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


CONCLUSIONS
nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. cumbiej@onid.orst.edu.
Jason S
JS
Cumbie
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. ivanchem@science.oregonstate.edu.
Maria G
MG
Ivanchenko
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.|Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA. megrawm@science.oregonstate.edu.
Molly
M
Megraw
D017360:Arabidopsis / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D036103:Nanotechnology / Q000295:instrumentation / Q000379:methods*; D018517:Plant Roots / Q000235:genetics; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D012984:Software; D024363:Transcription Initiation Site