RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome

Summary: 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 ...

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Main Authors:	Weizhong Chen, Zhangming Yan, Simin Li, Norman Huang, Xuerui Huang, Jin Zhang, Sheng Zhong
Format:	Article
Language:	English
Published:	Elsevier 2018-06-01
Series:	iScience
Online Access:	http://www.sciencedirect.com/science/article/pii/S2589004218300816

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spelling	doaj-580036cb3e0d436ba4914ea5b0f1bfa72020-11-25T01:10:08ZengElsevieriScience2589-00422018-06-014204215RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the GenomeWeizhong Chen0Zhangming Yan1Simin Li2Norman Huang3Xuerui Huang4Jin Zhang5Sheng Zhong6Department of Bioengineering, University of California San Diego, San Diego, CA 92093, USADepartment of Bioengineering, University of California San Diego, San Diego, CA 92093, USADepartment of Pharmacology, University of California San Diego, San Diego, CA 92093, USADepartment of Bioengineering, University of California San Diego, San Diego, CA 92093, USADivision of Biological Sciences, University of California San Diego, San Diego, CA 92093, USADepartment of Pharmacology, University of California San Diego, San Diego, CA 92093, USA; Corresponding authorDepartment of Bioengineering, University of California San Diego, San Diego, CA 92093, USA; Corresponding authorSummary: 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 immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs are located in sufficient proximity to the nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles. : Genetics; Molecular Genetics; Data Analysis in Structural Biology Subject Areas: Genetics, Molecular Genetics, Data Analysis in Structural Biologyhttp://www.sciencedirect.com/science/article/pii/S2589004218300816
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Weizhong Chen Zhangming Yan Simin Li Norman Huang Xuerui Huang Jin Zhang Sheng Zhong
spellingShingle	Weizhong Chen Zhangming Yan Simin Li Norman Huang Xuerui Huang Jin Zhang Sheng Zhong RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome iScience
author_facet	Weizhong Chen Zhangming Yan Simin Li Norman Huang Xuerui Huang Jin Zhang Sheng Zhong
author_sort	Weizhong Chen
title	RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
title_short	RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
title_full	RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
title_fullStr	RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
title_full_unstemmed	RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
title_sort	rnas as proximity-labeling media for identifying nuclear speckle positions relative to the genome
publisher	Elsevier
series	iScience
issn	2589-0042
publishDate	2018-06-01
description	Summary: 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 immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs are located in sufficient proximity to the nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles. : Genetics; Molecular Genetics; Data Analysis in Structural Biology Subject Areas: Genetics, Molecular Genetics, Data Analysis in Structural Biology
url	http://www.sciencedirect.com/science/article/pii/S2589004218300816
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RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome

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