XRN2

5'-3' exoribonuclease 2

This gene encodes a 5'-3' exonuclease that promotes transcription termination at cotranscriptional cleavage sites. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

Member of: DE-1 DE-1.18 Developmental clusters: GC4

Biological processes 34 terms

5'-3' RNA exonuclease activity (GO:0004534)5'-3' RNA exonuclease activity (GO:0004534)5'-3' RNA exonuclease activity (GO:0004534)5'-3' RNA exonuclease activity (GO:0004534)5'-3' exonuclease activity (GO:0008409)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA catabolic process (GO:0006401)RNA metabolic process (GO:0016070)RNA metabolic process (GO:0016070)RNA processing (GO:0006396)co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway (GO:0180010)exonuclease activity (GO:0004527)hippocampus development (GO:0021766)identical protein binding (GO:0042802)membrane (GO:0016020)neuron differentiation (GO:0030182)nuclear-transcribed mRNA catabolic process (GO:0000956)nuclease activity (GO:0004518)nucleic acid binding (GO:0003676)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)rRNA processing (GO:0006364)retina development in camera-type eye (GO:0060041)spermatogenesis (GO:0007283)spermatogenesis (GO:0007283)termination of RNA polymerase II transcription (GO:0006369)transcription termination site sequence-specific DNA binding (GO:0001147)

Expression (TPM)

TFs regulating XRN2 0 TFs

Transcription factors with Perturb-seq knockdown data for XRN2. 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 = XRN2 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 XRN2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of XRN2, 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
chr20:21,100,747–21,102,570	201.5 kb	Distal (>10kb) Multiome	378
chr20:21,105,059–21,106,031	197.6 kb	Distal (>10kb) Multiome	99
chr20:21,125,297–21,126,818	177.4 kb	Distal (>10kb) Multiome	907
chr20:21,189,624–21,190,699	113.1 kb	Distal (>10kb) Multiome	265
chr20:21,302,879–21,304,081	94 bp	At TSS Multiome	1114
chr20:21,391,406–21,392,099	88.3 kb	Distal (>10kb) Multiome	156
chr20:21,395,661–21,397,622	92.8 kb	Distal (>10kb) Multiome	295
chr20:21,505,233–21,506,733	203.1 kb	Distal (>10kb) Multiome	641
chr20:21,513,907–21,516,021	211.8 kb	Distal (>10kb) Multiome	331
chr20:21,518,360–21,519,896	216.0 kb	Distal (>10kb) Multiome	128
chr20:21,521,001–21,522,917	218.1 kb	Distal (>10kb) Multiome	278
chr20:21,579,739–21,580,220	276.7 kb	Distal (>10kb) Multiome	15

Genome Browser

Genomic view of the XRN2 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.