MSX2

msh homeobox 2 | CRS2, FPP, HOX8, MSH, PFM, PFM1

This gene encodes a member of the muscle segment homeobox gene family. The encoded protein is a transcriptional repressor whose normal activity may establish a balance between survival and apoptosis of neural crest-derived cells required for proper craniofacial morphogenesis. The encoded protein may also have a role in promoting cell growth under certain conditions and may be an important target for the RAS signaling pathways. Mutations in this gene are associated with parietal foramina 1 and craniosynostosis type 2. [provided by RefSeq, Jul 2008]

Member of: DE-7 DE-7.1 Developmental clusters: GC2

Biological processes 32 terms

DNA binding (GO:0003677)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription repressor activity (GO:0001217)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)animal organ morphogenesis (GO:0009887)cardiac conduction system development (GO:0003161)chromatin (GO:0000785)cranial suture morphogenesis (GO:0060363)embryonic morphogenesis (GO:0048598)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear speck (GO:0016607)nucleus (GO:0005634)nucleus (GO:0005634)osteoblast differentiation (GO:0001649)osteoblast differentiation (GO:0001649)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)transcription cis-regulatory region binding (GO:0000976)transcription cis-regulatory region binding (GO:0000976)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating MSX2 0 TFs

Transcription factors with Perturb-seq knockdown data for MSX2. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = MSX2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to MSX2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of MSX2, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr5:174,337,216–174,338,119	386.9 kb	Distal (>10kb) Multiome HiCAR	161
chr5:174,419,108–174,419,879	304.9 kb	Distal (>10kb) Multiome HiCAR	411
chr5:174,425,721–174,426,822	298.5 kb	Distal (>10kb) Multiome HiCAR	121
chr5:174,520,242–174,520,957	204.0 kb	Distal (>10kb) Multiome	312
chr5:174,532,420–174,533,094	191.8 kb	Distal (>10kb) Multiome	557
chr5:174,618,170–174,619,118	105.9 kb	Distal (>10kb) Multiome	166
chr5:174,692,956–174,693,590	31.3 kb	Distal (>10kb) Multiome	245
chr5:174,718,149–174,718,524	6.1 kb	Proximal (<10kb)	66
chr5:174,719,921–174,721,697	3.4 kb	Proximal (<10kb) Multiome	369
chr5:174,723,922–174,725,281	63 bp	At TSS Multiome	443
chr5:174,725,885–174,726,052	1.3 kb	Proximal (<10kb)	44
chr5:174,726,212–174,726,912	1.9 kb	Proximal (<10kb) Multiome	73
chr5:174,733,156–174,733,366	8.6 kb	Proximal (<10kb)	52
chr5:174,735,335–174,736,623	11.4 kb	Distal (>10kb) Multiome	338
chr5:174,793,746–174,794,221	69.3 kb	Distal (>10kb) Multiome	321
chr5:174,910,260–174,910,733	185.9 kb	Distal (>10kb) Multiome	200

Genome Browser

Genomic view of the MSX2 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.