Integrated workflow for discovery of microprotein-coding small open reading frames
STAR Protocols, 2023 Summary: Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100–150 amino acids, are an emerging class of functional biomolecules.
Kevin Cao +3 more
doaj +1 more source
Visualizing the periodic Ribo-seq reads with RiboPlotR [PDF]
, 2019 ABSTRACTBackgroundRibo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small
Wu, Hsin-Yen Larry, Hsu, Polly Yingshan
openaire +1 more source
Riborex: fast and flexible identification of differential translation from Ribo-seq data. [PDF]
Bioinformatics, 2017 Abstract Motivation Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample.
Li W +4 more
europepmc +4 more sources
Ribosome signatures aid bacterial translation initiation site identification [PDF]
, 2017 Background: While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem.
Chyżyńska, Katarzyna +5 more
core +2 more sources
The contribution of Alu exons to the human proteome. [PDF]
, 2016 BackgroundAlu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important ...
Jiang, Peng +7 more
core +1 more source
RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints
Life, 2021 Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs ...
Bo Song, Mengyun Jiang, Lei Gao
doaj +1 more source
REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes [PDF]
, 2017 Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes.
Giess, Adam +5 more
core +1 more source
What can Ribo-seq and proteomics tell us about the non-canonical proteome?
, 2023 AbstractRibosome profiling (Ribo-seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of non-canonical sites of ribosome translation outside of the currently annotated coding sequences (CDSs).
Prensner JR +8 more
europepmc +3 more sources
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs [PDF]
, 2017 Alternative translation initiation mechanisms such as leaky scanning and reinitiation potentiate the polycistronic nature of human transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stimuli.
Fijalkowska, Daria +5 more
core +1 more source
De novo functional transcriptomics with RNA-seq and Ribo-seq
, 2023 Our genome sequencing and assembly capabilities have hugely increased. However, annotating our genome is still challenging. Genes can produce multiple isoforms, which may have different expression levels and roles. Transcript functions can be elucidated by profiling ribosome positions with the protocol Ribo-seq.
Albanese, Roberto +5 more
openaire +1 more source