title: Long noncoding RNAs are rarely translated in two human cell lines.
abstract: Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA- fractions in the cell lines K562 and GM12878. We used the machine-learning algorithm RuleFit3 to regress the peptide data against RNA expression data. The most important covariate for predicting translation was, surprisingly, the Cytosol polyA- fraction in both cell lines. LncRNAs are ~13-fold less likely to produce detectable peptides than similar mRNAs, indicating that ~92% of GENCODE v7 lncRNAs are not translated in these two ENCODE cell lines. Intersecting 9640 lncRNA loci with 79,333 peptides yielded 85 unique peptides matching 69 lncRNAs. Most cases were due to a coding transcript misannotated as lncRNA. Two exceptions were an unprocessed pseudogene and a bona fide lncRNA gene, both with open reading frames (ORFs) compromised by upstream stop codons. All potentially translatable lncRNA ORFs had only a single peptide match, indicating low protein abundance and/or false-positive peptide matches. We conclude that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome.
authors.affiliation: Department of Statistics, University of California, Berkeley, California 94720, USA.
authors.forename: Balázs
authors.initials: B
authors.lastname: Bánfai
authors.forename: Hui
authors.initials: H
authors.lastname: Jia
authors.forename: Jainab
authors.initials: J
authors.lastname: Khatun
authors.forename: Emily
authors.initials: E
authors.lastname: Wood
authors.forename: Brian
authors.initials: B
authors.lastname: Risk
authors.forename: William E
authors.initials: WE
authors.lastname: Gundling
authors.forename: Anshul
authors.initials: A
authors.lastname: Kundaje
authors.forename: Harsha P
authors.initials: HP
authors.lastname: Gunawardena
authors.forename: Yanbao
authors.initials: Y
authors.lastname: Yu
authors.forename: Ling
authors.initials: L
authors.lastname: Xie
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Krajewski
authors.forename: Brian D
authors.initials: BD
authors.lastname: Strahl
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
authors.forename: Peter
authors.initials: P
authors.lastname: Bickel
authors.forename: Morgan C
authors.initials: MC
authors.lastname: Giddings
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.forename: Leonard
authors.initials: L
authors.lastname: Lipovich
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002460:Cell Line; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D020014:K562 Cells; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010455:Peptides / Q000235:genetics; D014176:Protein Biosynthesis; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D062085:RNA, Long Noncoding; D012333:RNA, Messenger