lin-42 PAS domain-containing protein;Period protein homolog lin-42 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: lin-42
Official Full Name: PAS domain-containing protein;Period protein homolog lin-42
Primary source: WormBase:WBGene00018572
Locus tag: CELE_F47F6.1
See related: AllianceGenome:WB:WBGene00018572
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. Involved in negative regulation of dauer larval development; negative regulation of miRNA transcription; and regulation of development, heterochronic. Located in cytoplasm and nucleus. Is expressed in several structures, including H1L.app; H1R.app; H2L.ppp; hypodermal cell; and pharynx. Human ortholog(s) of this gene implicated in advanced sleep phase syndrome; advanced sleep phase syndrome 1; alcohol dependence; cocaine dependence; and fetal alcohol spectrum disorder. Orthologous to human PER1 (period circadian regulator 1) and PER2 (period circadian regulator 2). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See lin-42 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 11

Sequence:: Chromosome: II; NC_003280.10 (1233236..1252359, complement)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans.
Title: Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans.
Temporal scaling in C. elegans larval development.
Title: Temporal scaling in C. elegans larval development.
These results establish a new role for the conserved, important Period protein homolog LIN-42 in regulating early germline development.
Title: The Period protein homolog LIN-42 regulates germline development in C. elegans.
The method was validated with a lin-42 mutant strain that shows delayed development relative to wild-type animals and with a daf-2 mutant that shows an extended second larval stage
Title: A High-Throughput Method for the Analysis of Larval Developmental Phenotypes in Caenorhabditis elegans.
A key function of lin-42 in developmental timing is to dampen pri-miRNAs levels, preventing their premature expression as mature miRNAs.
Title: Caenorhabditis elegans period homolog lin-42 regulates the timing of heterochronic miRNA expression.
lin-42 functions to negatively regulate the transcriptional output of multiple miRNAs and mRNAs and therefore coordinates the expression levels of genes that dictate temporal cell fate
Title: LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription.
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Title: The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Inactivation of the heterochronic gene lin-42a leads to arrhythmic molts and abnormal epidermal stem cell dynamics. Oscillatory expression in the epidermis peaks during the molts; forced expression leads to anachronistic larval molts and adult lethargy.
Title: LIN-42/PERIOD controls cyclical and developmental progression of C. elegans molts.
The C. elegans developmental timing protein LIN-42 regulates diapause in response to environmental cues.
Title: The C. elegans developmental timing protein LIN-42 regulates diapause in response to environmental cues.
LIN-42 has a dynamic expression pattern; its levels oscillate relative to the molts during postembryonic development.
Title: Novel heterochronic functions of the Caenorhabditis elegans period-related protein LIN-42.

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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

F47F6.1 (e-PCR)
- UniSTS:322147

F47F6.2 (e-PCR)
- UniSTS:311655

STS2-107 (e-PCR)
- UniSTS:241772

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of dauer larval development	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of dauer larval development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of dauer larval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of miRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of development, heterochronic	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PAS domain-containing protein;Period protein homolog lin-42

NP_001022176.1

Confirmed by transcript evidence

NP_001022177.1

Confirmed by transcript evidence

NP_001022178.1

Confirmed by transcript evidence

NP_001309559.1

Partially confirmed by transcript evidence

NP_001309560.1

Confirmed by transcript evidence

NP_001309561.1

Partially confirmed by transcript evidence

NP_001309562.1

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_003280.10 Reference assembly

Range

1233236..1252359 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001027006.7 → NP_001022177.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022177.1

Status: REVIEWED

UniProtKB/Swiss-Prot

H2L053, P91313, Q65ZG8

Conserved Domains (2) summary

cd00130
Location:168 → 271

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam14598
Location:169 → 271

PAS_11; PAS domain
NM_001027005.4 → NP_001022176.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022176.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q65ZG8
NM_001322704.3 → NP_001309559.1 PAS domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MAY5

Conserved Domains (1) summary

cd00130
Location:225 → 328

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
NM_001322705.3 → NP_001309560.1 Period protein homolog lin-42 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MAT8
NM_001322706.3 → NP_001309562.1 Period protein homolog lin-42 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MCB3
NM_001027007.3 → NP_001022178.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022178.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q65ZG8

Conserved Domains (2) summary

cd00130
Location:168 → 271

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam14598
Location:169 → 271

PAS_11; PAS domain
NM_001322707.3 → NP_001309561.1 PAS domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MBE1

Conserved Domains (1) summary

cd00130
Location:225 → 328

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...