PAF1

PAF1 component of Paf1/RNA polymerase II complex | F23149_1, FLJ11123, PD2

This gene encodes a subunit of the polymerase associated factor (PAF1) complex. The PAF1 complex interacts with RNA polymerase II and plays a role in transcription elongation as well as histone modifications including ubiquitylation and methylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

Biological processes 29 terms

Cdc73/Paf1 complex (GO:0016593)Cdc73/Paf1 complex (GO:0016593)Cdc73/Paf1 complex (GO:0016593)RNA polymerase II complex binding (GO:0000993)RNA polymerase II complex binding (GO:0000993)cellular response to lipopolysaccharide (GO:0071222)cellular response to lipopolysaccharide (GO:0071222)chromatin binding (GO:0003682)chromatin binding (GO:0003682)cytoplasm (GO:0005737)endodermal cell fate commitment (GO:0001711)endodermal cell fate commitment (GO:0001711)fibrillar center (GO:0001650)mRNA 3'-end processing (GO:0031124)membrane (GO:0016020)negative regulation of myeloid cell differentiation (GO:0045638)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of cell cycle G1/S phase transition (GO:1902808)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein localization to nucleus (GO:0034504)stem cell population maintenance (GO:0019827)transcription elongation by RNA polymerase II (GO:0006368)transcription elongation by RNA polymerase II (GO:0006368)

Expression (TPM)

TFs regulating PAF1 0 TFs

Transcription factors with Perturb-seq knockdown data for PAF1. 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 = PAF1 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 PAF1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PAF1, 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
chr19:39,125,485–39,126,290	265.4 kb	Distal (>10kb) Multiome	866
chr19:39,307,021–39,308,955	83.6 kb	Distal (>10kb) Multiome	358
chr19:39,320,514–39,321,175	70.3 kb	Distal (>10kb) Multiome	364
chr19:39,341,491–39,342,890	48.9 kb	Distal (>10kb) Multiome	934
chr19:39,390,544–39,391,970	11 bp	At TSS Multiome	1003
chr19:39,397,520–39,398,126	6.7 kb	Proximal (<10kb) Multiome	711
chr19:39,402,336–39,404,125	12.8 kb	Distal (>10kb) Multiome	826
chr19:39,406,270–39,408,010	15.6 kb	Distal (>10kb) Multiome	804
chr19:39,409,417–39,410,433	18.6 kb	Distal (>10kb) Multiome	884
chr19:39,411,293–39,414,170	21.3 kb	Distal (>10kb) Multiome	1109
chr19:39,428,269–39,428,993	37.5 kb	Distal (>10kb) Multiome	479
chr19:39,435,526–39,436,258	44.9 kb	Distal (>10kb) Multiome	930
chr19:39,445,191–39,446,019	54.4 kb	Distal (>10kb) Multiome	927
chr19:39,480,241–39,481,284	89.6 kb	Distal (>10kb) Multiome	880
chr19:39,497,736–39,498,430	106.9 kb	Distal (>10kb) Multiome	558
chr19:39,502,647–39,503,265	111.8 kb	Distal (>10kb) Multiome	835
chr19:39,506,926–39,507,691	116.1 kb	Distal (>10kb) Multiome	748
chr19:39,514,761–39,515,964	124.1 kb	Distal (>10kb) Multiome	370
chr19:39,532,304–39,533,247	141.7 kb	Distal (>10kb) Multiome	760
chr19:39,539,469–39,540,414	149.0 kb	Distal (>10kb) Multiome	772

Genome Browser

Genomic view of the PAF1 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.