lin-39 Homeobox protein lin-39 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: lin-39
Official Full Name: Homeobox protein lin-39
Primary source: WormBase:WBGene00003024
Locus tag: CELE_C07H6.7
See related: AllianceGenome:WB:WBGene00003024
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 cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of DNA-templated transcription; positive regulation of mesodermal cell fate specification; and positive regulation of vulval development. Located in nucleus. Is expressed in several structures, including P3.p; hypodermis; neurons; ventral cord blast cell; and vulval precursor cell. Orthologous to several human genes including HOXA5 (homeobox A5). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See lin-39 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 6

Sequence:: Chromosome: III; NC_003281.10 (7528641..7536632, complement)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hox proteins interact to pattern neuronal subtypes in Caenorhabditis elegans males.
Title: Hox proteins interact to pattern neuronal subtypes in Caenorhabditis elegans males.
A terminal selector prevents a Hox transcriptional switch to safeguard motor neuron identity throughout life.
Title: A terminal selector prevents a Hox transcriptional switch to safeguard motor neuron identity throughout life.
the HOX protein LIN-39 regulates the vulval precursor cell cycle at two levels. First, LIN-39 acts as a permissive factor by maintaining the expression of the cell cycle machinery in the vulval precursor cells, keeping them competent to proliferate. Second, LIN-39 triggers the lateral NOTCH signaling pathway in the adjacent 2 degrees vulval precursor cells, which over comes the cell cycle inhibition by LIN-31 Forkhead.
Title: The C. elegans hox gene lin-39 controls cell cycle progression during vulval development.
Here we describe a nonautonomous role of mab-5 in regulating both QR and QL descendant migrations, a role masked by redundancy with lin-39 A third Hox gene, egl-5/Abdominal-B, also likely nonautonomously regulates Q descendant migrations.We find that increased levels of MAB-5 in body wall muscle (BWM) can drive the spon-1 promoter adjacent to the Q cells, and
Title: Nonautonomous Roles of MAB-5/Hox and the Secreted Basement Membrane Molecule SPON-1/F-Spondin in Caenorhabditis elegans Neuronal Migration.
Data indicate that the hypodermal fate regulator LIN-26, and the GATA factor ELT-6 positively regulate lin-39 expression in the embryonic precursors to the Vulval Precursor Cells (VPCs).
Title: Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6.
LIN-39 establishes neuroblast anterior polarity by binding to the mig-13 promoter and promoting mig-13 expression, whereas MAB-5 inhibits neuroblast anterior polarity by associating with the lin-39 promoter and downregulating lin-39 and mig-13 expression.
Title: Transmembrane protein MIG-13 links the Wnt signaling and Hox genes to the cell polarity in neuronal migration.
Data show that the C. elegans hox gene lin-39 regulates epidermal morphogenesis via its novel target, the essential zinc finger protein VAB-23.
Title: LIN-39 and the EGFR/RAS/MAPK pathway regulate C. elegans vulval morphogenesis via the VAB-23 zinc finger protein.
LIN-39 and EFL-3 function in a cell type-specific context to regulate transcription of the egl-1 BH3-only cell death gene and to determine cell fate during development.
Title: Hox and a newly identified E2F co-repress cell death in Caenorhabditis elegans.
suggest that the GLI protein family involved in several key developmental processes in both invertebrates and vertebrates regulates somatic cell fates through influencing, at least in part, the expression of specific Hox genes, such as lin-39
Title: TRA-1/GLI controls the expression of the Hox gene lin-39 during C. elegans vulval development.
Transcriptional upregulation of lin-39 is dependent on Ras signaling.
Title: Transcriptional upregulation of the C. elegans Hox gene lin-39 during vulval cell fate specification.

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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

STS3-163 (e-PCR)
- UniSTS:242005

C07H6.7 (e-PCR)
- UniSTS:321917

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mesodermal cell fate specification	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of vulval development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of vulval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleoplasm	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