Revealing lncRNA structures and interactions by sequencing-based approaches

X Qian, J Zhao, PY Yeung, QC Zhang… - Trends in biochemical …, 2019 - cell.com
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level
of gene function and regulation. Thus, characterizing the structures and interactions of …

Rock, scissors, paper: How RNA structure informs function

SM Assmann, HL Chou, PC Bevilacqua - The Plant Cell, 2023 - academic.oup.com
RNA can fold back on itself to adopt a wide range of structures. These range from relatively
simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with …

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

E Rheinbay, MM Nielsen, F Abascal, JA Wala… - Nature, 2020 - nature.com
The discovery of drivers of cancer has traditionally focused on protein-coding genes,,–. Here
we present analyses of driver point mutations and structural variants in non-coding regions …

A pan-cancer analysis of synonymous mutations

Y Sharma, M Miladi, S Dukare, K Boulay… - Nature …, 2019 - nature.com
Synonymous mutations have been viewed as silent mutations, since they only affect the
DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless …

lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs

YR Miao, W Liu, Q Zhang, AY Guo - Nucleic acids research, 2018 - academic.oup.com
Long non-coding RNAs (lncRNAs) are emerging as important regulators in different
biological processes through various ways. Because the related data, especially mutations …

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

L Mularoni, R Sabarinathan, J Deu-Pons… - Genome biology, 2016 - Springer
Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the
major challenges of cancer research. This challenge is more acute and far from solved for …

Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting

A Hosseini Rad SM, AD McLellan - International journal of molecular …, 2020 - mdpi.com
The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to
transmission and replication in humans. Although the mutation rate is limited, recently …

Single nucleotide variations: biological impact and theoretical interpretation

P Katsonis, A Koire, SJ Wilson, TK Hsu, RC Lua… - Protein …, 2014 - Wiley Online Library
Genome‐wide association studies (GWAS) and whole‐exome sequencing (WES) generate
massive amounts of genomic variant information, and a major challenge is to identify which …

Discovery of cancer driver long noncoding RNAs across 1112 tumour genomes: new candidates and distinguishing features

A Lanzós, J Carlevaro-Fita, L Mularoni, F Reverter… - Scientific reports, 2017 - nature.com
Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold
missing drivers of tumourigenesis, but few such “driver lncRNAs” are known. Until now, they …

Simultaneous DNA and RNA mapping of somatic mitochondrial mutations across diverse human cancers

JB Stewart, B Alaei-Mahabadi, R Sabarinathan… - PLoS …, 2015 - journals.plos.org
Somatic mutations in the nuclear genome are required for tumor formation, but the functional
consequences of somatic mitochondrial DNA (mtDNA) mutations are less understood. Here …