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protein coding gene - lid2 (SPBP19A11.06) - histone demethylase (H3-trimethyl-K4 specific), Lid2 complex subunit Lid2

Gene summary

Standard name
lid2
Systematic ID
SPBP19A11.06
Product
histone demethylase (H3-trimethyl-K4 specific), Lid2 complex subunit Lid2
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
SPBP4H10.01
UniProt ID
Q9HDV4
ORFeome ID
49/49H05
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 2863808..2868411 forward strand

Annotation

Disease association

MONDO:0970951 - El Hayek-Chahrour neurodevelopmental disorder

References:

MONDO:0020850 - intellectual disability, autosomal recessive 65

References:

MONDO:0010355 - syndromic X-linked intellectual disability Claes-Jensen type

References:

GO biological process

GO:0033696 - heterochromatin boundary formation

References:

GO:0006355 - regulation of DNA-templated transcription

References:

GO:0031048 - regulatory ncRNA-mediated heterochromatin formation

References:

GO cellular component

GO:0048189 - Lid2 complex

References:

GO:0031934 - mating-type region heterochromatin

References:

GO:0005634 - nucleus

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GO:0005721 - pericentric heterochromatin

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GO molecular function

GO:0003682 - chromatin binding

References:

GO:0003677 - DNA binding

References:

GO:0034647 - histone H3K4me/H3K4me2/H3K4me3 demethylase activity

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Modification

MOD:00046 - O-phospho-L-serine

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MOD:00047 - O-phospho-L-threonine

References:

Multi-locus phenotype

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

References:

Genotypes:

Protein features

PBO:0111840 - ARID domain

PBO:0111833 - jmjC domain

PBO:0111834 - jmjN domain

PBO:0111832 - zf-C5HC2 type

PBO:0111780 - zf-PHD finger

PBO:0111743 - zinc finger protein

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0001352 - abnormal chromatin organization during vegetative growth

References:

Genotypes:

FYPO:0000059 - abnormal mitotic cell cycle

References:

Genotypes:

FYPO:0000452 - abnormal protein localization to chromatin during vegetative growth

References:

Genotypes:

FYPO:0007335 - abolished chromatin silencing at centromere inner repeat

References:

Genotypes:

FYPO:0007334 - abolished chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0007336 - abolished chromatin silencing at silent mating-type cassette

References:

Genotypes:

FYPO:0004170 - abolished histone H3-K9 dimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0003411 - decreased chromatin silencing at centromere inner repeat

References:

Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0002368 - decreased histone H3-K4 trimethylation during vegetative growth

References:

Genotypes:

FYPO:0000877 - decreased histone H3-K9 dimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0002386 - decreased protein localization to pericentric heterochromatin at centromere outer repeat region

References:

Genotypes:

FYPO:0004205 - decreased siRNA level

References:

Genotypes:

FYPO:0007339 - increased cen-dg RNA level

References:

Genotypes:

FYPO:0000220 - increased centromeric outer repeat transcript level

References:

Genotypes:

FYPO:0007345 - increased euchromatin-derived RNA level

References:

Genotypes:

FYPO:0007337 - increased histone H3-K4 methylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0007338 - increased histone H3-K4 trimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0000874 - increased histone H3-K9 dimethylation at centromere during vegetative growth

References:

Genotypes:

FYPO:0001490 - inviable elongated vegetative cell

References:

Genotypes:

FYPO:0002151 - inviable spore

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0001511 - inviable vegetative cell, abnormal cell shape, normal cell size

References:

Genotypes:

FYPO:0003087 - normal chromatin binding at mating-type region replication fork barrier

References:

Genotypes:

FYPO:0002335 - normal chromatin silencing

References:

Genotypes:

FYPO:0000703 - normal protein-protein interaction

References:

Genotypes:

FYPO:0000091 - sensitive to thiabendazole

References:

Genotypes:

FYPO:0001234 - slow vegetative cell population growth

References:

Genotypes:

FYPO:0003481 - viable elongated vegetative cell, elongated upon mitotic entry

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:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF00628PHDZnf_PHD-fingerPfam
PF01388ARIDARID_domPfam
PF02373JmjCJmjC_domPfam
PF02928zf-C5HC2Znf_C5HC2Pfam
PF08429PLU-1Lys_sp_deMease-like_domPfam
cd15518PHD_Ecm5p_Lid2p_likeCDD
cd15519PHD1_Lid2p_likeCDD
cd15520PHD3_Lid2p_likeCDD
cd16100ARIDCDD
PS01359ZF_PHD_1Zinc_finger_PHD-type_CSPROSITE patterns
PS50016ZF_PHD_2Znf_PHD-fingerPROSITE profiles
PS51011ARIDARID_domPROSITE profiles
PS51184JMJCJmjC_domPROSITE profiles
SM00249PHDZnf_PHDSMART
SM00558JmjCJmjC_domSMART
SM01014ARIDSMART
G3DSA:2.60.120.650:FF:000077CATH-FunFam
G3DSA:3.30.40.10:FF:001132CATH-FunFam
G3DSA:1.10.150.60ARID_dom_sfCATH-Gene3D
G3DSA:2.60.120.650CATH-Gene3D
G3DSA:3.30.40.10Znf_RING/FYVE/PHDCATH-Gene3D
SSF46774ARID_dom_sfSUPERFAMILY
SSF51197SUPERFAMILY
SSF57903Znf_FYVE_PHDSUPERFAMILY
PTHR10694PANTHER
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Polardisorder_predictionMobiDB-Polar
mobidb-lite-Polyampholytedisorder_predictionMobiDB-Polyampholyte
mobidb-lite-Positive-Polyelectrolytedisorder_predictionMobiDB-Positive-Polyelectrolyte

Orthologs

References / Literature

PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
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:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
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:32101745 - Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.
Lee SY et al. Cell Rep 2020 Feb 25;30(8):2686-2698.e8
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:14617822 - A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe.
Roguev A et al. Mol Cell Proteomics 2004 Feb;3(2):125-32
PMID:12488447 - High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts.
Roguev A et al. J Biol Chem 2003 Mar 07;278(10):8487-93
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: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:25838386 - Epigenetics. Restricted epigenetic inheritance of H3K9 methylation.
Audergon PN et al. Science 2015 Apr 03;348(6230):132-5
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
GO_REF:0000002 - Comments
PMID:22681890 - Hierarchical modularity and the evolution of genetic interactomes across species.
Ryan CJ et al. Mol Cell 2012 Jun 08;46(5):691-704
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
GO_REF:0000033 - Annotation inferences using phylogenetic trees
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: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: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
PMID:37851576 - The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast.
Mansouri-Noori F et al. Cell Rep 2023 Oct 31;42(10):113226
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:39476757 - Characterization of Ksg1 protein kinase-dependent phosphoproteome in the fission yeast S. pombe.
Cipak L et al. Biochem Biophys Res Commun 2024 Oct 25;736:150895