An easy, cost‐effective, and scalable method to deplete human ribosomal RNA for RNA‐seq

A Baldwin, AR Morris, N Mukherjee - Current Protocols, 2021 - Wiley Online Library
RNA sequencing (RNA‐seq) is a powerful and increasingly prevalent method to
characterize and quantify the transcriptome. Ribosomes are extremely abundant, however …

Regulation of mature mRNA levels by RNA processing efficiency

C Henfrey, S Murphy, M Tellier - NAR Genomics and …, 2023 - academic.oup.com
Transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA
cleavage and polyadenylation, regulate the production of mature mRNAs. The carboxyl …

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

AM Chakrabarti, IA Iosub, FCY Lee, J Ule… - Nucleic Acids …, 2023 - academic.oup.com
The structure of mRNA molecules plays an important role in its interactions with trans-acting
factors, notably RNA binding proteins (RBPs), thus contributing to the functional …

[PDF][PDF] Ablation of long noncoding RNA Hoxb3os exacerbates cystogenesis in mouse polycystic kidney disease

I Weisser, K Eckberg, S D'Amico… - Journal of the …, 2023 - journals.lww.com
Background: Autosomal dominant polycystic kidney disease (ADPKD) is a monogenic
disorder characterized by the formation of kidney cysts and is primarily caused by mutations …

Integration of lncRNA and mRNA transcriptome analyses reveals genes and pathways potentially involved in calf intestinal growth and development during the early …

EM Ibeagha-Awemu, DN Do, PL Dudemaine… - Genes, 2018 - mdpi.com
A better understanding of the factors that regulate growth and immune response of the
gastrointestinal tract (GIT) of calves will promote informed management practices in calf …

[HTML][HTML] RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation

R Backofen, J Engelhardt, A Erxleben, J Fallmann… - Journal of …, 2017 - Elsevier
The importance of RNA-based regulation is becoming more and more evident. Genome-
wide sequencing efforts have shown that the majority of the DNA in eukaryotic genomes is …

Functional impacts of non-coding RNA processing on enhancer activity and target gene expression

E Ntini, A Marsico - Journal of molecular cell biology, 2019 - academic.oup.com
Tight regulation of gene expression is orchestrated by enhancers. Through recent research
advancements, it is becoming clear that enhancers are not solely distal regulatory elements …

Activating the chromatin by noncoding RNAs

N Laham-Karam, P Laitinen, TA Turunen… - Antioxidants & redox …, 2018 - liebertpub.com
Significance: The extent and breadth of transcription have recently been uncovered and this
has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and …

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency

VR de Melo Costa, J Pfeuffer, A Louloupi, UAV Ørom… - BMC …, 2021 - Springer
Background Introns are generally removed from primary transcripts to form mature RNA
molecules in a post-transcriptional process called splicing. An efficient splicing of primary …

Epigenetic factors in breast cancer therapy

R Mathur, NK Jha, G Saini, SK Jha, SP Shukla… - Frontiers in …, 2022 - frontiersin.org
Epigenetic modifications are inherited differences in cellular phenotypes, such as cell gene
expression alterations, that occur during somatic cell divisions (also, in rare circumstances …