let-418 Protein let-418 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: let-418
Official Full Name: Protein let-418
Primary source: WormBase:WBGene00002637
Locus tag: CELE_F26F12.7
See related: AllianceGenome:WB:WBGene00002637
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 RNA polymerase II-specific DNA-binding transcription factor binding activity. Contributes to RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in embryonic digestive tract morphogenesis; negative regulation of transcription by RNA polymerase II; and negative regulation of vulval development. Part of RNA polymerase II transcription repressor complex. Is expressed in several structures, including P3.p hermaphrodite; anal region; head; nervous system; and reproductive system. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to several human genes including CHD3 (chromodomain helicase DNA binding protein 3). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See let-418 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 7

Sequence:: Chromosome: V; NC_003283.11 (5826833..5832831)

Chromosome V - NC_003283.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003283.11

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development.
Title: Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development.
These suppressors might represent direct competitors of LET-418 complexes for chromatin regulation of crucial genes involved in the transition to postembryonic development
Title: A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans.
germ cells deficient for spr-5 and let-418 mainly reprogram as neurons, suggesting that neuronal fate might be the first to be derepressed in early embryogenesis.
Title: LET-418/Mi2 and SPR-5/LSD1 cooperatively prevent somatic reprogramming of C. elegans germline stem cells.
LET-418/Mi2 could be part of a system that drives development and reproduction with concomitant life-reducing effects later in life.
Title: The Caenorhabditis elegans LET-418/Mi2 plays a conserved role in lifespan regulation.
the interaction between LIN-1 and LET-418/Mi-2 may link RTK/Ras signaling with chromatin remodeling and gene expression
Title: The Mi-2 nucleosome-remodeling protein LET-418 is targeted via LIN-1/ETS to the promoter of lin-39/Hox during vulval development in C. elegans.

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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

F26F12.7 (e-PCR)
- UniSTS:309975

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in embryonic digestive tract morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of vulval development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
part_of RNA polymerase II transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Protein let-418

NP_504523.1

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_003283.11 Reference assembly

Range

5826833..5832831

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_072122.6 → NP_504523.1 Protein let-418 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_504523.1

Status: REVIEWED

UniProtKB/Swiss-Prot

G5EBZ4

Conserved Domains (13) summary

smart00298
Location:489 → 543

CHROMO; Chromatin organization modifier domain

COG5034
Location:151 → 300

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd00024
Location:367 → 449

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cd00046
Location:622 → 780

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

sd00025
Location:295 → 323

zf-RanBP2; RanBP2-type Zn finger [structural motif]

cd15531
Location:258 → 300

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

pfam00176
Location:605 → 901

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:925 → 1040

Helicase_C; Helicase conserved C-terminal domain

pfam06461
Location:1276 → 1406

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1188 → 1238

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:95 → 147

CHDNT; CHDNT (NUC034) domain

pfam08074
Location:1524 → 1698

CHDCT2; CHDCT2 (NUC038) domain

cl22851
Location:320 → 362

PHD_SF; PHD finger superfamily