ArticleNucleic acids research2011
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 59 citations in OpenAlex.
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- Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.Molecular and cellular biology · 2016Article
- A genomic variant in IRF9 is associated with serum cytokine levels in pig.Immunogenetics · 2016Article
- Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization.Molecular and cellular biology · 2015Article
- A stationary wavelet entropy-based clustering approach accurately predicts gene expression.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- RNA sequencing: from tag-based profiling to resolving complete transcript structure.Cellular and molecular life sciences : CMLS · 2014Review
- The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals.Genes & development · 2014Article
- Integrated transcriptome analysis of mouse spermatogenesis.BMC genomics · 2014Article
- Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells.Applied microbiology and biotechnology · 2014Article
- Hepatic-specific accessibility of Igf1 gene enhancers is independent of growth hormone signaling.Molecular endocrinology (Baltimore, Md.) · 2013Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Alternative promoters that are differentially used in various cellular contexts and tissue types add to the transcriptional complexity in mammalian genome. Identification of alternative promoters and the annotation of their activity in different tissues is one of the major challenges in understanding the transcriptional regulation of the mammalian genes and their isoforms. To determine the use of alternative promoters in different tissues, we performed ChIP-seq experiments using antibody against RNA Pol-II, in five adult mouse tissues (brain, liver, lung, spleen and kidney). Our analysis identified 38 639 Pol-II promoters, including 12 270 novel promoters, for both protein coding and non-coding mouse genes. Of these, 6384 promoters are tissue specific which are CpG poor and we find that only 34% of the novel promoters are located in CpG-rich regions, suggesting that novel promoters are mostly tissue specific. By identifying the Pol-II bound promoter(s) of each annotated gene in a given tissue, we found that 37% of the protein coding genes use alternative promoters in the five mouse tissues. The promoter annotations and ChIP-seq data presented here will aid ongoing efforts of characterizing gene regulatory regions in mammalian genomes.
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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.