Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
Motivation: Pre-mRNA cleavage and polyadenylation are essential steps for 3′-end
maturation and subsequent stability and degradation of mRNAs. This process is highly …
maturation and subsequent stability and degradation of mRNAs. This process is highly …
A survey on methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq, and single-cell RNA-seq
Alternative polyadenylation (APA) plays important roles in modulating mRNA stability,
translation, and subcellular localization, and contributes extensively to shaping eukaryotic …
translation, and subcellular localization, and contributes extensively to shaping eukaryotic …
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data
ED Shulman, R Elkon - Nucleic acids research, 2019 - academic.oup.com
Alternative polyadenylation (APA) is emerging as an important layer of gene regulation
because the majority of mammalian protein-coding genes contain multiple polyadenylation …
because the majority of mammalian protein-coding genes contain multiple polyadenylation …
APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms
Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. APA is
dynamically regulated under different growth and differentiation conditions. Here, we …
dynamically regulated under different growth and differentiation conditions. Here, we …
Poly (A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation
mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional
gene regulation and is often regulated in a tissue-and/or developmental stage-specific …
gene regulation and is often regulated in a tissue-and/or developmental stage-specific …
[HTML][HTML] Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease
EK Stroup, Z Ji - Nature communications, 2023 - nature.com
The genomic distribution of cleavage and polyadenylation (polyA) sites should be co-
evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation …
evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation …
[HTML][HTML] Biased alternative polyadenylation in human tissues
Background Alternative polyadenylation is one of the mechanisms in human cells that give
rise to a variety of transcripts from a single gene. More than half of the human genes have …
rise to a variety of transcripts from a single gene. More than half of the human genes have …
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples
Motivation Alternative polyadenylation (APA) has been widely recognized as a widespread
mechanism modulated dynamically. Studies based on 3′ end sequencing and/or RNA-seq …
mechanism modulated dynamically. Studies based on 3′ end sequencing and/or RNA-seq …
APASdb: a database describing alternative poly (A) sites and selection of heterogeneous cleavage sites downstream of poly (A) signals
L You, J Wu, Y Feng, Y Fu, Y Guo, L Long… - Nucleic acids …, 2015 - academic.oup.com
Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA)
3′-processing sites depending on the cell and tissue type and/or physiological and …
3′-processing sites depending on the cell and tissue type and/or physiological and …
scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data
Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to
transcriptome diversity and gene expression regulation by affecting mRNA stability …
transcriptome diversity and gene expression regulation by affecting mRNA stability …