Poster abstracts
Poster number 100 submitted by Arden Bui
AtRTD2 versus AtRTD3: how Serine/Arginine-rich 45 affects the sperm transcriptome in Arabidopsis thaliana based on 2 versions of transcriptome reference
Arden Bui (Biochemistry Program, Department of Biology, St. Bonaventure University, St. Bonaventure, NY 14778), Christopher Chin (Biochemistry Program, Department of Biology, St. Bonaventure University, St. Bonaventure, NY 14778), Xiao-Ning Zhang (Biochemistry Program, Department of Biology, St. Bonaventure University, St. Bonaventure, NY 14778)
Abstract:
In flowering plant, pollen grains are the male gametophyte that produces sperms. Studies have shown that there is a transcriptome switch during pollen mitosis II when producing mature pollen grains. Arabidopsis Serine/Arginine-rich 45 (SR45) is a splicing regulator that is highly expressed during pollen development. The sr45-1 null mutant plant exhibits pleiotropic phenotypes throughout the life cycle, including a mild sterility and a reduced seed set. To investigate SR45’s effects in reproduction, sperm cells were isolated from wild-type and the sr45-1 mutant mature pollen using FACS. Using the 3D RNA-seq App, the bulk sperm transcriptome was sequenced and compared between the two genotypes using 2 versions of Arabidopsis transcriptome reference: AtRTD2 and AtRTD3. From the RNA-seq data analyses, the majority of differentially expressed (DE) genes overlapped between AtRTD2 and AtRTD3. The analyses suggest that SR45 promoted the expression of genes for pollen tube development and suppressed the expression of genes involved in pollen sperm cell differentiation. Several sperm markers are used to validate this transcriptome profile. Differentially expressed transcripts are overrepresented in mRNA splicing and phosphorelay signal transduction using both AtRTD2 and AtRTD3. This suggests that SR45-dependent AS events may preferentially contribute to the sperm identity in mature pollen grains via maintaining a homeostasis in alternative splicing and phosphorelay signal transduction. About 30% overlap (28 genes) was found between differential alternatively spliced (DAS) genes using AtRTD2 versus AtRTD3. Some of the DAS genes showed significant switches in isoform abundance and potential structural changes in the predicted protein products. Among genes exhibiting isoform switches, both RAD4 and RAD51 are of interest. Transgenic lines with a constitutive promoter and transgenic lines with the native promoter were developed to explore possible isoform-specific functional differences between RAD4 and RAD51 isoforms.
References:
Honys, D. & Twell, D. (2004). Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biology, 5(11), R85.
Guo,W. et al. (2020) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA biology, 1–14.
Zhang, R., et al. (2022). A high-resolution single-molecule sequencing-based arabidopsis transcriptome using novel methods of iso-seq analysis. Genome Biology, 23(1).
Zhang R, et al. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res.45(9):5061-5073.
Keywords: transcriptome analysis, alternative splicing, Arabidopsis thaliana