title: Nuclear RNA Isolation and Sequencing.
abstract: Most transcriptome studies involve sequencing and quantification of steady-state mRNA by isolating and sequencing poly (A) RNA. Although this type of sequencing data is informative to determine steady-state mRNA levels it does not provide information on transcriptional output and thus may not always reflect changes in transcriptional regulation of gene expression. Furthermore, sequencing poly (A) RNA may miss transcribed regions of the genome not usually modified by polyadenylation which includes many long noncoding RNAs. Here, we describe nuclear-RNA sequencing (nucRNA-seq) which investigates the transcriptional landscape through sequencing and quantification of nuclear RNAs which are both unspliced and spliced transcripts for protein-coding genes and nuclear-retained long noncoding RNAs.
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada, M5S 3G5.
authors.forename: Navroop K
authors.initials: NK
authors.lastname: Dhaliwal
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada, M5S 3G5. ja.mitchell@utoronto.ca.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Mitchell
mesh_terms: D000818:Animals; D002458:Cell Fractionation / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D026723:Polyadenylation; D062085:RNA, Long Noncoding / Q000235:genetics / Q000302:isolation & purification; D015138:RNA, Nuclear / Q000235:genetics* / Q000302:isolation & purification*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D015138:RNA, Nuclear
keywords: Cellular fractionation; LncRNA; Massively parallel sequencing; Nuclear RNA; Transcriptome profiling