protein coding gene - clr6 (SPBC36.05c) - histone deacetylase (class I) H3-K9 specific complex subunit Clr6

Gene summary

Standard name

clr6

Systematic ID

SPBC36.05c

Product

histone deacetylase (class I) H3-K9 specific complex subunit Clr6

Organism

Schizosaccharomyces pombe (fission yeast)

UniProt ID

O59702

ORFeome ID

40/40G04

Characterisation status

biological role published

Feature type

mRNA gene

Genomic location

chromosome II: 849345..851476 reverse strand

Annotation

Protein features

Orthologs

• HDAC1 (HGNC:4852) Homo sapiens
• HDAC2 (HGNC:4853) Homo sapiens
• clr6 (SJAG_00581) Schizosaccharomyces japonicus
• RPD3 (YNL330C) Saccharomyces cerevisiae

References / Literature

PMID:12193658 - Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast.

Noma K et al. Proc Natl Acad Sci U S A 2002 Dec 10;99 Suppl 4(Suppl 4):16438-45

PMID:22540037 - Predicting the fission yeast protein interaction network.

Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67

PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.

Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7

PMID:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.

Skribbe M et al. Mol Cell 2025 Feb 19;

PMID:29618061 - Histone deacetylation promotes transcriptional silencing at facultative heterochromatin.

Watts BR et al. Nucleic Acids Res 2018 Jun 20;46(11):5426-5440

PMID:16688222 - Histone H2B mutations in inner region affect ubiquitination, centromere function, silencing and chromosome segregation.

Maruyama T et al. EMBO J 2006 Jun 07;25(11):2420-31

PMID:30824696 - Systematic analysis reveals the prevalence and principles of bypassable gene essentiality.

Li J et al. Nat Commun 2019 Mar 01;10(1):1002

PMID:11884604 - Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity.

Bjerling P et al. Mol Cell Biol 2002 Apr;22(7):2170-81

PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.

Strachan J et al. J Cell Sci 2023 Dec 01;136(23)

PMID:19546237 - TOR complex 2 controls gene silencing, telomere length maintenance, and survival under DNA-damaging conditions.

Schonbrun M et al. Mol Cell Biol 2009 Aug;29(16):4584-94

PMID:38048463 - Rex1BD and the 14-3-3 protein control heterochromatin organization at tandem repeats by linking RNAi and HDAC.

Gao J et al. Proc Natl Acad Sci U S A 2023 Dec 12;120(50):e2309359120

PMID:23028377 - Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast.

Choi ES et al. PLoS Genet 2012 Sep;8(9):e1002985

PMID:19040720 - Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

Shevchenko A et al. Genome Biol 2008;9(11):R167

GO_REF:0000033 - Annotation inferences using phylogenetic trees

PMID:20404084 - Transcriptional activation of the general amino acid permease gene per1 by the histone deacetylase Clr6 Is regulated by Oca2 kinase.

Kaufmann I et al. Mol Cell Biol 2010 Jul;30(13):3396-410

PMID:25002536 - A novel histone deacetylase complex in the control of transcription and genome stability.

Zilio N et al. Mol Cell Biol 2014 Sep 15;34(18):3500-14

PMID:23084836 - Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation.

Tanaka A et al. Mol Cell 2012 Nov 30;48(4):532-46

PMID:34496258 - Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription.

Heo DH et al. Cell Rep 2021 Sep 07;36(10):109671

PMID:30652128 - Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription.

Okita AK et al. Commun Biol 2019;2:17

PMID:25963819 - Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly.

Lucena R et al. J Cell Biol 2015 May 11;209(3):387-402

PMID:37459529 - Class I histone deacetylase complex: Structure and functional correlates.

Wang X et al. Proc Natl Acad Sci U S A 2023 Jul 25;120(30):e2307598120

PMID:32295063 - The Catalytic-Dependent and -Independent Roles of Lsd1 and Lsd2 Lysine Demethylases in Heterochromatin Formation in Schizosaccharomyces pombe .

Marayati BF et al. Cells 2020 Apr 13;9(4)

PMID:21511999 - Comparative functional genomics of the fission yeasts.

Rhind N et al. Science 2011 May 20;332(6032):930-6

PMID:38289024 - Heat stress-induced activation of MAPK pathway attenuates Atf1-dependent epigenetic inheritance of heterochromatin in fission yeast.

Sun L et al. Elife 2024 Jan 30;13

PMID:21253571 - H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases.

Hansen KR et al. PLoS Genet 2011 Jan 06;7(1):e1001268

PMID:37445861 - Resistance to Chemotherapeutic 5-Fluorouracil Conferred by Modulation of Heterochromatic Integrity through Ino80 Function in Fission Yeast.

Lim KK et al. Int J Mol Sci 2023 Jun 26;24(13)

PMID:29109278 - Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex.

He H et al. Proc Natl Acad Sci U S A 2017 Nov 21;114(47):12524-12529

PMID:29844133 - Loss of Elongation-Like Factor 1 Spontaneously Induces Diverse, RNase H-Related Suppressor Mutations in Schizosaccharomyces pombe .

Marayati BF et al. Genetics 2018 Aug;209(4):967-981

PMID:15483052 - BAF53/Arp4 homolog Alp5 in fission yeast is required for histone H4 acetylation, kinetochore-spindle attachment, and gene silencing at centromere.

Minoda A et al. Mol Biol Cell 2005 Jan;16(1):316-27

PMID:27343236 - Restriction of Retrotransposon Mobilization in Schizosaccharomyces pombe by Transcriptional Silencing and Higher-Order Chromatin Organization.

Murton HE et al. Genetics 2016 Aug;203(4):1669-78

PMID:15632061 - Global effects on gene expression in fission yeast by silencing and RNA interference machineries.

Hansen KR et al. Mol Cell Biol 2005 Jan;25(2):590-601

PMID:26205977 - Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast.

Matsuda A et al. Nat Commun 2015 Jul 24;6:7753

PMID:23771057 - Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast.

Alper BJ et al. EMBO J 2013 Aug 28;32(17):2321-35

PMID:26510788 - Escape from Mitotic Arrest: An Unexpected Connection Between Microtubule Dynamics and Epigenetic Regulation of Centromeric Chromatin in Schizosaccharomyces pombe.

George AA et al. Genetics 2015 Dec;201(4):1467-78

PMID:12773576 - A novel jmjC domain protein modulates heterochromatization in fission yeast.

Ayoub N et al. Mol Cell Biol 2003 Jun;23(12):4356-70

PMID:19693008 - Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs.

Zofall M et al. Nature 2009 Sep 17;461(7262):419-22

PMID:37076472 - Two assembly modes for SIN3 histone deacetylase complexes.

Wang C et al. Cell Discov 2023 Apr 19;9(1):42

PMID:26537787 - Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.

Køhler JB et al. Nat Commun 2015 Nov 05;6:8827

PMID:12526748 - A new role for the transcriptional corepressor SIN3; regulation of centromeres.

Silverstein RA et al. Curr Biol 2003 Jan 08;13(1):68-72

PMID:12773392 - Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity.

Nakayama J et al. EMBO J 2003 Jun 02;22(11):2776-87

PMID:15292231 - Regulation of Swi6/HP1-dependent heterochromatin assembly by cooperation of components of the mitogen-activated protein kinase pathway and a histone deacetylase Clr6.

Kim HS et al. J Biol Chem 2004 Oct 08;279(41):42850-9

PMID:12867036 - Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast.

Shankaranarayana GD et al. Curr Biol 2003 Jul 15;13(14):1240-6

PMID:31262821 - Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks.

Feng G et al. Proc Natl Acad Sci U S A 2019 Jul 16;116(29):14563-14572

PMID:19164572 - Msc1 links dynamic Swi6/HP1 binding to cell fate determination.

Lawrence RJ et al. Proc Natl Acad Sci U S A 2009 Jan 27;106(4):1163-8

PMID:20194963 - Transformation/transcription domain-associated protein (TRRAP)-mediated regulation of Wee1.

Calonge TM et al. Genetics 2010 May;185(1):81-93

PMID:24478943 - Pcf1, a large subunit of CAF-1, required for maintenance of checkpoint kinase Cds1 activity.

Kunoh T et al. Springerplus 2014;3:30

PMID:33511417 - Repression of a large number of genes requires interplay between homologous recombination and HIRA.

Misova I et al. Nucleic Acids Res 2021 Feb 26;49(4):1914-1934

PMID:34805795 - The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability.

Calvo IA et al. iScience 2021 Nov 19;24(11):103338

PMID:18354085 - Diminishing HDACs by drugs or mutations promotes normal or abnormal sister chromatid separation by affecting APC/C and adherin.

Kimata Y et al. J Cell Sci 2008 Apr 01;121(Pt 7):1107-18

PMID:17450151 - Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection.

Nicolas E et al. Nat Struct Mol Biol 2007 May;14(5):372-80

PMID:21211723 - Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci.

Yamane K et al. Mol Cell 2011 Jan 07;41(1):56-66

PMID:19443688 - Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast.

Fischer T et al. Proc Natl Acad Sci U S A 2009 Jun 02;106(22):8998-9003

PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.

Egan ED et al. RNA 2014 Jun;20(6):867-81

PMID:24957674 - Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.

Anver S et al. EMBO Rep 2014 Aug;15(8):894-902

PMID:32124033 - Mutation in histone deacetylase clr6 promotes the survival of S. pombe cds1 null mutant in response to hydroxyurea.

Khan S et al. Mol Genet Genomics 2020 May;295(3):695-703

PMID:18094683 - Host genome surveillance for retrotransposons by transposon-derived proteins.

Cam HP et al. Nature 2008 Jan 24;451(7177):431-6

PMID:20299449 - A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assembly.

Xhemalce B et al. Genes Dev 2010 Apr 01;24(7):647-52

PMID:19620282 - The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts.

Anderson HE et al. Mol Cell Biol 2009 Sep;29(18):5158-67

PMID:21979813 - Acetylation regulates monopolar attachment at multiple levels during meiosis I in fission yeast.

Kagami A et al. EMBO Rep 2011 Oct 28;12(11):1189-95

PMID:18818364 - Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

Roguev A et al. Science 2008 Oct 17;322(5900):405-10

PMID:26412298 - A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.

Beckley JR et al. Mol Cell Proteomics 2015 Dec;14(12):3132-41

PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.

Marguerat S et al. Cell 2012 Oct 26;151(3):671-83

PMID:37615341 - Schizosaccharomyces pombe Rtf2 is important for replication fork barrier activity of RTS1 via splicing of Rtf1 .

Budden AM et al. Elife 2023 Aug 24;12

PMID:19723888 - Inhibition of type I histone deacetylase increases resistance of checkpoint-deficient cells to genotoxic agents through mitotic delay.

Alao JP et al. Mol Cancer Ther 2009 Sep;8(9):2606-15

PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.

Lee J et al. Nat Commun 2017 Feb 20;8:14527

GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference

PMID:23091701 - Impaired coenzyme A synthesis in fission yeast causes defective mitosis, quiescence-exit failure, histone hypoacetylation and fragile DNA.

Nakamura T et al. Open Biol 2012 Sep;2(9):120117

PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623

PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).

Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36

PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.

Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7

PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.

Hayles J et al. Open Biol 2013 May 22;3(5):130053

PMID:33468217 - Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex.

Weigt M et al. Epigenetics Chromatin 2021 Jan 19;14(1):8

PMID:26404184 - High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification.

Nie M et al. Sci Rep 2015 Sep 25;5:14389

PMID:9755190 - Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast.

Grewal SI et al. Genetics 1998 Oct;150(2):563-76

PMID:16079916 - Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast.

Wirén M et al. EMBO J 2005 Aug 17;24(16):2906-18