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protein coding gene - lsd1 (SPBC146.09c) - histone demethylase SWIRM1

Gene summary

Standard name
lsd1
Systematic ID
SPBC146.09c
Product
histone demethylase SWIRM1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
swm1, saf110
UniProt ID
Q9Y802
ORFeome ID
47/47G02
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 1015936..1019241 reverse strand

Annotation

Comment

PBO:0000206 - deletion mutant expression profiling

References:

Disease association

MONDO:0700299 - ACTH-independent macronodular adrenal hyperplasia 3

References:

MONDO:0014751 - palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome

References:

GO biological process

GO:0140718 - facultative heterochromatin formation

References:

GO:0033696 - heterochromatin boundary formation

References:

GO:0071515 - mating-type locus imprinting

References:

GO:0031508 - pericentric heterochromatin formation

References:

GO:1902681 - regulation of replication fork arrest at rDNA repeats

References:

GO:0011000 - replication fork arrest at mating type locus

References:

GO:0030466 - silent mating-type cassette heterochromatin formation

References:

GO:0031509 - subtelomeric heterochromatin formation

References:

GO cellular component

GO:0000785 - chromatin

References:

GO:0033193 - Lsd1/2 complex

References:

GO:0031934 - mating-type region heterochromatin

References:

GO:0005634 - nucleus

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GO:0005721 - pericentric heterochromatin

References:

GO:0140720 - subtelomeric heterochromatin

References:

GO molecular function

GO:0140682 - FAD-dependent H3K4me/H3K4me3 demethylase activity

References:

GO:0140683 - histone H3K9me/H3K9me2 demethylase activity

References:

GO:0031491 - nucleosome binding

References:

GO:1990841 - promoter-specific chromatin binding

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00696 - phosphorylated residue

References:

MOD:01149 - sumoylated lysine

References:

MOD:01148 - ubiquitinylated lysine

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Multi-locus phenotype

FYPO:0007504 - abolished histone demethylase activity (H3-K9 specific)

References:

Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

References:

Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0002827 - decreased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0007478 - decreased epigenetic heterochromatin inheritance

References:

Genotypes:

FYPO:0003081 - decreased genetic imprinting at mating-type locus

References:

Genotypes:

FYPO:0005922 - decreased heterochromatin assembly at subtelomere

References:

Genotypes:

FYPO:0000888 - decreased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0002355 - decreased histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0004137 - decreased histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0003085 - decreased replication fork arrest at mating-type locus

References:

Genotypes:

FYPO:0001117 - decreased RNA level during vegetative growth

References:

Genotypes:

FYPO:0004085 - decreased vegetative cell growth

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0007339 - increased cen-dg RNA level

References:

Genotypes:

FYPO:0004376 - increased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0005225 - increased histone H3-K4 dimethylation during vegetative growth

References:

Genotypes:

FYPO:0000887 - increased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0006987 - increased histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0006361 - increased histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0006110 - increased silent mating-type cassette transcript-derived siRNA level

References:

Genotypes:

FYPO:0005917 - increased subtelomeric heterochromatin RNA level

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0001387 - loss of viability at high temperature

References:

Genotypes:

FYPO:0002336 - normal chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

References:

Genotypes:

FYPO:0000964 - normal growth on thiabendazole

References:

Genotypes:

FYPO:0007341 - normal histone H3-K4 trimethylation during vegetative growth

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

Protein features

PBO:0111771 - HMG box

Qualitative gene expression

PomGeneEx:0000018 - protein level increased

References:

PomGeneEx:0000011 - RNA level increased

References:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0004481 - abolished cell population growth at high temperature

References:

Genotypes:

FYPO:0008210 - abolished chromatin binding at promoter region

References:

Genotypes:

FYPO:0003080 - abolished genetic imprinting at mating-type locus

References:

Genotypes:

FYPO:0007504 - abolished histone demethylase activity (H3-K9 specific)

References:

Genotypes:

FYPO:0000469 - abolished mating type switching

References:

Genotypes:

FYPO:0001326 - altered RNA level during vegetative growth

References:

Genotypes:

FYPO:0000134 - branched, elongated, multiseptate cell

References:

Genotypes:

FYPO:0008211 - decreased antisense RNA level during heat stress

References:

Genotypes:

FYPO:0000082 - decreased cell population growth at high temperature

References:

Genotypes:

FYPO:0000251 - decreased cell population growth on galactose carbon source

References:

Genotypes:

FYPO:0001407 - decreased cell population growth on glucose carbon source

References:

Genotypes:

FYPO:0003092 - decreased chromatin binding at mating-type region replication fork barrier

References:

Genotypes:

FYPO:0003091 - decreased chromatin binding at rDNA replication fork barrier

References:

Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0002827 - decreased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0007478 - decreased epigenetic heterochromatin inheritance

References:

Genotypes:

FYPO:0003081 - decreased genetic imprinting at mating-type locus

References:

Genotypes:

FYPO:0005922 - decreased heterochromatin assembly at subtelomere

References:

Genotypes:

FYPO:0000888 - decreased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0002355 - decreased histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0004137 - decreased histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0001324 - decreased protein level during vegetative growth

References:

Genotypes:

FYPO:0007505 - decreased protein localization to chromatin at promoter

References:

Genotypes:

FYPO:0002387 - decreased protein localization to subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0003085 - decreased replication fork arrest at mating-type locus

References:

Genotypes:

FYPO:0003090 - decreased replication fork arrest at rDNA repeats

References:

Genotypes:

FYPO:0001117 - decreased RNA level during vegetative growth

References:

Genotypes:

FYPO:0004202 - decreased spliced cen-dg RNA level

References:

Genotypes:

FYPO:0000584 - decreased sporulation frequency

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0000636 - increased cell population growth rate

References:

Genotypes:

FYPO:0007339 - increased cen-dg RNA level

References:

Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

References:

Genotypes:

FYPO:0006299 - increased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0004376 - increased chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0005225 - increased histone H3-K4 dimethylation during vegetative growth

References:

Genotypes:

FYPO:0000875 - increased histone H3-K9 dimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0000887 - increased histone H3-K9 dimethylation at centromere outer repeat during vegetative growth

References:

Genotypes:

FYPO:0006361 - increased histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0000873 - increased histone H3-K9 dimethylation during vegetative growth

References:

Genotypes:

FYPO:0000881 - increased histone H3-K9 trimethylation at centromere inner repeat during vegetative growth

References:

Genotypes:

FYPO:0007507 - increased histone H3-K9 trimethylation at promoter during vegetative growth

References:

Genotypes:

FYPO:0007509 - increased histone H3-K9 trimethylation at silent mating-type cassette during vegetative growth

References:

Genotypes:

FYPO:0007508 - increased histone H3-K9 trimethylation at subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0007506 - increased protein localization to chromatin at promoter

References:

Genotypes:

FYPO:0004377 - increased protein localization to heterochromatin at silent mating-type cassette

References:

Genotypes:

FYPO:0003010 - increased protein localization to subtelomeric heterochromatin during vegetative growth

References:

Genotypes:

FYPO:0000825 - increased RNA level during vegetative growth

References:

Genotypes:

FYPO:0004689 - increased silent mating-type cassette cenH-derived RNA level

References:

Genotypes:

FYPO:0006110 - increased silent mating-type cassette transcript-derived siRNA level

References:

Genotypes:

FYPO:0004948 - increased spatial extent of centromeric heterochromatin assembly

References:

Genotypes:

FYPO:0005917 - increased subtelomeric heterochromatin RNA level

References:

Genotypes:

FYPO:0001387 - loss of viability at high temperature

References:

Genotypes:

FYPO:0001252 - multinucleate multiseptate vegetative cell

References:

Genotypes:

FYPO:0000674 - normal cell population growth at high temperature

References:

Genotypes:

FYPO:0002837 - normal centromeric outer repeat transcript-derived siRNA level

References:

Genotypes:

FYPO:0002335 - normal chromatin silencing

References:

Genotypes:

FYPO:0003082 - normal genetic imprinting at mating-type locus

References:

Genotypes:

FYPO:0001690 - normal growth on camptothecin

References:

Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

References:

Genotypes:

FYPO:0000963 - normal growth on hydroxyurea

References:

Genotypes:

FYPO:0000957 - normal growth on methyl methanesulfonate

References:

Genotypes:

FYPO:0000703 - normal protein-protein interaction

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0004325 - sensitive to 5-fluorouracil

References:

Genotypes:

FYPO:0002642 - sensitive to amphotericin B

References:

Genotypes:

FYPO:0000085 - sensitive to camptothecin

References:

Genotypes:

FYPO:0002640 - sensitive to clotrimazole

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0002641 - sensitive to micafungin

References:

Genotypes:

FYPO:0002328 - sensitive to terbinafine

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0002197 - viable vegetative cell with abnormal cell shape

References:

Genotypes:

FYPO:0001510 - viable vegetative cell, abnormal cell shape, normal cell size

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0000055 - no apparent S. cerevisiae ortholog

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF01593Amino_oxidaseAmino_oxidasePfam
PF04433SWIRMSWIRMPfam
PS50118HMG_BOX_2HMG_box_domPROSITE profiles
PS50934SWIRMSWIRMPROSITE profiles
G3DSA:1.10.30.10:FF:000067CATH-FunFam
G3DSA:1.10.10.10WH-like_DNA-bd_sfCATH-Gene3D
G3DSA:1.10.30.10HMG_box_dom_sfCATH-Gene3D
G3DSA:3.50.50.60FAD/NAD-bd_sfCATH-Gene3D
SSF46689Homeodomain-like_sfSUPERFAMILY
SSF47095HMG_box_dom_sfSUPERFAMILY
SSF51905FAD/NAD-bd_sfSUPERFAMILY
SSF54373SUPERFAMILY
PTHR10742L-amino-acid_oxidase-likePANTHER
CoilCOILS
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Negative-Polyelectrolytedisorder_predictionMobiDB-Negative-Polyelectrolyte
mobidb-lite-Polyampholytedisorder_predictionMobiDB-Polyampholyte

Orthologs

References / Literature

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:23163955 - Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe.
Yadav MP et al. BMC Res Notes 2012 Nov 19;5:643
PMID:25483073 - Chromosome segregation and organization are targets of 5'-Fluorouracil in eukaryotic cells.
Mojardín L et al. Cell Cycle 2015;14(2):206-18
PMID:25417108 - Dicer promotes transcription termination at sites of replication stress to maintain genome stability.
Castel SE et al. Cell 2014 Oct 23;159(3):572-83
PMID:27887640 - Functional and regulatory profiling of energy metabolism in fission yeast.
Malecki M et al. Genome Biol 2016 Nov 25;17(1):240
PMID:38181050 - The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe.
Liu H et al. PLoS Genet 2024 Jan 05;20(1):e1011107
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:22252817 - A genomewide screen in Schizosaccharomyces pombe for genes affecting the sensitivity of antifungal drugs that target ergosterol biosynthesis.
Fang Y et al. Antimicrob Agents Chemother 2012 Apr;56(4):1949-59
PMID:23260662 - Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast.
Holmes A et al. Cell Rep 2012 Dec 27;2(6):1513-20
PMID:25373780 - A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression.
Graml V et al. Dev Cell 2014 Oct 27;31(2):227-239
PMID:17440621 - Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1.
Opel M et al. PLoS One 2007 Apr 18;2(4):e386
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:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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: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: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: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:18957202 - Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin.
Li F et al. Cell 2008 Oct 17;135(2):272-83
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:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
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:17434129 - S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription.
Lan F et al. Mol Cell 2007 Apr 13;26(1):89-101
PMID:25838386 - Epigenetics. Restricted epigenetic inheritance of H3K9 methylation.
Audergon PN et al. Science 2015 Apr 03;348(6230):132-5
PMID:10759889 - Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library.
Ding DQ et al. Genes Cells 2000 Mar;5(3):169-90
PMID:16990277 - Fission yeast homologs of human histone H3 lysine 4 demethylase regulate a common set of genes with diverse functions.
Nicolas E et al. J Biol Chem 2006 Nov 24;281(47):35983-8
PMID:17371846 - Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries.
Gordon M et al. Mol Cell Biol 2007 Jun;27(11):4058-69
PMID:16537923 - Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast.
Todd BL et al. Mol Cell Biol 2006 Apr;26(7):2817-31
PMID:29610759 - Molecular signature of the imprintosome complex at the mating-type locus in fission yeast.
Raimondi C et al. Microb Cell 2018 Jan 16;5(4):169-183
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:27298342 - Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks.
Willis NA et al. Proc Natl Acad Sci U S A 2016 Jun 28;113(26):E3676-85
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.