{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Chen W"],"funding":["NICHD NIH HHS","NCI NIH HHS","NIH"],"pagination":["204-215"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6146591"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["4"],"pubmed_abstract":["It remains challenging to identify all parts of the nuclear genome that are in proximity to nuclear speckles, due to physical separation between the nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNA (snRNAs) and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA [nuclear speckle-associated RNA]), may extend to sufficient proximity to the genome. Leveraging a transcriptome-genome interaction assay (mapping of RNA-genome interactions [MARGI]), we identified clusters of nsaRNA-interacting genomic sequences (nsaPeaks). Posttranscriptional pre-mRNAs, which also accumulate to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Our combined DNA fluorescence in situ hybridization and immunofluo"],"journal":["iScience"],"pubmed_title":["RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome."],"pmcid":["PMC6146591"],"funding_grant_id":["DP1 HD087990","U01 CA200147","DP1HD087990","R35CA197622","R35 CA197622","U01CA200147"],"pubmed_authors":["Yan Z","Li S","Zhang J","Zhong S","Huang X","Chen W","Huang N"],"additional_accession":[]},"is_claimable":false,"name":"RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome.","description":"It remains challenging to identify all parts of the nuclear genome that are in proximity to nuclear speckles, due to physical separation between the nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNA (snRNAs) and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA [nuclear speckle-associated RNA]), may extend to sufficient proximity to the genome. Leveraging a transcriptome-genome interaction assay (mapping of RNA-genome interactions [MARGI]), we identified clusters of nsaRNA-interacting genomic sequences (nsaPeaks). Posttranscriptional pre-mRNAs, which also accumulate to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Our combined DNA fluorescence in situ hybridization and immunofluo","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Jun","modification":"2026-05-01T18:16:01.839Z","creation":"2026-04-18T03:08:25.406Z"},"accession":"S-EPMC6146591","cross_references":{"pubmed":["30240742"],"doi":["10.1016/j.isci.2018.06.005"]}}