A survey on methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq, and single-cell RNA-seq

W Ye, Q Lian, C Ye, X Wu - Genomics, Proteomics & …, 2023 - academic.oup.com
Alternative polyadenylation (APA) plays important roles in modulating mRNA stability,
translation, and subcellular localization, and contributes extensively to shaping eukaryotic …

Alternative polyadenylation is a Novel Strategy for the regulation of Gene expression in response to stresses in plants

J Wu, L Ma, Y Cao - International Journal of Molecular Sciences, 2023 - mdpi.com
Precursor message RNA requires processing to generate mature RNA. Cleavage and
polyadenylation at the 3′-end in the maturation of mRNA is one of key processing steps in …

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Y Long, B Zhang, S Tian, JJ Chan, J Zhou, Z Li… - Genome …, 2023 - genome.cshlp.org
Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with
different 3′ ends, which is dynamic across different cell types or conditions. Many …

Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy

MA Waldrop, SA Moore, KD Mathews… - Human …, 2022 - Wiley Online Library
DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with
high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of …

InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data

X Liu, H Chen, Z Li, X Yang, W Jin, Y Wang… - Nature …, 2024 - nature.com
Alternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has
been implicated in diverse biological processes and diseases, as it can produce noncoding …

Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease

AM Jobbins, N Haberman, N Artigas… - Nucleic Acids …, 2022 - academic.oup.com
Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and
the regulation of gene expression in eukaryotic cells. While defects in pre-mRNA processing …

FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues

Q Shi, X Li, Y Liu, Z Chen, X He - Nucleic Acids Research, 2024 - academic.oup.com
Regulatory processes at the RNA transcript level play a crucial role in generating
transcriptome diversity and proteome composition in human cells, impacting both …

ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues

X Ma, S Cheng, R Ding, Z Zhao, XD Zou… - Nucleic Acids …, 2023 - academic.oup.com
Functional interpretation of disease-associated non-coding variants remains a significant
challenge in the post-GWAS era. Our recent study has identified 3′ UTR alternative …

Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers

Z Zhao, Q Xu, R Wei, L Huang, W Wang… - Nucleic acids …, 2021 - academic.oup.com
Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through
various mechanisms depending on their genomic location. While somatic SNVs near …

The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens

D Oreper, S Klaeger, S Jhunjhunwala… - Seminars in …, 2023 - Elsevier
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer
therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of …