Intron retention: importance, challenges, and opportunities

JJL Wong, U Schmitz - Trends in Genetics, 2022 - cell.com
Recent landmark discoveries have underpinned the physiological importance of intron
retention (IR) across multiple domains of life and revealed an unexpected breath of functions …

[HTML][HTML] Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons

Y Yang, R Yang, B Kang, S Qian, X He, X Zhang - Cell reports, 2023 - cell.com
Dysregulation of alternative splicing has been repeatedly associated with
neurodevelopmental disorders, but the extent of cell-type-specific splicing in human neural …

Introns: the “dark matter” of the eukaryotic genome

KN Girardini, AM Olthof, RN Kanadia - Frontiers in Genetics, 2023 - frontiersin.org
The emergence of introns was a significant evolutionary leap that is a major distinguishing
feature between prokaryotic and eukaryotic genomes. While historically introns were …

Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex

J Katahira, T Ohmae, M Yasugi, R Sasaki… - Nucleic Acids …, 2023 - academic.oup.com
To facilitate selfish replication, viruses halt host gene expression in various ways. The
nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the …

FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1

S Cho, Y Chun, L He, CB Ramirez, KS Ganesh… - Molecular Cell, 2023 - cell.com
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell
growth that stimulates macromolecule synthesis through transcription, RNA processing, and …

hGRAD: A versatile “one-fits-all” system to acutely deplete RNA binding proteins from condensates

B Arnold, RJ Riegger, EK Okuda, I Slišković… - Journal of Cell …, 2023 - rupress.org
Nuclear RNA binding proteins (RBPs) are difficult to study because they often belong to
large protein families and form extensive networks of auto-and crossregulation. They are …

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

JK David, SK Maden, MA Wood, RF Thompson… - Genome biology, 2022 - Springer
Background There is growing interest in retained introns in a variety of disease contexts
including cancer and aging. Many software tools have been developed to detect retained …

SpliceWiz: interactive analysis and visualization of alternative splicing in R

ACH Wong, JJL Wong, JEJ Rasko… - Briefings in …, 2024 - academic.oup.com
Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform
diversity in eukaryotes. However, the analysis and visualization of AS events from RNA …

Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome

L Hannes, M Atzori, A Goldenberg, J Argente… - Genetics in …, 2024 - Elsevier
Purpose Oral-facial-digital (OFD) syndromes are genetically heterogeneous developmental
disorders, caused by pathogenic variants in genes involved in primary cilia formation and …

Alternative splicing analysis benchmark with DICAST

A Fenn, O Tsoy, T Faro, FLM Rößler… - NAR genomics and …, 2023 - academic.oup.com
Alternative splicing is a major contributor to transcriptome and proteome diversity in health
and disease. A plethora of tools have been developed for studying alternative splicing in …