Micropeptides encoded in transcripts previously identified as long noncoding RNAs: a new chapter in transcriptomics and proteomics

F Yeasmin, T Yada, N Akimitsu - Frontiers in genetics, 2018 - frontiersin.org
Integrative analysis using omics-based technologies results in the identification of a large
number of putative short open reading frames (sORFs) with protein-coding capacity within …

Alternative translation start sites and hidden coding potential of eukaryotic mRNAs

AV Kochetov - Bioessays, 2008 - Wiley Online Library
It is widely suggested that a eukaryotic mRNA typically contains one translation start site and
encodes a single functional protein product. However, according to current points of view on …

Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue

J Ma, CC Ward, I Jungreis, SA Slavoff… - Journal of proteome …, 2014 - ACS Publications
The existence of nonannotated protein-coding human short open reading frames (sORFs)
has been revealed through the direct detection of their sORF-encoded polypeptide (SEP) …

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes

S Nakagawa, Y Niimura, T Gojobori… - Nucleic acids …, 2008 - academic.oup.com
Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the
accurate annotation of genome sequences. Kozak reported that the nucleotide sequence …

DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction

Y Zhang, C Jia, MJ Fullwood… - Briefings in …, 2021 - academic.oup.com
The development of deep sequencing technologies has led to the discovery of novel
transcripts. Many in silico methods have been developed to assess the coding potential of …

Translational control of eukaryotic gene expression

KVD Kelen, R Beyaert, D Inzé… - Critical reviews in …, 2009 - Taylor & Francis
Translational control mechanisms are, besides transcriptional control and mRNA stability,
the most determining for final protein levels. A large number of accessory factors that assist …

Polymorphisms in E-cadherin (CDH1) result in a mis-localised cytoplasmic protein that is associated with Crohn's disease

AM Muise, TD Walters, WK Glowacka, AM Griffiths… - Gut, 2009 - gut.bmj.com
Background: Patients with Crohn's disease have defects in intestinal epithelial permeability
that are inadequately explained by known inflammatory bowel disease (IBD) susceptibility …

A novel intracellular isoform of matrix metalloproteinase-2 induced by oxidative stress activates innate immunity

DH Lovett, R Mahimkar, RL Raffai, L Cape… - PloS one, 2012 - journals.plos.org
Background Experimental and clinical evidence has pinpointed a critical role for matrix
metalloproteinase-2 (MMP-2) in ischemic ventricular remodeling and systolic heart failure …

Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process of ribosome scanning

K Li, J Kong, S Zhang, T Zhao, W Qian - Genome biology, 2022 - Springer
Background Eukaryotic ribosomes are widely presumed to scan mRNA for the AUG codon to
initiate translation in a strictly 5′–3′ movement (ie, strictly unidirectional scanning model) …

Alternative translation start sites are conserved in eukaryotic genomes

GA Bazykin, AV Kochetov - Nucleic acids research, 2011 - academic.oup.com
Alternative start AUG codons within a single transcript can contribute to diversity of the
proteome; however, their functional significance remains controversial. Here, we provide …