Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transc...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3510205?pdf=render |
| _version_ | 1818136593811111936 |
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| author | Jennifer A Mitchell Ieuan Clay David Umlauf Chih-Yu Chen Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano Peter Fraser |
| author_facet | Jennifer A Mitchell Ieuan Clay David Umlauf Chih-Yu Chen Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano Peter Fraser |
| author_sort | Jennifer A Mitchell |
| collection | DOAJ |
| description | In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq) in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq) of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A)-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs. |
| first_indexed | 2024-12-11T09:42:53Z |
| format | Article |
| id | doaj.art-0244b07b53fe4a4486c1b6e6aab8d9a8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T09:42:53Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0244b07b53fe4a4486c1b6e6aab8d9a82022-12-22T01:12:37ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01711e4927410.1371/journal.pone.0049274Nuclear RNA sequencing of the mouse erythroid cell transcriptome.Jennifer A MitchellIeuan ClayDavid UmlaufChih-Yu ChenCatherine A MoirChristopher H EskiwStefan SchoenfelderLyubomira ChakalovaTakashi NaganoPeter FraserIn addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq) in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq) of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A)-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.http://europepmc.org/articles/PMC3510205?pdf=render |
| spellingShingle | Jennifer A Mitchell Ieuan Clay David Umlauf Chih-Yu Chen Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano Peter Fraser Nuclear RNA sequencing of the mouse erythroid cell transcriptome. PLoS ONE |
| title | Nuclear RNA sequencing of the mouse erythroid cell transcriptome. |
| title_full | Nuclear RNA sequencing of the mouse erythroid cell transcriptome. |
| title_fullStr | Nuclear RNA sequencing of the mouse erythroid cell transcriptome. |
| title_full_unstemmed | Nuclear RNA sequencing of the mouse erythroid cell transcriptome. |
| title_short | Nuclear RNA sequencing of the mouse erythroid cell transcriptome. |
| title_sort | nuclear rna sequencing of the mouse erythroid cell transcriptome |
| url | http://europepmc.org/articles/PMC3510205?pdf=render |
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