding RNAs (ncRNAs) are now attracting increasing attention. Pioneering work in yeast and plant systems has revealed that non-coding RNAs can have a major influence on the deposition of histone and DNA modifications. This can introduce heritable variation into gene expression and, thus, be the basis of epigenetic phenomena. Mechanistically, such processes have been studied extensively in the fission yeast Schizosaccharomyces pombe, providing an important conceptual framework for possible modes of action of ncRNAs also in other organisms. In this review, we highlight mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast, and we draw parallels to studies in other eukaryotes that indicate evolutionary conservation.
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Affiliation(s)
- Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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27
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Tanaka TU, Clayton L, Natsume T. Three wise centromere functions: see no error, hear no break, speak no delay. EMBO Rep 2013; 14:1073-83. [PMID: 24232185 PMCID: PMC3849490 DOI: 10.1038/embor.2013.181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/18/2013] [Indexed: 12/17/2022] Open
Abstract
The main function of the centromere is to promote kinetochore assembly for spindle microtubule attachment. Two additional functions of the centromere, however, are becoming increasingly clear: facilitation of robust sister-chromatid cohesion at pericentromeres and advancement of replication of centromeric regions. The combination of these three centromere functions ensures correct chromosome segregation during mitosis. Here, we review the mechanisms of the kinetochore-microtubule interaction, focusing on sister-kinetochore bi-orientation (or chromosome bi-orientation). We also discuss the biological importance of robust pericentromeric cohesion and early centromere replication, as well as the mechanisms orchestrating these two functions at the microtubule attachment site.
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Affiliation(s)
- Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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28
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Marina DB, Shankar S, Natarajan P, Finn KJ, Madhani HD. A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes Dev 2013; 27:1851-6. [PMID: 24013500 PMCID: PMC3778239 DOI: 10.1101/gad.226019.113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) can trigger repressive chromatin, but how they recruit silencing factors remains unclear. In Schizosaccharomyces pombe, heterochromatin assembly on transcribed noncoding pericentromeric repeats requires both RNAi and RNAi-independent mechanisms. In Saccharomyces cerevisiae, which lacks a repressive chromatin mark (H3K9me [methylated Lys9 on histone H3]), unstable ncRNAs are recognized by the RNA-binding protein Nrd1. We show that the S. pombe ortholog Seb1 is associated with pericentromeric lncRNAs. Individual mutation of dcr1+ (Dicer) or seb1+ results in equivalent partial reductions of pericentromeric H3K9me levels, but a double mutation eliminates this mark. Seb1 functions independently of RNAi by recruiting the NuRD (nucleosome remodeling and deacetylase)-related chromatin-modifying complex SHREC (Snf2-HDAC [histone deacetylase] repressor complex).
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Affiliation(s)
- Diana B Marina
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
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29
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Wang J, Tadeo X, Hou H, Tu PG, Thompson J, Yates JR, Jia S. Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries. Genes Dev 2013; 27:1886-902. [PMID: 24013502 PMCID: PMC3778242 DOI: 10.1101/gad.221010.113] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heterochromatin spreading leads to gene silencing, and boundary elements constrain such spreading. IRC inverted repeats are required for boundary function at centromeric heterochromatin in fission yeast. Jia and colleagues now identify BET family homolog Bdf2 as required for heterochromatin boundary function at IRCs. Bdf2 interacts with boundary protein Epe1, recognizes acetylated histone H4 tails, and antagonizes Sir2-mediated deacetylation of histone H4K16. This study illustrates a mechanism for establishing chromosome boundaries through recruitment of a factor that protects euchromatic histone modifications. Heterochromatin spreading leads to the silencing of genes within its path, and boundary elements have evolved to constrain such spreading. In fission yeast, heterochromatin at centromeres I and III is flanked by inverted repeats termed IRCs, which are required for proper boundary functions. However, the mechanisms by which IRCs prevent heterochromatin spreading are unknown. Here, we identified Bdf2, which is homologous to the mammalian bromodomain and extraterminal (BET) family double bromodomain proteins involved in diverse types of cancers, as a factor required for proper boundary function at IRCs. Bdf2 is enriched at IRCs through its interaction with the boundary protein Epe1. The bromodomains of Bdf2 recognize acetylated histone H4 tails and antagonize Sir2-mediated deacetylation of histone H4K16. Furthermore, abolishing H4K16 acetylation (H4K16ac) with an H4K16R mutation promotes heterochromatin spreading, and mimicking H4K16ac by an H4K16Q mutation blocks heterochromatin spreading at IRCs. Our results thus illustrate a mechanism of establishing chromosome boundaries at specific sites through the recruitment of a factor that protects euchromatic histone modifications. They also reveal a previously unappreciated function of H4K16ac in cooperation with H3K9 methylation to regulate heterochromatin spreading.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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30
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Huang Y, Zhang JL, Yu XL, Xu TS, Wang ZB, Cheng XC. Molecular functions of small regulatory noncoding RNA. BIOCHEMISTRY (MOSCOW) 2013; 78:221-30. [PMID: 23586714 DOI: 10.1134/s0006297913030024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recently, using large-scale genomic sequencing, a great number of small noncoding RNAs (ncRNA) has been discovered. Short ncRNAs can be classified into three major classes--small interfering RNA (siRNA), microRNA (miRNA), and piwi-interacting RNA (piRNA). These short ncRNAs ranging from 20 to 300 nt in size are now recognized as a new paradigm of gene regulation for controlling many biological processes. In this paper, we review the biogenesis and recent research on the functions of small regulatory non-coding RNAs and aim at understanding their important functions in living organisms.
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Affiliation(s)
- Yong Huang
- Animal Science and Technology College, He Nan University of Science and Technology, Luoyang City, Henan Province, PR China.
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31
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Nakamura T, Pluskal T, Nakaseko Y, Yanagida M. Impaired coenzyme A synthesis in fission yeast causes defective mitosis, quiescence-exit failure, histone hypoacetylation and fragile DNA. Open Biol 2013; 2:120117. [PMID: 23091701 PMCID: PMC3472395 DOI: 10.1098/rsob.120117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 08/22/2012] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of coenzyme A (CoA) requires a five-step process using pantothenate and cysteine in the fission yeast Schizosaccharomyces pombe. CoA contains a thiol (SH) group, which reacts with carboxylic acid to form thioesters, giving rise to acyl-activated CoAs such as acetyl-CoA. Acetyl-CoA is essential for energy metabolism and protein acetylation, and, in higher eukaryotes, for the production of neurotransmitters. We isolated a novel S. pombe temperature-sensitive strain ppc1-537 mutated in the catalytic region of phosphopantothenoylcysteine synthetase (designated Ppc1), which is essential for CoA synthesis. The mutant becomes auxotrophic to pantothenate at permissive temperature, displaying greatly decreased levels of CoA, acetyl-CoA and histone acetylation. Moreover, ppc1-537 mutant cells failed to restore proliferation from quiescence. Ppc1 is thus the product of a super-housekeeping gene. The ppc1-537 mutant showed combined synthetic lethal defects with five of six histone deacetylase mutants, whereas sir2 deletion exceptionally rescued the ppc1-537 phenotype. In synchronous cultures, ppc1-537 cells can proceed to the S phase, but lose viability during mitosis failing in sister centromere/kinetochore segregation and nuclear division. Additionally, double-strand break repair is defective in the ppc1-537 mutant, producing fragile broken DNA, probably owing to diminished histone acetylation. The CoA-supported metabolism thus controls the state of chromosome DNA.
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Affiliation(s)
- Takahiro Nakamura
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
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32
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Noncoding RNAs prevent spreading of a repressive histone mark. Nat Struct Mol Biol 2013; 20:994-1000. [PMID: 23872991 DOI: 10.1038/nsmb.2619] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 05/30/2013] [Indexed: 01/04/2023]
Abstract
Transcription of eukaryotic genomes is more widespread than was previously anticipated and results in the production of many non-protein-coding RNAs (ncRNAs) whose functional relevance is poorly understood. Here we demonstrate that ncRNAs can counteract the encroachment of heterochromatin into neighboring euchromatin. We have identified a long ncRNA (termed BORDERLINE) that prevents spreading of the HP1 protein Swi6 and histone H3 Lys9 methylation beyond the pericentromeric repeat region of Schizosaccharomyces pombe chromosome 1. BORDERLINE RNAs act in a sequence-independent but locus-dependent manner and are processed by Dicer into short RNAs referred to as brdrRNAs. In contrast to canonical centromeric short interfering RNAs, brdrRNAs are rarely loaded onto Argonaute. Our analyses reveal an unexpected regulatory activity of ncRNAs in demarcating an epigenetically distinct chromosomal domain that could also be operational in other eukaryotes.
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33
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Narayanan A, Iordanskiy S, Das R, Van Duyne R, Santos S, Jaworski E, Guendel I, Sampey G, Dalby E, Iglesias-Ussel M, Popratiloff A, Hakami R, Kehn-Hall K, Young M, Subra C, Gilbert C, Bailey C, Romerio F, Kashanchi F. Exosomes derived from HIV-1-infected cells contain trans-activation response element RNA. J Biol Chem 2013; 288:20014-33. [PMID: 23661700 PMCID: PMC3707700 DOI: 10.1074/jbc.m112.438895] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 05/03/2013] [Indexed: 12/20/2022] Open
Abstract
Exosomes are nano-sized vesicles produced by healthy and virus-infected cells. Exosomes derived from infected cells have been shown to contain viral microRNAs (miRNAs). HIV-1 encodes its own miRNAs that regulate viral and host gene expression. The most abundant HIV-1-derived miRNA, first reported by us and later by others using deep sequencing, is the trans-activation response element (TAR) miRNA. In this study, we demonstrate the presence of TAR RNA in exosomes from cell culture supernatants of HIV-1-infected cells and patient sera. TAR miRNA was not in Ago2 complexes outside the exosomes but enclosed within the exosomes. We detected the host miRNA machinery proteins Dicer and Drosha in exosomes from infected cells. We report that transport of TAR RNA from the nucleus into exosomes is a CRM1 (chromosome region maintenance 1)-dependent active process. Prior exposure of naive cells to exosomes from infected cells increased susceptibility of the recipient cells to HIV-1 infection. Exosomal TAR RNA down-regulated apoptosis by lowering Bim and Cdk9 proteins in recipient cells. We found 10(4)-10(6) copies/ml TAR RNA in exosomes derived from infected culture supernatants and 10(3) copies/ml TAR RNA in the serum exosomes of highly active antiretroviral therapy-treated patients or long term nonprogressors. Taken together, our experiments demonstrated that HIV-1-infected cells produced exosomes that are uniquely characterized by their proteomic and RNA profiles that may contribute to disease pathology in AIDS.
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Affiliation(s)
- Aarthi Narayanan
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Sergey Iordanskiy
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Ravi Das
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Rachel Van Duyne
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Steven Santos
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Elizabeth Jaworski
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Irene Guendel
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Gavin Sampey
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Elizabeth Dalby
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Maria Iglesias-Ussel
- the Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Anastas Popratiloff
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Ramin Hakami
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Kylene Kehn-Hall
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Mary Young
- the Washington Metropolitan Women's Interagency HIV Study, Division of Infectious Diseases, Georgetown University Medical Center, Washington, D. C. 20007, and
| | - Caroline Subra
- the Department of Microbiology, Infectiology, and Immunology, Medicine Faculty, Laval University Center Hospitalier Universitaire de Quebec Research Center, City of Quebec, Quebec G1R2J6, Canada
| | - Caroline Gilbert
- the Department of Microbiology, Infectiology, and Immunology, Medicine Faculty, Laval University Center Hospitalier Universitaire de Quebec Research Center, City of Quebec, Quebec G1R2J6, Canada
| | - Charles Bailey
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Fabio Romerio
- the Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Fatah Kashanchi
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
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34
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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35
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Sharma V, Misteli T. Non-coding RNAs in DNA damage and repair. FEBS Lett 2013; 587:1832-9. [PMID: 23684639 DOI: 10.1016/j.febslet.2013.05.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) are increasingly recognized as central players in diverse biological processes. Upon DNA damage, the DNA damage response (DDR) elicits a complex signaling cascade, which includes the induction of multiple ncRNA species. Recent studies indicate that DNA-damage induced ncRNAs contribute to regulation of cell cycle, apoptosis and DNA repair, and thus play a key role in maintaining genome stability. This review summarizes the emerging role of ncRNAs in DNA damage and repair.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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36
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Heinemann JA, Agapito-Tenfen SZ, Carman JA. A comparative evaluation of the regulation of GM crops or products containing dsRNA and suggested improvements to risk assessments. ENVIRONMENT INTERNATIONAL 2013; 55:43-55. [PMID: 23523853 DOI: 10.1016/j.envint.2013.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/08/2013] [Accepted: 02/22/2013] [Indexed: 05/20/2023]
Abstract
Changing the nature, kind and quantity of particular regulatory-RNA molecules through genetic engineering can create biosafety risks. While some genetically modified organisms (GMOs) are intended to produce new regulatory-RNA molecules, these may also arise in other GMOs not intended to express them. To characterise, assess and then mitigate the potential adverse effects arising from changes to RNA requires changing current approaches to food or environmental risk assessments of GMOs. We document risk assessment advice offered to government regulators in Australia, New Zealand and Brazil during official risk evaluations of GM plants for use as human food or for release into the environment (whether for field trials or commercial release), how the regulator considered those risks, and what that experience teaches us about the GMO risk assessment framework. We also suggest improvements to the process.
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Affiliation(s)
- Jack A Heinemann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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37
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Structural analysis of Stc1 provides insights into the coupling of RNAi and chromatin modification. Proc Natl Acad Sci U S A 2013; 110:E1879-88. [PMID: 23613586 DOI: 10.1073/pnas.1212155110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs can modulate gene expression by directing modifications to histones that alter chromatin structure. In fission yeast, siRNAs produced via the RNAi pathway direct modifications associated with heterochromatin formation. siRNAs associate with the RNAi effector protein Argonaute 1 (Ago1), targeting the Ago1-containing RNA-induced transcriptional silencing (RITS) complex to homologous nascent transcripts. This promotes recruitment of the Clr4 complex (CLRC), which mediates methylation of histone H3 on lysine 9 (H3K9me) in cognate chromatin. A key question is how the RNAi and chromatin modification machineries are connected. Stc1 is a small protein recently shown to associate with both Ago1 and CLRC and to play a pivotal role in mediating the RNAi-dependent recruitment of CLRC to chromatin. To understand its mode of action, we have performed a detailed structural and functional analysis of the Stc1 protein. Our analyses reveal that the conserved N-terminal region of Stc1 represents an unusual tandem zinc finger domain, with similarities to common LIM domains but distinguished by a lack of preferred relative orientation of the two zinc fingers. We demonstrate that this tandem zinc finger domain is involved in binding Ago1, whereas the nonconserved C-terminal region mediates association with CLRC. These findings elucidate the molecular basis for the coupling of RNAi to chromatin modification in fission yeast.
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38
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Leshkowitz D, Horn-Saban S, Parmet Y, Feldmesser E. Differences in microRNA detection levels are technology and sequence dependent. RNA (NEW YORK, N.Y.) 2013; 19:527-38. [PMID: 23431331 PMCID: PMC3677263 DOI: 10.1261/rna.036475.112] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Identification and quantification of small RNAs are challenging because of their short length, high sequence similarities within microRNA (miRNA) families, and the existence of miRNA isoforms and O-methyl 3' modifications. In this study, the detection performance of three high-throughput commercial platforms, Agilent and Affymetrix microarrays and Illumina next-generation sequencing, was systematically and comprehensively compared. The ability to detect miRNAs was shown to depend strongly on the platform and on miRNA modifications and sequence. Using synthetic transcripts, including mature, precursor, and O-methyl-modified miRNAs spiked into human RNA, a large intensity variation in all spiked-in miRNAs and a reduced capacity in detecting O-methyl-modified miRNAs were observed between the tested platforms. In addition, endogenous human miRNA expression levels were assessed across the platforms. Detected miRNA expression levels were not consistent between platforms. Although biases in miRNA detection were previously described, here the end-point result, i.e., detection intensity, of these biases was investigated on multiple platforms in a controlled fashion. A detailed exploration of a large number of attributes, including base composition, sequence structure, and isoform miRNA attributes, suggests their impact on miRNA expression detection level. This study provides a basis for understanding the attributes that should be considered to adjust platform-dependent detection biases.
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Affiliation(s)
- Dena Leshkowitz
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
| | - Shirley Horn-Saban
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
| | - Yisrael Parmet
- Industrial Engineering and Management Department, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ester Feldmesser
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
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39
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Abstract
The gene expression programs that establish and maintain specific cell states in humans are controlled by thousands of transcription factors, cofactors, and chromatin regulators. Misregulation of these gene expression programs can cause a broad range of diseases. Here, we review recent advances in our understanding of transcriptional regulation and discuss how these have provided new insights into transcriptional misregulation in disease.
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Affiliation(s)
- Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts
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40
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Hall SE, Chirn GW, Lau NC, Sengupta P. RNAi pathways contribute to developmental history-dependent phenotypic plasticity in C. elegans. RNA (NEW YORK, N.Y.) 2013; 19:306-319. [PMID: 23329696 PMCID: PMC3677242 DOI: 10.1261/rna.036418.112] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/26/2012] [Indexed: 05/30/2023]
Abstract
Early environmental experiences profoundly influence adult phenotypes through complex mechanisms that are poorly understood. We previously showed that adult Caenorhabditis elegans that transiently passed through the stress-induced dauer larval stage (post-dauer adults) exhibit significant changes in gene expression profiles, chromatin states, and life history traits when compared with adults that bypassed the dauer stage (control adults). These wild-type, isogenic animals of equivalent developmental stages exhibit different signatures of molecular marks that reflect their distinct developmental trajectories. To gain insight into the mechanisms that contribute to these developmental history-dependent phenotypes, we profiled small RNAs from post-dauer and control adults by deep sequencing. RNA interference (RNAi) pathways are known to regulate genome-wide gene expression both at the chromatin and post-transcriptional level. By quantifying changes in endogenous small interfering RNA (endo-siRNA) levels in post-dauer as compared with control animals, our analyses identified a subset of genes that are likely targets of developmental history-dependent reprogramming through a complex RNAi-mediated mechanism. Mutations in specific endo-siRNA pathways affect expected gene expression and chromatin state changes for a subset of genes in post-dauer animals, as well as disrupt their increased brood size phenotype. We also find that both chromatin state and endo-siRNA distribution in dauers are unique, and suggest that remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Our results indicate a role for endo-siRNA pathways as a contributing mechanism to early experience-dependent phenotypic plasticity in adults, and describe how developmental history can program adult physiology and behavior via epigenetic mechanisms.
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Affiliation(s)
- Sarah E. Hall
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Gung-Wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Piali Sengupta
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
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Chowdhury D, Choi YE, Brault ME. Charity begins at home: non-coding RNA functions in DNA repair. Nat Rev Mol Cell Biol 2013; 14:181-9. [PMID: 23385724 DOI: 10.1038/nrm3523] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the past decade, evolutionarily conserved microRNAs (miRNAs) have been characterized as regulators of almost every cellular process and signalling pathway. There is now emerging evidence that this new class of regulators also impinges on the DNA damage response (DDR). Both miRNAs and other small non-coding RNAs (ncRNAs) are induced at DNA breaks and mediate the repair process. These intriguing observations raise the possibility that crosstalk between ncRNAs and the DDR might provide a means of efficient and accurate DNA repair and facilitate the maintenance of genomic stability.
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Affiliation(s)
- Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.
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Claycomb JM. Caenorhabditis elegans small RNA pathways make their mark on chromatin. DNA Cell Biol 2013; 31 Suppl 1:S17-33. [PMID: 23046453 DOI: 10.1089/dna.2012.1611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Endogenous small-RNA-mediated gene silencing pathways are generally recognized for their functions in halting gene expression by the degradation of a transcript or by translational inhibition. However, another important mode of gene regulation by small RNAs is mediated at the level of chromatin modulation. Over the past decade a great deal of progress on understanding the molecular mechanisms by which small RNAs can influence chromatin has been made for fungi, ciliated protozoans, and plants, while less is known about the functions and consequences of such chromatin-directed small RNA pathways in animals. Several recent studies in the nematode Caenorhabditis elegans have provided mechanistic insights into small RNA pathways that impact chromatin throughout development. The "worm" has been instrumental in uncovering the mechanisms of RNA interference and remains a powerful system for dissecting the molecular means by which small RNA pathways impact chromatin in animals. This review summarizes our current knowledge of the various chromatin-directed small RNA pathways in C. elegans and provides insights for future study.
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Affiliation(s)
- Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Tang KF, Ren H. The role of dicer in DNA damage repair. Int J Mol Sci 2012; 13:16769-78. [PMID: 23222681 PMCID: PMC3546719 DOI: 10.3390/ijms131216769] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 11/09/2012] [Accepted: 11/12/2012] [Indexed: 01/07/2023] Open
Abstract
Dicer is the key component of the RNA interference pathway. Our group and others have reported that knockdown or knockout of Dicer leads to DNA damage in mammalian cells. Two groups recently showed that efficiency of DNA damage repair was greatly reduced in Dicer-deficient cells and that Dicer-dependent small RNAs (~21 nucleotides) produced from the sequences in the vicinity of DNA double-strand break sites were essential for DNA damage repair. Moreover, accumulating data have suggested that miroRNAs play pivotal roles in DNA damage repair. In this review, we discuss the molecular mechanisms by which loss of Dicer leads to DNA damage, as well as the role of Dicer in tumorigenesis.
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Affiliation(s)
- Kai-Fu Tang
- Authors to whom correspondence should be addressed; E-Mails: (K.-F.T.); (H.R.); Tel.: +86-577-8883-1271 (K.-F.T.); +86-236-369-3029 (H.R.); Fax: +86-577-8883-1359 (K.-F.T.); +86-236-370-3790 (H.R.)
| | - Hong Ren
- Authors to whom correspondence should be addressed; E-Mails: (K.-F.T.); (H.R.); Tel.: +86-577-8883-1271 (K.-F.T.); +86-236-369-3029 (H.R.); Fax: +86-577-8883-1359 (K.-F.T.); +86-236-370-3790 (H.R.)
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Normal DNA methylation dynamics in DICER1-deficient mouse embryonic stem cells. PLoS Genet 2012; 8:e1002919. [PMID: 22969435 PMCID: PMC3435250 DOI: 10.1371/journal.pgen.1002919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 07/09/2012] [Indexed: 11/19/2022] Open
Abstract
Reduced DNA methylation has been reported in DICER1-deficient mouse ES cells. Reductions seen at pericentric satellite repeats have suggested that siRNAs are required for the proper assembly of heterochromatin. More recent studies have postulated that the reduced methylation is an indirect effect: the loss of Mir290 cluster miRNAs leads to upregulation of the transcriptional repressor RBL2 that targets the downregulation of DNA methyltransferase (Dnmt) genes. However, the observations have been inconsistent. We surmised that the inconsistency could be related to cell line “age,” given that DNA methylation is lost progressively with passage in DNMT-deficient ES cells. We therefore subjected Dicer1−/− ES cells to two experimental regimes to rigorously test the level of functional DNMT activity. First, we cultured them for a prolonged period. If DNMT activity was reduced, further losses of methylation would occur. Second, we measured their DNMT activity in a rebound DNA methylation assay: DNA methylation was stripped from Cre/loxP conditionally mutant Dicer1 ES cells using a shRNA targeting Dnmt1 mRNA. Cre expression then converted these cells to Dicer1−/−, allowing for DNMT1 recovery and forcing the cells to remethylate in the absence of RNAi. In both cases, we found functional DNMT activity to be normal. Finally, we also show that the level of RBL2 protein is not at excess levels in Dicer1−/− ES cells as has been assumed. These studies reveal that reduced functional DNMT activity is not a salient feature of DICER1-deficient ES cells. We suggest that the reduced DNA methylation sometimes observed in these cells could be due to stochastic alterations in DNA methylation patterns that could offer growth or survival advantages in culture, or to the dysregulation of pathways acting in opposition to the DNMT pathway. In mammalian cells, DNA methylation is required for the maintenance of genome stability. Recent studies have shown that the genome-wide levels of DNA methylation can be reduced in DICER1-deficient mouse embryonic stem (ES) cells, suggesting that the activity of DNA methylating enzymes (DNMTs) may be regulated by small RNA molecules. The enzyme DICER1 catalyses the production of these small RNAs that serve as sequence-specific guides for modifying chromatin or transcription. However, these observations of defective DNA methylation have been inconsistent. We surmised that this inconsistency could be due to cell line “age,” because it can take many cell divisions before reduced DNMT activity may result in loss of DNA methylation. To test this idea, we rigorously assayed the functional level of DNMT activity in DICER1-deficient ES cells. First, we tested their ability to maintain DNA methylation over prolonged culture. Second, we tested their ability to rebound in DNA methylation after first stripping it from the genome. In both cases functional DNMT activity was entirely normal. We suggest that losses of DNA methylation sometimes seen in DICER1-deficient ES cells is stochastic and could involve cell line adaptation.
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Abstract
Despite many challenges, great progress has been made in identifying kinetochore proteins and understanding their overall functions relative to spindles and centromeric DNA. In contrast, less is known about the specialized centromeric chromatin environment and how it may be involved in regulating the assembly of kinetochore proteins. Multiple independent lines of evidence have implicated transcription and the resulting RNA as an important part of this process. Here, we summarize recent literature demonstrating the roles of centromeric RNA in regulating kinetochore assembly and maintenance. We also review literature suggesting that the process of centromeric transcription may be as important as the resulting RNA and that such transcription may be involved in recruiting the centromeric histone variant CENH3.
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Affiliation(s)
- Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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CSR-1 RNAi pathway positively regulates histone expression in C. elegans. EMBO J 2012; 31:3821-32. [PMID: 22863779 DOI: 10.1038/emboj.2012.216] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 07/13/2012] [Indexed: 02/08/2023] Open
Abstract
Endogenous small interfering RNAs (endo-siRNAs) have been discovered in many organisms, including mammals. In C. elegans, depletion of germline-enriched endo-siRNAs found in complex with the CSR-1 Argonaute protein causes sterility and defects in chromosome segregation in early embryos. We discovered that knockdown of either csr-1, the RNA-dependent RNA polymerase (RdRP) ego-1, or the dicer-related helicase drh-3, leads to defects in histone mRNA processing, resulting in severe depletion of core histone proteins. The maturation of replication-dependent histone mRNAs, unlike that of other mRNAs, requires processing of their 3'UTRs through an endonucleolytic cleavage guided by the U7 snRNA, which is lacking in C. elegans. We found that CSR-1-bound antisense endo-siRNAs match histone mRNAs and mRNA precursors. Consistently, we demonstrate that CSR-1 directly binds to histone mRNA in an ego-1-dependent manner using biotinylated 2'-O-methyl RNA oligonucleotides. Moreover, we demonstrate that increasing the dosage of histone genes rescues the lethality associated with depletion of CSR-1 and EGO-1. These results support a positive and direct effect of RNAi on histone gene expression.
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Meagher RB, Müssar KJ. The influence of DNA sequence on epigenome-induced pathologies. Epigenetics Chromatin 2012; 5:11. [PMID: 22818522 PMCID: PMC3439399 DOI: 10.1186/1756-8935-5-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/20/2012] [Indexed: 01/13/2023] Open
Abstract
Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype) with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, "genotype predisposes epitype", and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated) and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly determines the inherited positioning of numerous and diverse post-translational modifications of histone side chains within nucleosomes. We discuss the medical and scientific implications of these observations on future research and on the development of solutions to epigenetically induced disorders.
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Affiliation(s)
- Richard B Meagher
- Genetics Department, Davison Life Sciences Building, University of Georgia, Athens, GA, 30605, USA.
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Abstract
Pericentromeric heterochromatin formation is mediated by repressive histone H3 lysine 9 methylation (H3K9Me) and its recognition by HP1 proteins. Intriguingly, in many organisms, RNAi is coupled to this process through poorly understood mechanisms. In Schizosaccharomyces pombe, the H3-K9 methyltransferase Clr4 and the heterochromatin protein 1 (HP1) ortholog Swi6 are critical for RNAi, whereas RNAi stimulates H3K9Me. In addition to the endoribonuclease Dcr1, RNAi in S. pombe requires two interacting protein complexes, the RITS complex, which contains an Argonaute subunit, and the RDRC complex, which contains an RNA-dependent RNA polymerase subunit. We previously identified Ers1 (essential for RNAi-dependent silencing) as an orphan protein that genetically acts in the RNAi pathway. Using recombinant proteins, we show here that Ers1 directly and specifically interacts with HP1/Swi6. Two-hybrid assays indicate that Ers1 also directly interacts with several RNAi factors. Consistent with these interactions, Ers1 associates in vivo with the RITS complex, the RDRC complex, and Dcr1, and it promotes interactions between these factors. Ers1, like Swi6, is also required for RNAi complexes to associate with pericentromeric noncoding RNAs. Overexpression of Ers1 results in a dominant-negative phenotype that can be specifically suppressed by increasing levels of the RDRC subunit Hrr1 or of Dcr1, further supporting a functional role for Ers1 in promoting the assembly of the RNAi machinery. Through the interactions described here, Ers1 may promote RNAi by tethering the corresponding enzyme complexes to HP1-coated chromatin, thereby placing them in proximity to the nascent noncoding RNA substrate.
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Holoch D, Moazed D. RNAi in fission yeast finds new targets and new ways of targeting at the nuclear periphery. Genes Dev 2012; 26:741-5. [PMID: 22508721 DOI: 10.1101/gad.191155.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNAi in Schizosaccharomyces pombe is critical for centromeric heterochromatin formation. It has remained unclear, however, whether RNAi also regulates the expression of protein-coding loci. In the April 1, 2012, issue of Genes & Development, Woolcock and colleagues (pp. 683-667) reported an elegant mechanism for the conditional RNAi-mediated repression of stress response genes involving association with Dcr1 at the nuclear pore. Unexpectedly, the initial targeting of RNAi components to these genes does not require small RNA guides.
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Affiliation(s)
- Daniel Holoch
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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50
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Mmi1 RNA surveillance machinery directs RNAi complex RITS to specific meiotic genes in fission yeast. EMBO J 2012; 31:2296-308. [PMID: 22522705 DOI: 10.1038/emboj.2012.105] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/29/2012] [Indexed: 12/24/2022] Open
Abstract
RNA interference (RNAi) silences gene expression by acting both at the transcriptional and post-transcriptional levels in a broad range of eukaryotes. In the fission yeast Schizosaccharomyces pombe the RNA-Induced Transcriptional Silencing (RITS) RNAi complex mediates heterochromatin formation at non-coding and repetitive DNA. However, the targeting and role of RITS at other genomic regions, including protein-coding genes, remain unknown. Here we show that RITS localizes to specific meiotic genes and mRNAs. Remarkably, RITS is guided to these meiotic targets by the RNA-binding protein Mmi1 and its associated RNA surveillance machinery that together degrade selective meiotic mRNAs during vegetative growth. Upon sexual differentiation, RITS localization to the meiotic genes and mRNAs is lost. Large-scale identification of Mmi1 RNA targets reveals that RITS subunit Chp1 associates with the vast majority of them. In addition, loss of RNAi affects the effective repression of sexual differentiation mediated by the Mmi1 RNA surveillance machinery. These findings uncover a new mechanism for recruiting RNAi to specific meiotic genes and suggest that RNAi participates in the control of sexual differentiation in fission yeast.
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