This gene produces a precursor transcript from which a long non-coding RNA is derived by RNase P cleavage of a tRNA-like small ncRNA (known as mascRNA) from its 3' end. The resultant mature transcript lacks a canonical poly(A) tail but is instead stabilized by a 3' triple helical structure. This transcript is retained in the nucleus where it is thought to form molecular scaffolds for ribonucleoprotein complexes. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer metastasis and cell migration, and it is involved in cell cycle regulation. Its upregulation in multiple cancerous tissues has been associated with the proliferation and metastasis of tumor cells. [provided by RefSeq, Mar 2015]
Transcription factors with Perturb-seq knockdown data for MALAT1. 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 = MALAT1 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 MALAT1, 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 |
|---|---|---|---|---|
| chr11:65,213,383–65,213,853 | 284.0 kb | Distal (>10kb) Multiome | 174 | |
| chr11:65,225,439–65,226,037 | 272.0 kb | Distal (>10kb) Multiome | 522 | |
| chr11:65,261,186–65,262,526 | 235.8 kb | Distal (>10kb) Multiome | 777 | |
| chr11:65,314,302–65,316,053 | 181.9 kb | Distal (>10kb) Multiome | 803 | |
| chr11:65,333,360–65,334,372 | 163.8 kb | Distal (>10kb) Multiome | 654 | |
| chr11:65,354,023–65,355,987 | 143.0 kb | Distal (>10kb) Multiome | 677 | |
| chr11:65,366,306–65,366,977 | 131.1 kb | Distal (>10kb) Multiome HiCAR | 309 | |
| chr11:65,381,835–65,382,758 | 115.4 kb | Distal (>10kb) Multiome | 984 | |
| chr11:65,386,320–65,387,097 | 111.0 kb | Distal (>10kb) Multiome | 757 | |
| chr11:65,416,383–65,417,015 | 81.1 kb | Distal (>10kb) Multiome | 664 | |
| chr11:65,417,855–65,419,687 | 78.5 kb | Distal (>10kb) Multiome | 1018 | |
| chr11:65,421,858–65,423,533 | 75.2 kb | Distal (>10kb) Multiome HiCAR | 1197 | |
| chr11:65,454,735–65,455,360 | 42.5 kb | Distal (>10kb) Multiome | 573 | |
| chr11:65,477,100–65,477,990 | 20.0 kb | Distal (>10kb) Multiome | 991 | |
| chr11:65,487,451–65,488,490 | 9.9 kb | Proximal (<10kb) Multiome | 706 | |
| chr11:65,496,515–65,498,726 | 56 bp | At TSS Multiome | 1059 | |
| chr11:65,498,911–65,499,611 | 1.3 kb | Proximal (<10kb) | 965 | |
| chr11:65,506,702–65,508,865 | 9.6 kb | Proximal (<10kb) Multiome | 864 | |
| chr11:65,524,475–65,525,724 | 27.4 kb | Distal (>10kb) Multiome | 711 | |
| chr11:65,538,923–65,541,339 | 43.2 kb | Distal (>10kb) Multiome | 733 | |
| chr11:65,546,285–65,547,091 | 49.1 kb | Distal (>10kb) Multiome | 529 | |
| chr11:65,553,318–65,554,003 | 56.0 kb | Distal (>10kb) Multiome | 195 | |
| chr11:65,569,718–65,570,745 | 72.7 kb | Distal (>10kb) Multiome | 930 | |
| chr11:65,571,973–65,573,008 | 74.8 kb | Distal (>10kb) Multiome | 420 | |
| chr11:65,573,788–65,575,269 | 76.7 kb | Distal (>10kb) Multiome | 742 | |
| chr11:65,575,601–65,576,322 | 78.4 kb | Distal (>10kb) Multiome | 527 | |
| chr11:65,591,808–65,592,698 | 94.6 kb | Distal (>10kb) Multiome | 169 | |
| chr11:65,606,536–65,607,917 | 109.5 kb | Distal (>10kb) Multiome | 376 | |
| chr11:65,613,478–65,614,645 | 116.6 kb | Distal (>10kb) Multiome | 702 | |
| chr11:65,614,954–65,616,793 | 117.9 kb | Distal (>10kb) Multiome | 830 | |
| chr11:65,637,768–65,638,920 | 140.5 kb | Distal (>10kb) Multiome | 740 | |
| chr11:65,641,918–65,642,633 | 144.5 kb | Distal (>10kb) Multiome | 155 | |
| chr11:65,646,814–65,647,818 | 149.6 kb | Distal (>10kb) Multiome | 270 | |
| chr11:65,652,106–65,653,317 | 155.1 kb | Distal (>10kb) Multiome | 901 | |
| chr11:65,662,517–65,663,930 | 165.4 kb | Distal (>10kb) Multiome | 839 | |
| chr11:65,711,437–65,712,942 | 214.6 kb | Distal (>10kb) Multiome | 1143 | |
| chr11:65,720,215–65,720,955 | 223.0 kb | Distal (>10kb) Multiome | 821 | |
| chr11:65,779,808–65,781,988 | 282.4 kb | Distal (>10kb) Multiome | 764 | |
| chr11:65,785,898–65,789,101 | 290.8 kb | Distal (>10kb) Multiome | 478 |
Genomic view of the MALAT1 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.