LIN-39

WormBase ID: WBGene00003024

WormBase description: Is an ortholog of several human genes including HOXA4 (homeobox A4); HOXB5 (homeobox B5); and HOXC4 (homeobox C4). Exhibits proximal promoter sequence-specific DNA binding activity. Is involved in several processes, including positive regulation of mesodermal cell fate specification; positive regulation of transcription, DNA-templated; and positive regulation of vulval development. Localizes to nucleus. Is expressed in several structures, including hypodermis; male-specific anatomical entity; neurons; somatic nervous system; and ventral cord blast cell. Human ortholog(s) of this gene are implicated in several diseases, including brachydactyly-syndactyly syndrome; diabetes mellitus (multiple); and dysostosis (multiple).

Reporter verification: Whole-genome sequencing indicated that the GFP tags another TF, LIN-39 rather than MAB-5
Primers used to verify fosmid reporter: 5'-CGAGAAGCGACAACGAACAG-3'

Strain name: RW10350

Strain genotype: unc-119 (ed3) III; itIs37 (pie-1p::mCherry::H2B::pie-1 3'UTR + unc-119(+)); stIs10116 (his-72p::his-24::mCherry::let-858 3'UTR + unc-119(+)); stIs10309 (lin-39::TY1::eGFP::3xFLAG(P000007_E01))

Expression pattern: Lineage-specific, Tissue-specific (Skin and Muscle)

Lineage expression pattern

350 stage

600 stage

3D expression pattern

4-cells

8-cells

15-cells

28-cells

~50-cells

~100-cells

~200-cells

~350-cells

~500-cells

~600-cells

600-cells

bean-stage

Inferred TF relationships

Based on expression similarity (strong, medium, weak): SNAI-1, SYD-9, LIN-22, RNT-1, CEH-40, HLH-1, EGL-5, NHR-23, CEH-20, VAB-7, UNC-62, LIN-26, UNC-120, GMEB-1, NHR-102, LIN-1, HBL-1, M03D4.4, VAB-15, TLP-1, CEH-13, HMBX-1, PAL-1, HAM-2, IRX-1, ELT-1, F23B12.7, Y75B8A.6, CEBP-1, NHR-25, CEH-74, ATF-7, CES-2, CRH-2


Based on ChIP-seq (directly from ModERN database, targets from L1 stage ChIP-seq data are underlined)

Targeting: RNT-1, UNC-62, TLP-1, CEBP-1, ATHP-1, CAMT-1, CEH-18, CEH-38, EFL-1, EFL-3, EGL-44, EGRH-1, FOS-1, HLH-11, HLH-30, MDL-1, MEF-2, MEP-1, NHR-10

Targeted by: RNT-1, HLH-1, UNC-62, UNC-120, ELT-1, CEH-18, CEH-36, ELT-2, LSY-2, NFYA-1, REF-2, UNC-55, BLMP-1, C16A3.4, DSC-1, EFL-1, MEP-1, NHR-85, PAG-3, SWSN-7, TBX-2, UNC-130, ZTF-11

Based on reannotated ChIP-seq (peaks are assigned to a target if it is located within 2 kb relative to the transcription start site; targets from L1 stage ChIP-seq data are underlined)

Targeting: UNC-62, TLP-1, CEBP-1, ATHP-1, CAMT-1, CEH-18, CEH-5, EFL-1, EGL-44, HLH-30, K10B3.5, MDL-1, MEF-2, NHR-10

Targeted by: RNT-1, HLH-1, UNC-62, UNC-120, LSY-2, NFYA-1, REF-2, UNC-55, BLMP-1, MEP-1, NHR-85, SWSN-7, TBX-2, ZTF-11