lin-53 putative histone-binding protein lin-53 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: lin-53
Official Full Name: putative histone-binding protein lin-53
Primary source: WormBase:WBGene00003036
Locus tag: CELE_K07A1.12
See related: AllianceGenome:WB:WBGene00003036
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables histone deacetylase binding activity. Involved in several processes, including cell fate specification; embryonic digestive tract morphogenesis; and nematode male tail tip morphogenesis. Acts upstream of or within mitochondrial unfolded protein response. Located in nucleus. Part of DRM complex and NuRD complex. Is expressed in several structures, including P3.p hermaphrodite; P4.p hermaphrodite; P5.p hermaphrodite; P6.p hermaphrodite; and P7.p hermaphrodite. Orthologous to human RBBP4 (RB binding protein 4, chromatin remodeling factor) and RBBP7 (RB binding protein 7, chromatin remodeling factor). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See lin-53 in Genome Data Viewer

Location:: chromosome: I

Exon count:: 3

Sequence:: Chromosome: I; NC_003279.8 (9618196..9619760, complement)

Chromosome I - NC_003279.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003279.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo holocentromere formation on artificial chromosomes in Caenorhabditis elegans embryos.
Title: RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo holocentromere formation on artificial chromosomes in Caenorhabditis elegans embryos.
The LIN-53 is required for maintaining lifespan and muscle integrity through discrete chromatin regulatory mechanisms.
Title: The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans.
RbAp46/48LIN-53 localizes to the centromere during metaphase in a CENP-AHCP-3- and M18BP1KNL-2-dependent manner, suggesting CENP-AHCP-3 loading may occur before anaphase.
Title: RbAp46/48(LIN-53) Is Required for Holocentromere Assembly in Caenorhabditis elegans.
this study finds that lin-53 showed a synthetic interaction with eaf-1(tm3976) where knockdown of lin-53 in an eaf-1(tm3976) mutant resulted in sterile worms.
Title: Identification of a genetic interaction between the tumor suppressor EAF2 and the retinoblastoma protein (Rb) signaling pathway in C. elegans and prostate cancer cells.
through ectopic expression of single transcription factors (che-1) study found the identity of mitotic germ cells can be directly converted into that of specific neuron types; this reprogramming requires removal of LIN-53
Title: Direct conversion of C. elegans germ cells into specific neuron types.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

K07A1.12 (e-PCR)
- UniSTS:311444

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryo development ending in birth or egg hatching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic digestive tract morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mitochondrial unfolded protein response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in nematode male tail tip morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of DRM complex	IDA Inferred from Direct Assay more info	PubMed
part_of ESC/E(Z) complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: putative histone-binding protein lin-53

NP_492552.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003279.8 Reference assembly

Range

9618196..9619760 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_060151.9 → NP_492552.1 putative histone-binding protein lin-53 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_492552.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A2JDY3, O62411, P90916

Conserved Domains (4) summary

COG2319
Location:115 → 400

WD40; WD40 repeat [General function prediction only]

cd00200
Location:118 → 395

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam12265
Location:16 → 83

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

sd00039
Location:124 → 170

7WD40; WD40 repeat [structural motif]