This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]
Transcription factors with Perturb-seq knockdown data for YBX1. 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 = YBX1 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 |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of YBX1, 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.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr1:42,455,770–42,457,060 | 226.1 kb | Distal (>10kb) Multiome | 881 | |
| chr1:42,462,753–42,463,783 | 219.2 kb | Distal (>10kb) Multiome | 581 | |
| chr1:42,657,991–42,659,026 | 24.0 kb | Distal (>10kb) Multiome | 952 | |
| chr1:42,681,723–42,683,347 | 95 bp | At TSS Multiome | 924 | |
| chr1:42,739,796–42,740,734 | 57.9 kb | Distal (>10kb) Multiome | 365 | |
| chr1:42,765,982–42,767,804 | 84.8 kb | Distal (>10kb) Multiome | 899 | |
| chr1:42,816,354–42,817,722 | 134.8 kb | Distal (>10kb) Multiome | 721 | |
| chr1:42,845,973–42,847,060 | 164.1 kb | Distal (>10kb) Multiome | 723 | |
| chr1:42,923,882–42,925,144 | 242.1 kb | Distal (>10kb) Multiome | 878 | |
| chr1:42,957,739–42,959,536 | 276.6 kb | Distal (>10kb) Multiome | 943 |
Genomic view of the YBX1 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.