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Genomewide characterization of non-polyadenylated RNAs
BACKGROUND: RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188798/ https://www.ncbi.nlm.nih.gov/pubmed/21324177 http://dx.doi.org/10.1186/gb-2011-12-2-r16 |
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author | Yang, Li Duff, Michael O Graveley, Brenton R Carmichael, Gordon G Chen, Ling-Ling |
author_facet | Yang, Li Duff, Michael O Graveley, Brenton R Carmichael, Gordon G Chen, Ling-Ling |
author_sort | Yang, Li |
collection | PubMed |
description | BACKGROUND: RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight into the nature and expression of transcripts that lack poly(A) tails. RESULTS: We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from HeLa cells and H9 human embryonic stem cells (hESCs). Using stringent criteria, we found that while the majority of transcripts are poly(A)+, a significant portion of transcripts are either poly(A)- or bimorphic, being found in both the poly(A)+ and poly(A)- populations. Further analyses revealed that many mRNAs may not contain classical long poly(A) tails and such messages are overrepresented in specific functional categories. In addition, we surprisingly found that a few excised introns accumulate in cells and thus constitute a new class of non-polyadenylated long non-coding RNAs. Finally, we have identified a specific subset of poly(A)- histone mRNAs, including two histone H1 variants, that are expressed in undifferentiated hESCs and are rapidly diminished upon differentiation; further, these same histone genes are induced upon reprogramming of fibroblasts to induced pluripotent stem cells. CONCLUSIONS: We offer a rich source of data that allows a deeper exploration of the poly(A)- landscape of the eukaryotic transcriptome. The approach we present here also applies to the analysis of the poly(A)- transcriptomes of other organisms. |
format | Online Article Text |
id | pubmed-3188798 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31887982011-10-07 Genomewide characterization of non-polyadenylated RNAs Yang, Li Duff, Michael O Graveley, Brenton R Carmichael, Gordon G Chen, Ling-Ling Genome Biol Research BACKGROUND: RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight into the nature and expression of transcripts that lack poly(A) tails. RESULTS: We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from HeLa cells and H9 human embryonic stem cells (hESCs). Using stringent criteria, we found that while the majority of transcripts are poly(A)+, a significant portion of transcripts are either poly(A)- or bimorphic, being found in both the poly(A)+ and poly(A)- populations. Further analyses revealed that many mRNAs may not contain classical long poly(A) tails and such messages are overrepresented in specific functional categories. In addition, we surprisingly found that a few excised introns accumulate in cells and thus constitute a new class of non-polyadenylated long non-coding RNAs. Finally, we have identified a specific subset of poly(A)- histone mRNAs, including two histone H1 variants, that are expressed in undifferentiated hESCs and are rapidly diminished upon differentiation; further, these same histone genes are induced upon reprogramming of fibroblasts to induced pluripotent stem cells. CONCLUSIONS: We offer a rich source of data that allows a deeper exploration of the poly(A)- landscape of the eukaryotic transcriptome. The approach we present here also applies to the analysis of the poly(A)- transcriptomes of other organisms. BioMed Central 2011 2011-02-16 /pmc/articles/PMC3188798/ /pubmed/21324177 http://dx.doi.org/10.1186/gb-2011-12-2-r16 Text en Copyright ©2011 Yang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Yang, Li Duff, Michael O Graveley, Brenton R Carmichael, Gordon G Chen, Ling-Ling Genomewide characterization of non-polyadenylated RNAs |
title | Genomewide characterization of non-polyadenylated RNAs |
title_full | Genomewide characterization of non-polyadenylated RNAs |
title_fullStr | Genomewide characterization of non-polyadenylated RNAs |
title_full_unstemmed | Genomewide characterization of non-polyadenylated RNAs |
title_short | Genomewide characterization of non-polyadenylated RNAs |
title_sort | genomewide characterization of non-polyadenylated rnas |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188798/ https://www.ncbi.nlm.nih.gov/pubmed/21324177 http://dx.doi.org/10.1186/gb-2011-12-2-r16 |
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