Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain
Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investi...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
National Academy of Sciences (U.S.)
2016
|
| Online Access: | http://hdl.handle.net/1721.1/100788 |
| _version_ | 1826198064543563776 |
|---|---|
| author | Goff, Loyal A. Groff, Abigail F. Sauvageau, Martin Trayes-Gibson, Zachary Sanchez-Gomez, Diana B. Morse, Michael Martin, Ryan D. Elcavage, Lara E. Liapis, Stephen C. Gonzalez-Celeiro, Meryem Plana, Olivia Li, Eric Gerhardinger, Chiara Tomassy, Giulio S. Arlotta, Paola Rinn, John L. |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Goff, Loyal A. Groff, Abigail F. Sauvageau, Martin Trayes-Gibson, Zachary Sanchez-Gomez, Diana B. Morse, Michael Martin, Ryan D. Elcavage, Lara E. Liapis, Stephen C. Gonzalez-Celeiro, Meryem Plana, Olivia Li, Eric Gerhardinger, Chiara Tomassy, Giulio S. Arlotta, Paola Rinn, John L. |
| author_sort | Goff, Loyal A. |
| collection | MIT |
| description | Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that several lncRNAs are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. We further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncRNA loci. Finally, we found that 4 of the 13 lncRNAs significantly affect the expression of several neighboring protein-coding genes in a cis-like manner. By providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncRNA locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease. |
| first_indexed | 2024-09-23T10:58:18Z |
| format | Article |
| id | mit-1721.1/100788 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:58:18Z |
| publishDate | 2016 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/1007882022-09-27T16:16:11Z Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain Goff, Loyal A. Groff, Abigail F. Sauvageau, Martin Trayes-Gibson, Zachary Sanchez-Gomez, Diana B. Morse, Michael Martin, Ryan D. Elcavage, Lara E. Liapis, Stephen C. Gonzalez-Celeiro, Meryem Plana, Olivia Li, Eric Gerhardinger, Chiara Tomassy, Giulio S. Arlotta, Paola Rinn, John L. Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Goff, Loyal A. Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that several lncRNAs are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. We further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncRNA loci. Finally, we found that 4 of the 13 lncRNAs significantly affect the expression of several neighboring protein-coding genes in a cis-like manner. By providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncRNA locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease. National Science Foundation (U.S.) (Postdoctoral Research Fellowship in Biology DBI-0905973) 2016-01-11T00:40:04Z 2016-01-11T00:40:04Z 2015-06 2014-07 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/100788 Goff, Loyal A., Abigail F. Groff, Martin Sauvageau, Zachary Trayes-Gibson, Diana B. Sanchez-Gomez, Michael Morse, Ryan D. Martin, et al. “Spatiotemporal Expression and Transcriptional Perturbations by Long Noncoding RNAs in the Mouse Brain.” Proc Natl Acad Sci USA 112, no. 22 (June 1, 2015): 6855–6862. en_US http://dx.doi.org/10.1073/pnas.1411263112 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) National Academy of Sciences (U.S.) |
| spellingShingle | Goff, Loyal A. Groff, Abigail F. Sauvageau, Martin Trayes-Gibson, Zachary Sanchez-Gomez, Diana B. Morse, Michael Martin, Ryan D. Elcavage, Lara E. Liapis, Stephen C. Gonzalez-Celeiro, Meryem Plana, Olivia Li, Eric Gerhardinger, Chiara Tomassy, Giulio S. Arlotta, Paola Rinn, John L. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title | Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title_full | Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title_fullStr | Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title_full_unstemmed | Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title_short | Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain |
| title_sort | spatiotemporal expression and transcriptional perturbations by long noncoding rnas in the mouse brain |
| url | http://hdl.handle.net/1721.1/100788 |
| work_keys_str_mv | AT goffloyala spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT groffabigailf spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT sauvageaumartin spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT trayesgibsonzachary spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT sanchezgomezdianab spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT morsemichael spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT martinryand spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT elcavagelarae spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT liapisstephenc spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT gonzalezceleiromeryem spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT planaolivia spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT lieric spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT gerhardingerchiara spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT tomassygiulios spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT arlottapaola spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain AT rinnjohnl spatiotemporalexpressionandtranscriptionalperturbationsbylongnoncodingrnasinthemousebrain |