High-Throughput Nuclease Probing of RNA Structures Using FragSeq.
High-throughput sequencing of cDNA (RNA-Seq) can be used to generate nuclease accessibility data for many distinct transcripts in the same mixture simultaneously. Such assays accelerate RNA structure analysis and provide researchers with new technologies to tackle biological questions on a transcriptome-wide scale. FragSeq is an experimental assay for transcriptome-wide RNA structure probing using RNA-Seq, coupled with data analysis tools that allow quantitative determination of nuclease accessibility at single-base resolution. We provide a practical guide to designing and carrying out FragSeq experiments and data analysis.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. andrew.uzilov@gmail.com.
Andrew V
AV
Uzilov
Research and Development, Pacific Biosciences, Menlo Park, CA, USA.
Jason G
JG
Underwood
D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D059367:RNA Cleavage; D015347:RNA Probes; D012260:Ribonucleases / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software; D059467:Transcriptome; D064878:Web Browser; D057188:Workflow
D015347:RNA Probes; D012313:RNA; D012260:Ribonucleases
Bioinformatics; FragSeq; Nuclease accessibility; Nuclease probing; RNA structure prediction; RNA structure probing; RNA-Seq; Transcriptome