Transcriptomics,Genomics

Dataset Information

91

Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq


ABSTRACT: We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs. 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. By integrating the ChIP-seq, RNA-seq and small RNA-seq data (previously uploaded to GEO as GSM450615 by our collaborator) with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified previously electronically annotated TSSs at a high resolution, and predicted some novel TSSs.

ORGANISM(S): Macaca mulatta  

SUBMITTER: Dali Han  Jing Li   Philipp Khaitovich   Jing-Dong J Han   Zheng Yan   Haiyang Hu   Yixing Han   Yuan Gao   Bin Xie   Nan Qiao   Yi Liu    

PROVIDER: E-GEOD-24538 | ArrayExpress| 2012-11-06

SECONDARY ACCESSION(S): SRP003782SRP003781GSE24538PRJNA132563

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq.

Liu Yi Y   Han Dali D   Han Yixing Y   Yan Zheng Z   Xie Bin B   Li Jing J   Qiao Nan N   Hu Haiyang H   Khaitovich Philipp P   Gao Yuan Y   Han Jing-Dong J JD  

Nucleic acids research 20101014 4


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  ...[more]

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