Alternative splicing regulatory networks: functions, mechanisms, and evolution

J Ule, BJ Blencowe - Molecular cell, 2019 - cell.com
High-throughput sequencing-based methods and their applications in the study of
transcriptomes have revolutionized our understanding of alternative splicing. Networks of …

Differential fates of introns in gene expression due to global alternative splicing

A Kumari, S Sedehizadeh, JD Brook, P Kozlowski… - Human genetics, 2022 - Springer
The discovery of introns over four decades ago revealed a new vision of genes and their
interrupted arrangement. Throughout the years, it has appeared that introns play essential …

[HTML][HTML] Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

KA Reimer, CA Mimoso, K Adelman, KM Neugebauer - Molecular cell, 2021 - cell.com
Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To
determine how co-transcriptional splicing is integrated with transcription elongation and 3 …

The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis

Q Lv, J Qiu, J Liu, Z Li, W Zhang, Q Wang… - The Plant …, 2020 - Wiley Online Library
Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the
most famous medicinal plants in Eastern China. Here, we report a chromosome‐level …

Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers

K Eldjárn Hjörleifsson, DK Sullivan, NP Swarna… - BioRxiv, 2022 - biorxiv.org
In single-cell and single-nucleus RNA sequencing, the coexistence of nascent
(unprocessed) and mature (processed) mRNA poses challenges in accurate read mapping …

A novel role of U1 snRNP: splice site selection from a distance

RN Singh, NN Singh - Biochimica et Biophysica Acta (BBA)-Gene …, 2019 - Elsevier
Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes.
However, understanding the mechanism by which exon-intron boundaries are defined …

Timing is everything: advances in quantifying splicing kinetics

HE Merens, K Choquet, AR Baxter-Koenigs… - Trends in Cell …, 2024 - cell.com
Splicing is a highly regulated process critical for proper pre-mRNA maturation and the
maintenance of a healthy cellular environment. Splicing events are impacted by ongoing …

Recursive splicing discovery using lariats in total RNA sequencing

ER Hoppe, DB Udy, RK Bradley - Life Science Alliance, 2023 - life-science-alliance.org
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in
segments via multiple splicing reactions. Relatively few recursive splice sites have been …

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq

DK Sullivan, KE Hjörleifsson, NP Swarna… - Nucleic Acids …, 2024 - academic.oup.com
In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent
(unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in …

The unusual gene architecture of polyubiquitin is created by dual-specific splice sites

C Duan, T Mooney, L Buerer, C Bowers, S Rong… - Genome Biology, 2024 - Springer
Background The removal of introns occurs through the splicing of a 5′ splice site (5′ ss)
with a 3′ splice site (3′ ss). These two elements are recognized by distinct components of …