A Bioinformatics Methodology for the Annotation and Analysis of Sperm Chromatin Remodeling Proteins in Sequenced Drosophila Species

Author

Zain A. AlviFollow

Date of Award

Spring 12-16-2016

Degree Type

Dissertation

Degree Name

PhD Molecular Bioscience

Department

Biology

Advisor

Angela V. Klaus, Ph.D ; Tin-Chun Chu, Ph.D

Committee Member

Jane L. Ko, Ph.D

Committee Member

Carolyn Bentivegna, Ph.D

Committee Member

Brian Nichols, Ph.D

Committee Member

Valeria Schawaroch, Ph.D

Keywords

spermatogenesis, Tpl94D, transition proteins, RNA-Seq, gene expression, DEG

Abstract

Spermatogenesis is the process by which mature functional spermatozoa are formed, and is initiated in the stem cell niche of the testes. During the post-meiotic stage of spermatogenesis, spermiogenesis, transition proteins facilitate the transformation of chromatin from a histone-based nucleosome structure to a protamine-based nucleosome structure. This study is aimed at analyzing genomic, transcript, and protein sequences of transition proteins in 13 sequenced Drosophila species. The Drosophila melanogaster spermatid specific transition protein-like protein (Tpl^94D) was used as the reference sequence in this study. An extensive bioinformatics approach was employed in establishing the Tpl^94D orthologs. We identified Tpl^94D orthologs in the melanogaster subgenus (D. simulans, D. sechellia, D. erecta, and D. yakuba), D. ananassae, D. miranda, and D. pseudoobscura. In contrast, no Tpl^94D orthologs were identified in D. persmilis, D. willistoni, or the Drosophila subgenus (D. mojavensis, D. virilis, and D. grimshawi) due to their evolutionary distance from D. melanogaster. Differential gene expression analysis of the testes versus the ovaries showed high expression of Tpl^94D orthologs in the testes for in D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. miranda, and D. pseudoobscura. Further RNA-Seq analysis using the NIH Isoform Two-Step Analysis revealed higher testes expression for D. melanogaster Tpl^94D isoform A (164 amino acids) than D. melanogaster Tpl^94D isoform B (163 amino acids). We confirmed the conservation of a HMG box/DNA binding domain among transition protein (Tpl^94D ) orthologs and Drosophila male specific transcript protamine-like protein (MST35Ba/MST35Bb) orthologs. Overall, this study represents the first large-scale, single-genus invertebrate dataset for transition proteins and provides the basis for a fine-grained analysis of their evolution.

Recommended Citation

Alvi, Zain A., "A Bioinformatics Methodology for the Annotation and Analysis of Sperm Chromatin Remodeling Proteins in Sequenced Drosophila Species" (2016). Seton Hall University Dissertations and Theses (ETDs). 2253.
https://scholarship.shu.edu/dissertations/2253