REF-2

WormBase ID: WBGene00004335

WormBase description: Is an ortholog of human ZIC2 (Zic family member 2); ZIC3 (Zic family member 3); and ZIC4 (Zic family member 4). Exhibits RNA polymerase II regulatory region sequence-specific DNA binding activity and RNA polymerase II transcription factor binding activity. Is involved in DNA-templated transcription, initiation; nematode larval development; and neuron fate specification. Localizes to cytoplasm and nucleus. Is expressed in several structures, including IL1 neuron; P3.p male; neuroblasts; rectal epithelial cell; and ventral nerve cord.

Reporter verification: Verified by PCR and sequencing
Primers used to verify fosmid reporter: 5'-AAATGCGTCAATCGGAACAC-3'

Strain name: SYS109

Cross: OP520 x JIM113

Strain genotype: ujIs113 (pie-1p::mCherry::H2B; nhr-2p::mCherry::his-24::let858 3'UTR; unc-119(+)) II; wgIs520 (ref-2::TY1::EGFP::3xFLAG + unc-119(+))

Expression pattern: Lineage-specific, Anterior-biased, Transient-expression

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): LIM-6, SEM-2, MED-2, TTX-3, TAB-1, CEH-41, LIN-1, CEH-32, Y56A3A.28, HLH-30, CEH-51, SOX-2, UNC-39


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

Targeting: SEM-2, HLH-30, SOX-2, UNC-39, ALR-1, BCL-11, CEBP-1, CEH-20, CEH-22, CEH-30, CEH-31, CEH-38, CEH-39, CEH-43, CEH-44, CEH-45, CEH-48, CES-2, CRH-2, DAF-19, DAF-3, DMD-5, DUXL-1, EFL-1, EFL-3, EGL-18, EGL-44, EGL-46, EGL-5, EGRH-1, ELT-3, ELT-6, ETS-5, FOS-1, GMEB-1, GMEB-2, HBL-1, HLH-2, K09A11.1, LAG-1, LIM-7, LIN-13, LIN-39, MDL-1, MEP-1, MLS-2, NHR-10, NHR-102, NHR-23, NHR-49, PAX-3, POP-1, RCOR-1, SDZ-38, SEL-8, SKN-1, SWSN-7, TAG-68, TBX-2, UNC-37, UNC-42, UNC-62, Y55F3AM.14, ZIP-8, ZTF-6

Targeted by: NFYA-1, ZIP-8, IRX-1, LSY-2, NHR-85, VAB-15

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: HLH-30, SOX-2, ALR-1, CEBP-1, CEH-20, CEH-22, CEH-31, CEH-39, CEH-48, CEH-74, CES-2, CRH-2, DAF-19, DMD-5, DUXL-1, EFL-1, EFL-3, EGL-46, EGL-5, ELT-3, ELT-6, ETS-5, GMEB-1, GMEB-2, HLH-2, LAG-1, LIN-13, LIN-39, MDL-1, MEP-1, MLS-2, NHR-10, NHR-23, NHR-49, POP-1, RCOR-1, SKN-1, SVH-5, SWSN-7, TBX-2, UNC-37, UNC-42, UNC-62

Targeted by: ZIP-8, IRX-1, LSY-2, NHR-85, VAB-15