ArticleJournal of mathematical biology2017
RNA Pol II transcription model and interpretation of GRO-seq data.
Article in Journal of mathematical biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- LIET model: capturing the kinetics of RNA polymerase from loading to termination.Nucleic acids research · 2025Article
- CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.Nature communications · 2023Article
- Connectome and regulatory hubs of CAGE highly active enhancers.Scientific reports · 2023Article
- The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling.JCI insight · 2021Article
- TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Article
- A generative model for the behavior of RNA polymerase.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
A mixture model and statistical method is proposed to interpret the distribution of reads from a nascent transcriptional assay, such as global run-on sequencing (GRO-seq) data. The model is annotation agnostic and leverages on current understanding of the behavior of RNA polymerase II. Briefly, it assumes that polymerase loads at key positions (transcription start sites) within the genome. Once loaded, polymerase either remains in the initiation form (with some probability) or transitions into an elongating form (with the remaining probability). The model can be fit genome-wide, allowing patterns of Pol II behavior to be assessed on each distinct transcript. Furthermore, it allows for the first time a principled approach to distinguishing the initiation signal from the elongation signal; in particular, it implies a data driven method for calculating the pausing index, a commonly used metric that informs on the behavior of RNA polymerase II. We demonstrate that this approach improves on existing analyses of GRO-seq data and uncovers a novel biological understanding of the impact of knocking down the Male Specific Lethal (MSL) complex in Drosophilia melanogaster.
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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.