NEAT1

nuclear paraspeckle assembly transcript 1 | LINC00084, MENepsilon/beta, TP53LC15, TncRNA, VINC, NCRNA00084

This gene produces a long non-coding RNA (lncRNA) transcribed from the multiple endocrine neoplasia locus. This lncRNA is retained in the nucleus where it forms the core structural component of the paraspeckle sub-organelles. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer progression. [provided by RefSeq, Mar 2015]

Member of: DE-8 DE-8.3 Developmental clusters: GC2

Biological processes 18 terms

RISC complex (GO:0016442)RISC complex binding (GO:1905172)chromatin organization (GO:0006325)chromatin-protein adaptor activity (GO:0140463)lncRNA-mediated post-transcriptional gene silencing (GO:0000512)miRNA binding (GO:0035198)miRNA inhibitor activity via base-pairing (GO:0140869)miRNA-mediated post-transcriptional gene silencing (GO:0035195)molecular condensate scaffold activity (GO:0140693)molecular condensate scaffold activity (GO:0140693)nuclear body organization (GO:0030575)paraspeckles (GO:0042382)paraspeckles (GO:0042382)paraspeckles (GO:0042382)positive regulation of inflammatory response (GO:0050729)positive regulation of miRNA catabolic process (GO:2000627)positive regulation of synoviocyte proliferation (GO:1901647)regulation of mRNA export from nucleus (GO:0010793)

Expression (TPM)

TFs regulating NEAT1 0 TFs

Transcription factors with Perturb-seq knockdown data for NEAT1. 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 = NEAT1 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 NEAT1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NEAT1, 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
chr11:65,134,120–65,135,530	287.8 kb	Distal (>10kb) Multiome	997
chr11:65,180,773–65,182,676	241.1 kb	Distal (>10kb) Multiome	832
chr11:65,184,109–65,184,542	238.4 kb	Distal (>10kb) Multiome	85
chr11:65,213,383–65,213,853	209.1 kb	Distal (>10kb) Multiome	174
chr11:65,225,439–65,226,037	197.1 kb	Distal (>10kb) Multiome	522
chr11:65,261,186–65,262,526	161.0 kb	Distal (>10kb) Multiome	777
chr11:65,314,302–65,316,053	107.0 kb	Distal (>10kb) Multiome	803
chr11:65,333,360–65,334,372	88.9 kb	Distal (>10kb) Multiome	654
chr11:65,354,023–65,355,987	68.1 kb	Distal (>10kb) Multiome	677
chr11:65,366,306–65,366,977	56.2 kb	Distal (>10kb) Multiome	309
chr11:65,381,835–65,382,758	40.6 kb	Distal (>10kb) Multiome	984
chr11:65,386,320–65,387,097	36.2 kb	Distal (>10kb) Multiome	757
chr11:65,416,383–65,417,015	6.2 kb	Proximal (<10kb) Multiome	664
chr11:65,417,855–65,419,687	3.7 kb	Proximal (<10kb) Multiome	1018
chr11:65,421,243–65,421,721	1.1 kb	Proximal (<10kb)	747
chr11:65,421,858–65,423,533	331 bp	At TSS Multiome	1197
chr11:65,425,230–65,425,666	2.5 kb	Proximal (<10kb)	440
chr11:65,454,735–65,455,360	32.4 kb	Distal (>10kb) Multiome	573
chr11:65,477,100–65,477,990	54.8 kb	Distal (>10kb) Multiome	991
chr11:65,487,451–65,488,490	65.0 kb	Distal (>10kb) Multiome HiCAR	706
chr11:65,496,515–65,498,726	74.8 kb	Distal (>10kb) Multiome HiCAR	1059
chr11:65,506,702–65,508,865	84.5 kb	Distal (>10kb) Multiome	864
chr11:65,524,475–65,525,724	102.2 kb	Distal (>10kb) Multiome	711
chr11:65,538,923–65,541,339	118.1 kb	Distal (>10kb) Multiome	733
chr11:65,546,285–65,547,091	123.9 kb	Distal (>10kb) Multiome	529
chr11:65,553,318–65,554,003	130.9 kb	Distal (>10kb) Multiome	195
chr11:65,569,718–65,570,745	147.5 kb	Distal (>10kb) Multiome	930
chr11:65,571,973–65,573,008	149.7 kb	Distal (>10kb) Multiome	420
chr11:65,573,788–65,575,269	151.6 kb	Distal (>10kb) Multiome	742
chr11:65,575,601–65,576,322	153.2 kb	Distal (>10kb) Multiome	527
chr11:65,591,808–65,592,698	169.4 kb	Distal (>10kb) Multiome	169
chr11:65,606,536–65,607,917	184.4 kb	Distal (>10kb) Multiome	376
chr11:65,613,478–65,614,645	191.4 kb	Distal (>10kb) Multiome	702
chr11:65,614,954–65,616,793	192.8 kb	Distal (>10kb) Multiome	830
chr11:65,637,768–65,638,920	215.3 kb	Distal (>10kb) Multiome	740
chr11:65,641,918–65,642,633	219.4 kb	Distal (>10kb) Multiome	155
chr11:65,646,814–65,647,818	224.5 kb	Distal (>10kb) Multiome	270
chr11:65,652,106–65,653,317	230.0 kb	Distal (>10kb) Multiome	901
chr11:65,662,517–65,663,930	240.3 kb	Distal (>10kb) Multiome	839
chr11:65,711,437–65,712,942	289.5 kb	Distal (>10kb) Multiome	1143
chr11:65,720,215–65,720,955	297.9 kb	Distal (>10kb) Multiome	821

Genome Browser

Genomic view of the NEAT1 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.