Dissertation
WHOLE TRANSCRIPTOME TERMINI SITE SEQUENCING, ALTERNATIVE POLYADENYLATION SITE MAPPING AND RE-ANNOTATION OF X. TROPICALIS GENES
Doctor of Philosophy (PhD), Washington State University
01/2016
Handle:
https://hdl.handle.net/2376/117540
Abstract
Alterative polyadenylation (APA) is one of the crucial factors affecting post-transcriptional stability, localization and translation of transcripts. Global APA changes have been associated with embryo development, cancer activation and other important biological processes. Although Xenopus tropicalis is an important amphibian model for developmental biology, no global APA profiles have been reported in the species.
The Whole Transcriptome Termini Site Sequencing (WTTS-seq) method captured the 3’-ends of transcripts, which were used to study poly(A) (pA) sites in X. tropicalis. This unique method not only detected pA, but it also profiled gene expression in one strike. We found that the Spearman correlation was 0.965 between gene expression values of WTTS-seq technical replicates, and 0.912 between WTTS-seq and RNA-seq (RNA sequencing). More than 85% of the detected pAs were located within 5 bp of the center of each pA cluster.
However, one major obstacle in WTTS-seq data analysis is the incomplete genome annotation of X. tropicalis 3’UTR (3’ untranslated region). Among the annotated genes on Xenbase9.0, only 50.3% possessed 3’UTR. Therefore, to improve the current Xenbase9.0 genome annotation, we integrated comprehensive datasets including Iso-seq, WTTS-seq, RNA-seq, and NCBI mRNA. We named this annotation WSU9.1, which is posted at http://134.121.247.55/jbrowse/tropicalis/ for the benefit of the research community. Compared to Xenbase9.0 annotation, 68.5% of genes in the WSU9.1 annotation had 3’UTR annotated. Furthermore, we increased the 3’UTR length from 534 bp to 806 bp and improved the annotation rate of WTTS-seq detected pAs from 71% to 80%.
In brief, our WTTS-seq and other datasets significantly improved the annotation of protein coding genes in X. tropicalis, especially in the 3’UTR. The analysis of APA dynamics and regulation during the early embryo development of X. tropicalis can be greatly facilitated with this improved 3’UTR annotation. Combining APA dynamics with changes in miRNA binding sites (small RNA sequencing data available in SRA database) will also open new doors in the future research of X. tropicalis embryo development.
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Details
- Title
- WHOLE TRANSCRIPTOME TERMINI SITE SEQUENCING, ALTERNATIVE POLYADENYLATION SITE MAPPING AND RE-ANNOTATION OF X. TROPICALIS GENES
- Creators
- RUI LI
- Contributors
- Zhihua Jiang (Advisor)John J. Wyrick (Committee Member)Min Du (Committee Member)Omar Cornejo (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Department of Animal Sciences
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Number of pages
- 126
- Identifiers
- 99900581831401842
- Language
- English
- Resource Type
- Dissertation