NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.

TitleNanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
Publication TypeJournal Article
Year of Publication2015
AuthorsCumbie, JS, Ivanchenko, MG, Megraw, M
JournalBMC Genomics
Volume16
Pagination597
Date Published2015
ISSN1471-2164
KeywordsArabidopsis, Genes, Plant, Genome, Plant, Nanotechnology, Plant Roots, Promoter Regions, Genetic, Sequence Analysis, DNA, Software, Transcription Initiation Site
Abstract

BACKGROUND: Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties.

RESULTS: Here we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots.

CONCLUSION: nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.

[Link to Protocol, Additional Data, and Supplementary Materials]

[Link to CapFilter Software]

DOI10.1186/s12864-015-1670-6
Alternate JournalBMC Genomics
PubMed ID26268438
PubMed Central IDPMC4534009
Grant ListGM097188 / GM / NIGMS NIH HHS / United States