ArticlePloS one2012
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic acids research · 2024Article
- Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma.Nucleic acids research · 2023Article
- Review
- Involvement of GRK2 in modulating nalfurafine-induced reduction of excessive alcohol drinking in mice.Neuroscience letters · 2021Article
- Chromatin Conformation in Development and Disease.Frontiers in cell and developmental biology · 2021Review
- mTORC1 pathway is involved in the kappa opioid receptor activation-induced increase in excessive alcohol drinking in mice.Pharmacology, biochemistry, and behavior · 2020Article
- The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice.PLoS biology · 2020Article
- Nuclear transcriptional changes in hypothalamus of Pomc enhancer knockout mice after excessive alcohol drinking.Genes, brain, and behavior · 2019Article
- Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.Bioinformatics (Oxford, England) · 2019Article
- Fetal γ-globin genes are regulated by theBlood · 2018Article
- KLF4 Nuclear Export Requires ERK Activation and Initiates Exit from Naive Pluripotency.Stem cell reports · 2018Article
- Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo.Nature communications · 2018Article
- Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome.Cell reports · 2017Article
- Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes.Genome research · 2017Article
- Use of RNA sequencing to evaluate rheumatic disease patients.Arthritis research & therapy · 2015Review
- Human and murine erythropoiesis.Current opinion in hematology · 2015Review
- Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production.Nucleus (Austin, Tex.) · 2015Article
- Developmental transcriptome analysis of human erythropoiesis.Human molecular genetics · 2014Article
- Temporally and spatially restricted gene expression profiling.Current genomics · 2014Article
- RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.