Reducing reference usage in detection of regulated RNA processing
Abstract/Contents
- Abstract
- RNA sequencing methods have become increasingly sensitive, high-throughput, and cost- effective, resulting in an unprecedented volume of sequencing data accessible to the public. RNA processing events, such as alternative splicing or alternative polyadenylation, leave distinct signatures in RNA-seq reads. However, RNA-seq data is critically underutilized: sequence variation from RNA processing, beyond simple annotated alternative splicing, is most often ignored. We introduce a new statistical method to detect regulated RNA processing from single- cell RNA-seq data, that does not rely on existing gene annotations. Using this method, we detect cell type-specific RNA processing differences in human lung. We also discover developmentally regulated RNA processing changes, including global 3'UTR length changes, in both human spermatogenesis and Arabidopsis thaliana root development. We also demonstrate the use of a fully reference-free statistical method for discovery of regulated sequence variation in plant RNA-seq data. By fully removing the reliance on alignment to detect regulated changes, we can discover condition- and cell type-dependent RNA processing events even when an isoform or entire gene is missing from the reference.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2023; ©2023 |
| Publication date | 2023; 2023 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Meyer, Elisabeth |
|---|---|
| Degree supervisor | Salzman, Julia |
| Thesis advisor | Salzman, Julia |
| Thesis advisor | Das, Rhiju |
| Thesis advisor | Gao, Alex |
| Thesis advisor | Straight, Aaron, 1966- |
| Degree committee member | Das, Rhiju |
| Degree committee member | Gao, Alex |
| Degree committee member | Straight, Aaron, 1966- |
| Associated with | Stanford University, School of Medicine |
| Associated with | Stanford University, Department of Biochemistry |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Elisabeth Meyer. |
|---|---|
| Note | Submitted to the Department of Biochemistry. |
| Thesis | Thesis Ph.D. Stanford University 2023. |
| Location | https://purl.stanford.edu/wg415sg5199 |
Access conditions
- Copyright
- © 2023 by Elisabeth Meyer
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