Observation of dually decoded regions of the human genome using ribosome profiling data.

Journal Article (Journal Article)

The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with subcodon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames.

Full Text

Duke Authors

Cited Authors

  • Michel, AM; Choudhury, KR; Firth, AE; Ingolia, NT; Atkins, JF; Baranov, PV

Published Date

  • November 2012

Published In

Volume / Issue

  • 22 / 11

Start / End Page

  • 2219 - 2229

PubMed ID

  • 22593554

Pubmed Central ID

  • PMC3483551

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

Digital Object Identifier (DOI)

  • 10.1101/gr.133249.111


  • eng

Conference Location

  • United States