Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

By A. Bazzini, Timothy G. Johnstone, Romain Christiano, Sebastian D. Mackowiak, Benedikt Obermayer, E. Fleming, Charles E. Vejnar, Miler T. Lee, Nikolaus Rajewsky, T. Walther and 1 more. EMBO Journal, 2014

614 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2531820717268ddb00c428aad2e5f198ce8f280b

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In Molecular Biology

Citations in the corpus

A Micropeptide Encoded by a Putative Long Non-coding RNA Regulates Muscle Performance (2015, neutral): “Recent genome-wide studies have suggested that hundreds of functional micropeptides may be encoded in vertebrate long noncoding RNAs (lncRNAs) (Andrews andRothnagel, 2014; Bazzini et al., 2014).”
Mechanisms of long noncoding RNA function in development and disease (2016, background): “In general, RNA transcripts containing short (\100 nt) non-conserved ORFs, which have no homology to known peptide sequences and do not match to peptides identified in mass spectrometry screens are considered noncoding [6].”
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition (2016, neutral): “2016 The Authors developmental time points in zebrafish embryos (2, 6, 12, 24 and 48 hpf) (Bazzini et al, 2014).”
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs (2016, background): “In this regard, linear long noncoding (lnc) RNAs are not generally translated into proteins, but a subset of them appear to be a source of functional small or micropeptides due to the presence of short open reading frames (ORFs).(40) For example, a micropeptide encoded by a noncoding RNA was recentl”
Non-coding RNA: what is functional and what is junk? (2015, neutral): “It is also worthwhile noting that certain annotated lncRNAs may actually encode short functional peptides (Ingolia et al., 2011, 2014; Magny et al., 2013; Bazzini et al., 2014), although FIGURE 1 | Estimate of RNA levels in a typical mammalian cell.”
Detecting actively translated open reading frames in ribosome profiling data (2015, methodology): “Consequently, this subset of ribosomal footprints displays a striking bias toward the translated frame 1,6,9 , which can be used to infer, for each read, the position of the peptidyl-site (P-site) compartment of the translating ribosome 9 .”