ArticleNucleic acids research2011
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-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 14 papers.
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Who cites it
14 citing papers in PubMed, 20 citations in OpenAlex.
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- Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.PLoS genetics · 2015Article
- Advanced Applications of RNA Sequencing and Challenges.Bioinformatics and biology insights · 2015Review
- Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes.BMC genomics · 2014Article
- Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene.The Journal of nutritional biochemistry · 2013Article
- Monoubiquitination of filamin B regulates vascular endothelial growth factor-mediated trafficking of histone deacetylase 7.Molecular and cellular biology · 2013Article
- RhesusBase: a knowledgebase for the monkey research community.Nucleic acids research · 2013Article
- Human-specific histone methylation signatures at transcription start sites in prefrontal neurons.PLoS biology · 2012Article
- Transposase mediated construction of RNA-seq libraries.Genome research · 2012Article
- Quantitative proteomic approaches to studying histone modifications.Current chemical genomics · 2011Article
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rhesus macaque is a widely used primate model organism. Its genome annotations are however still largely comparative computational predictions derived mainly from human genes, which precludes studies on the macaque-specific genes, gene isoforms or their regulations. Here we took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. We generated 14,013,757 sequence tags by H3K4me3 ChIP-Seq and obtained 17,322,358 paired end reads for mRNA, and 10,698,419 short reads for sRNA from the macaque brain. By integrating these data with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified 17,933 of previously electronically annotated TSSs at 500-bp resolution. We also predicted approximately 10,000 novel TSSs. These provide an important rich resource for close examination of the species-specific transcript structures and transcription regulations in the Rhesus macaque genome. Our approach exemplifies a relatively inexpensive way to generate a reasonably reliable TSS map for a large genome. It may serve as a guiding example for similar genome annotation efforts targeted at other model organisms.
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