Emerging roles of histone modifications and HDACs in RNA splicing

R Rahhal, E Seto - Nucleic acids research, 2019 - academic.oup.com
Histone modifications and RNA splicing, two seemingly unrelated gene regulatory
processes, greatly increase proteome diversity and profoundly influence normal as well as …

The determinants of alternative RNA splicing in human cells

TV Ramanouskaya, VV Grinev - Molecular Genetics and Genomics, 2017 - Springer
Alternative splicing represents an important level of the regulation of gene function in
eukaryotic organisms. It plays a critical role in virtually every biological process within an …

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

R Tuladhar, Y Yeu, J Tyler Piazza, Z Tan… - Nature …, 2019 - nature.com
The introduction of insertion-deletions (INDELs) by non-homologous end-joining (NHEJ)
pathway underlies the mechanistic basis of CRISPR-Cas9-directed genome editing …

Recursive splicing in long vertebrate genes

CR Sibley, W Emmett, L Blazquez, A Faro… - Nature, 2015 - nature.com
It is generally believed that splicing removes introns as single units from precursor
messenger RNA transcripts. However, some long Drosophila melanogaster introns contain …

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

A Tareen, M Kooshkbaghi, A Posfai, WT Ireland… - Genome biology, 2022 - Springer
Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep
mutational scanning experiments on proteins and massively parallel reporter assays on …

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

AN Brooks, MO Duff, G May, L Yang… - Genome …, 2015 - genome.cshlp.org
Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA
sequence elements and activate or repress adjacent exons. Here, we used RNA …

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

L de la Fuente, Á Arzalluz-Luque, M Tardáguila… - Genome Biology, 2020 - Springer
Recent advances in long-read sequencing solve inaccuracies in alternative transcript
identification of full-length transcripts in short-read RNA-Seq data, which encourages the …

The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors

JW Lu, TD Plank, F Su, XJ Shi, C Liu… - The Journal of …, 2016 - Am Soc Clin Investig
Inflammatory myofibroblastic tumors (IMTs) are characterized by myofibroblast proliferation
and an inflammatory cell infiltrate. Little is known about the molecular pathways that …

Altered splicing factor and alternative splicing events in a mouse model of diet-and polychlorinated biphenyl-induced liver disease

BJ Petri, KM Piell, B Wahlang, KZ Head… - Environmental …, 2023 - Elsevier
Non-alcoholic fatty liver disease (NAFLD) is associated with human environmental exposure
to polychlorinated biphenyls (PCBs). Alternative splicing (AS) is dysregulated in steatotic …

Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing

T Horn, A Gosliga, C Li, M Enculescu… - npj Systems Biology and …, 2023 - nature.com
Alternative splicing is an important step in eukaryotic mRNA pre-processing which increases
the complexity of gene expression programs, but is frequently altered in disease. Previous …