ArticleMolecular systems biology2016
Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation.
Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Deep learning in structural bioinformatics: current applications and future perspectives.Briefings in bioinformatics · 2024Review
- Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.Genome research · 2023Article
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.Genomics, proteomics & bioinformatics · 2022Article
- CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference.Nucleic acids research · 2022Article
- Molecular and evolutionary processes generating variation in gene expression.Nature reviews. Genetics · 2021Review
- Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice.Frontiers in cell and developmental biology · 2021Article
- Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.Methods in enzymology · 2021Article
- Pan-tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation.Molecular systems biology · 2020Article
- Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles.BioMed research international · 2020Article
- DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.Bioinformatics (Oxford, England) · 2019Article
- Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver.G3 (Bethesda, Md.) · 2018Article
- A compendium of conserved cleavage and polyadenylation events in mammalian genes.Genome research · 2018Article
- Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation.Molecular systems biology · 2016Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative polyadenylation (APA), which is regulated by both cis-elements and trans-factors, plays an important role in post-transcriptional regulation of eukaryotic gene expression. However, comparing to the extensively studied transcription and alternative splicing, the extent of APA divergence during evolution and the relative cis- and trans-contribution remain largely unexplored. To directly address these questions for the first time in mammals, by using deep sequencing-based methods, we measured APA divergence between C57BL/6J and SPRET/EiJ mouse strains as well as allele-specific APA pattern in their F1 hybrids. Among the 24,721 polyadenylation sites (pAs) from 7,271 genes expressing multiple pAs, we identified 3,747 pAs showing significant divergence between the two strains. After integrating the allele-specific data from F1 hybrids, we demonstrated that these events could be predominately attributed to cis-regulatory effects. Further systematic sequence analysis of the regions in proximity to cis-divergent pAs revealed that the local RNA secondary structure and a poly(U) tract in the upstream region could negatively modulate the pAs usage.
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