ArticleGenome research2019
Sequence determinants of polyadenylation-mediated regulation.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- Cross-domain signal grammars of transcription termination.Advanced biotechnology · 2026Review
- Promoter identity shapes splicing outcomes and fidelity.Nature communications · 2026Article
- Annotating the genome at single-nucleotide resolution with DNA foundation models.Nature methods · 2025Article
- RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation.Nature genetics · 2025Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Delineating yeast cleavage and polyadenylation signals using deep learning.Genome research · 2024Article
- Article
- Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease.Nature communications · 2023Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.NAR genomics and bioinformatics · 2023Article
- Deciphering the impact of genetic variation on human polyadenylation using APARENT2.Genome biology · 2022Article
- A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons.Nucleic acids research · 2022Article
- Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.Entropy (Basel, Switzerland) · 2021Review
- New function of a well-known promoter: Enhancer activity of minimal CMV promoter enables efficient dual-cassette transgene expression.The journal of gene medicine · 2021Article
- Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences.Genome biology · 2021Article
- Article
- Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes.Genome research · 2021Article
- The Advances in Deep Learning Modeling of Polyadenylation Codes.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning mutagenesis data set, we gain mechanistic insight into various modes of action by which the cleavage efficiency affects the sensitivity or robustness of the PAS to mutation. Furthermore, we employ motif discovery to identify both known and novel sequence motifs associated with PAS-mediated regulation. By leveraging the large scale of our data, we train a deep learning model for the highly accurate prediction of RNA levels from DNA sequence alone (
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.