Pooled sequencing links variation in transcription factor binding and chromatin accessibility to disease risk
Abstract/Contents
- Abstract
- The second chapter of this thesis focuses on identifying cis-regulatory variants that affect transcription factor (TF) binding. Broadly, we discovered thousands of cis-acting binding quantitative trait loci (bQTLs) that affect TF binding, that CTCF can recruit multiple TFs, and that bQTLs can link genetic variation to 3D-genome architecture and complex disease traits. This chapter uses a pooling-based experimental approach and a custom analysis pipeline to map QTLs that affect TF binding. Chromatin immuno-precipitation followed by high-throughput sequencing (ChIP-seq) in a population of 60-71 genotyped individuals, allows for the genetic mapping of variants affecting TF binding in a systematic way. Those variants that affect binding are likely causal for modifying the binding of the TF to the protein and are therefore, a priori more likely to affect disease phenotypes. Therefore, this framework provides a candidate molecular mechanism by which the variant is acting. The custom pipeline I developed can be used for any pooled data such as ChIP-seq, without any modifications to the pipeline. All scripts and documentation are freely available and can be found here: https://github.com/tehranchi/public . This chapter is from work published in Cell in April 2016. The third chapter uses the same pooling approach and analysis pipeline to investigate a more broad class of QTLs that affect chromatin accessibility (caQTLs). Because these caQTLs mark regions of open chromatin and subsequently actively transcribed regions, they may also contain bQTLs that modify transcription factor binding. Therefore, this approach can be used together with software that can predict TF binding in open regions to obtain a more comprehensive understanding of the binding landscape. Similar to chapter 2, this method focuses on finding cis-regulatory variants that affect chromatin accessibility. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) was performed in 10 global populations of genotyped individuals to allow for the mapping of variants affecting chromatin accessibility. Briefly, in this chapter we found tens of thousands of caQTLs per population, we fine-map shared caQTLs and used them to identify CTCF as the major motif relevant to open chromatin, and we find that caQTLs can link transcription factor binding to chromatin architecture and complex disease traits. This large-scale project with 1000 individuals in total, would not be tractable in the lab without pooling. Using the pooling approach drastically saves time and cost associated with sequencing and reagents. This chapter corresponds to work from a manuscript currently in prep.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2016 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Tehranchi, Ashley |
|---|---|
| Associated with | Stanford University, Department of Biology. |
| Primary advisor | Fraser, Hunter B |
| Thesis advisor | Fraser, Hunter B |
| Thesis advisor | Petrov, Dmitri Alex, 1969- |
| Thesis advisor | Pritchard, Jonathan D |
| Thesis advisor | Snyder, Michael, Ph. D |
| Advisor | Petrov, Dmitri Alex, 1969- |
| Advisor | Pritchard, Jonathan D |
| Advisor | Snyder, Michael, Ph. D |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Ashley Tehranchi. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2016. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2016 by Ashley Tehranchi
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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