Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages
Abstract Gene transcription is controlled and modulated by regulatory regions, including enhancers and promoters. These regions are abundant in non-coding bidirectional transcription that results in generally unstable RNA. Using nascent RNA transcription data across hundreds of human samples, we ide...
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| Format: | Article |
| Language: | English |
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BMC
2025-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11568-z |
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| author | Rutendo F. Sigauke Lynn Sanford Zachary L. Maas Taylor Jones Jacob T. Stanley Hope A. Townsend Mary A. Allen Robin D. Dowell |
| author_facet | Rutendo F. Sigauke Lynn Sanford Zachary L. Maas Taylor Jones Jacob T. Stanley Hope A. Townsend Mary A. Allen Robin D. Dowell |
| author_sort | Rutendo F. Sigauke |
| collection | DOAJ |
| description | Abstract Gene transcription is controlled and modulated by regulatory regions, including enhancers and promoters. These regions are abundant in non-coding bidirectional transcription that results in generally unstable RNA. Using nascent RNA transcription data across hundreds of human samples, we identified over 800,000 regions containing bidirectional transcription. We then identify tissue specific, highly correlated transcription between bidirectional and gene regions. The identified correlated pairs, a bidirectional region and a gene, are enriched for disease associated SNPs and often supported by independent 3D data. We present these resources as a database called DBNascent ( https://nascent.colorado.edu/ ) which serves as a resource for future studies into gene regulation, enhancer associated RNAs, and transcription factors. |
| format | Article |
| id | doaj-art-6d2b11b297d348529dee81a3c672df4c |
| institution | OA Journals |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-6d2b11b297d348529dee81a3c672df4c2025-08-20T02:19:58ZengBMCBMC Genomics1471-21642025-04-0126111510.1186/s12864-025-11568-zAtlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkagesRutendo F. Sigauke0Lynn Sanford1Zachary L. Maas2Taylor Jones3Jacob T. Stanley4Hope A. Townsend5Mary A. Allen6Robin D. Dowell7BioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderAbstract Gene transcription is controlled and modulated by regulatory regions, including enhancers and promoters. These regions are abundant in non-coding bidirectional transcription that results in generally unstable RNA. Using nascent RNA transcription data across hundreds of human samples, we identified over 800,000 regions containing bidirectional transcription. We then identify tissue specific, highly correlated transcription between bidirectional and gene regions. The identified correlated pairs, a bidirectional region and a gene, are enriched for disease associated SNPs and often supported by independent 3D data. We present these resources as a database called DBNascent ( https://nascent.colorado.edu/ ) which serves as a resource for future studies into gene regulation, enhancer associated RNAs, and transcription factors.https://doi.org/10.1186/s12864-025-11568-zNascent RNA sequencingBidirectional transcriptionEnhancer RNA |
| spellingShingle | Rutendo F. Sigauke Lynn Sanford Zachary L. Maas Taylor Jones Jacob T. Stanley Hope A. Townsend Mary A. Allen Robin D. Dowell Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages BMC Genomics Nascent RNA sequencing Bidirectional transcription Enhancer RNA |
| title | Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages |
| title_full | Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages |
| title_fullStr | Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages |
| title_full_unstemmed | Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages |
| title_short | Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages |
| title_sort | atlas of nascent rna transcripts reveals tissue specific enhancer to gene linkages |
| topic | Nascent RNA sequencing Bidirectional transcription Enhancer RNA |
| url | https://doi.org/10.1186/s12864-025-11568-z |
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