Quantitative profiling of peptides from RNAs classified as noncoding.
Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences--including introns and several classes of noncoding RNAs (ncRNAs)--do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here we use computational methods to identify the products of non-canonical translation in mouse neurons by analysing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from antisense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential.
1] Proteomics Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Sudhakaran
S
Prabakaran
Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Martin
M
Hemberg
1] Proteomics Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Ruchi
R
Chauhan
Proteomics Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Dominic
D
Winter
F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Ry Y
RY
Tweedie-Cullen
F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Christian
C
Dittrich
F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Elizabeth
E
Hong
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Jeremy
J
Gunawardena
1] Proteomics Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
Hanno
H
Steen
1] Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Gabriel
G
Kreiman
1] Proteomics Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Judith A
JA
Steen
D000818:Animals; D019295:Computational Biology; D023281:Genomics; D007438:Introns; D051379:Mice / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D008810:Mice, Inbred C57BL; D009474:Neurons / Q000378:metabolism; D010455:Peptides / Q000235:genetics* / Q000378:metabolism; D014176:Protein Biosynthesis; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism
D010455:Peptides; D022661:RNA, Untranslated