HMGN1

high mobility group nucleosome binding domain 1 | FLJ27265, FLJ31471, MGC104230, MGC117425, HMG14

The protein encoded by this gene binds nucleosomal DNA and is associated with transcriptionally active chromatin. Along with a similar protein, HMG17, the encoded protein may help maintain an open chromatin configuration around transcribable genes. [provided by RefSeq, Aug 2011]

Member of: DE-1

Biological processes 13 terms

DNA binding (GO:0003677)chromatin (GO:0000785)chromatin (GO:0000785)chromatin binding (GO:0003682)chromatin organization (GO:0006325)cytoplasm (GO:0005737)nucleoplasm (GO:0005654)nucleosomal DNA binding (GO:0031492)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription, elongation (GO:0032786)protein binding (GO:0005515)

Expression (TPM)

TFs regulating HMGN1 0 TFs

Transcription factors with Perturb-seq knockdown data for HMGN1. 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 = HMGN1 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 HMGN1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HMGN1, 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
chr21:39,182,840–39,184,214	165.4 kb	Distal (>10kb) Multiome	1028
chr21:39,312,364–39,314,680	35.3 kb	Distal (>10kb) Multiome	1121
chr21:39,332,179–39,332,739	16.7 kb	Distal (>10kb) Multiome	188
chr21:39,348,209–39,350,114	174 bp	At TSS Multiome	923
chr21:39,380,111–39,380,888	31.3 kb	Distal (>10kb) Multiome	663
chr21:39,387,404–39,389,039	39.7 kb	Distal (>10kb) Multiome	713
chr21:39,429,900–39,431,278	81.6 kb	Distal (>10kb) Multiome	277
chr21:39,445,343–39,446,179	96.7 kb	Distal (>10kb) Multiome	837
chr21:39,451,559–39,452,036	102.7 kb	Distal (>10kb) Multiome	267
chr21:39,612,590–39,613,211	263.8 kb	Distal (>10kb) Multiome	208

Genome Browser

Genomic view of the HMGN1 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.