The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

Abstract

Summary Mechanistic roles for many lncRNAs are poorly understood in part because their direct interactions with genomic loci and proteins are difficult to assess. Using a method to purify endogenous RNAs and their associated factors, we mapped the genomic binding sites for two highly expressed human lncRNAs, NEAT1 and MALAT1. We show that NEAT1 and MALAT1 localize to hundreds of genomic sites in human cells, primarily over active genes. NEAT1 and MALAT1 exhibit colocalization to many of these loci, but display distinct gene body binding patterns at these sites, suggesting independent but complementary functions for these RNAs. We also identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function, in addition to unique associated proteins. Transcriptional inhibition or stimulation alters localization of NEAT1 on active chromatin sites, implying that underlying DNA sequence does not target NEAT1 to chromatin and that localization responds to cues involved in the transcription process.

Specific RNP capture with antisense LNA/DNA mixmers

“…The recently described CHART-MS (capture hybridization analysis of RNA targets) (West et al 2014), CHIRP-MS (chromatin isolation by RNA purification) (Chu et al 2015), and RAP-MS (RNA antisense purification) (McHugh et al 2015) are all based on so-called "tiling approaches," which use sets of overlapping biotinylated DNA oligonucleotides that cover the length of the whole transcript. The advantage of the tiling approaches is that RNA integrity is less critical than for specific RNP capture, which uses just one oligonucleotide to capture the RNA of interest.…”

“…Antisense oligonucleotides have been extensively used to purify specific RNAs and their protein partners (Lamond et al 1989;West et al 2014;Chu et al 2015;McHugh et al 2015), as exemplified by the recent determination of the Xist RNA-bound proteome using biotinylated DNA oligonucleotides covering the entire transcript length (referred to as "tiling approach") (Chu et al 2015;McHugh et al 2015). While such a strategy enables targeting of RNA lacking full integrity, the "tiling approach" cannot be used to analyze distinct transcript isoforms or particular regions of interest from within a given RNA.…”

“…While such a strategy enables targeting of RNA lacking full integrity, the "tiling approach" cannot be used to analyze distinct transcript isoforms or particular regions of interest from within a given RNA. Some of these tiling approaches used extensive formaldehyde crosslinking, copurifying indirect RNA interactors via protein-protein interactions (West et al 2014;Chu et al 2015).…”

Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue

“…MALAT1 appears to involve RNA recombination and is located at the active transcription sites. 18 Increase of expression of MALAT1 is associated with poor prognosis of several human malignancies. Multiple mechanisms were proposed for the oncogenic activity of MALAT1.…”

Integrative analysis of competing endogenous RNA networks reveals the functional lncRNAs in heart failure

“…Interestingly, we found two lncRNAs (NEAT1 and AC005154.6) were all crucial in each feature (Figure 2D), indicating that the two lncRNA might function as a crucial regulators in the pathology processes of heart failure. NEAT1 is the lncRNA that localizes to hundreds of genomic sites in cells, primarily over active genes 18. Some studies had found that NEAT1 functioned in multiple biological processes, such as altering the epigenetic landscape of target gene promoters, regulating cell proliferation and implicating in miRNA‐associated pathways 19, 20, 21.…”