Regulation of gene expression by cis-acting long non-coding RNAs

N Gil, I Ulitsky - Nature Reviews Genetics, 2020 - nature.com
Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from
thousands of loci in mammalian genomes. Cis-acting lncRNAs, which constitute a …

A mechanistic view of long noncoding RNAs in cancer

L Winkler, N Dimitrova - Wiley Interdisciplinary Reviews: RNA, 2022 - Wiley Online Library
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of
biological processes in normal and disease states. In particular, lncRNAs have garnered …

Evaluation of deep learning in non-coding RNA classification

N Amin, A McGrath, YPP Chen - Nature Machine Intelligence, 2019 - nature.com
Non-coding (nc) RNA plays a vital role in biological processes and has been associated
with diseases such as cancer. Classification of ncRNAs is necessary for understanding the …

A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis

P Cai, ABC Otten, B Cheng, MA Ishii, W Zhang… - Genome …, 2020 - genome.cshlp.org
Genome-wide association studies indicate that many disease susceptibility regions reside in
non-protein-coding regions of the genome. Long noncoding RNAs (lncRNAs) are a major …

Reverse-genetics studies of lncRNAs—what we have learnt and paths forward

F Gao, Y Cai, P Kapranov, D Xu - Genome biology, 2020 - Springer
Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in
multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized …

Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability

A Rom, L Melamed, N Gil, MJ Goldrich, R Kadir… - Nature …, 2019 - nature.com
Chromodomain helicase DNA binding protein 2 (Chd2) is a chromatin remodeller implicated
in neurological disease. Here we show that Chaserr, a highly conserved long noncoding …

Genetic determinants of survival in progressive supranuclear palsy: a genome-wide association study

E Jabbari, S Koga, RR Valentino, RH Reynolds… - The Lancet …, 2021 - thelancet.com
Background The genetic basis of variation in the progression of primary tauopathies has not
been determined. We aimed to identify genetic determinants of survival in progressive …

Single-cell causal network inferred by cross-mapping entropy

L Li, R Xia, W Chen, Q Zhao, P Tao… - Briefings in …, 2023 - academic.oup.com
Gene regulatory networks (GRNs) reveal the complex molecular interactions that govern cell
state. However, it is challenging for identifying causal relations among genes due to noisy …

Mammalian RNA decay pathways are highly specialized and widely linked to translation

AC Tuck, A Rankova, AB Arpat, LA Liechti, D Hess… - Molecular Cell, 2020 - cell.com
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many
diseases. This complex system is challenging to study, particularly in mammals, where it …

TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data

J Kim, S T. Jakobsen, KN Natarajan… - Nucleic acids …, 2021 - academic.oup.com
Accurate prediction of gene regulatory rules is important towards understanding of cellular
processes. Existing computational algorithms devised for bulk transcriptomics typically …