Investigating the Structural and Functional Roles of Transcriptionally Active Rice Transposons

Investigating the Structural and Functional Roles of Transcriptionally Active Rice Transposons

Alvin Sherman Library

Transposable elements (TEs) are crucial contributors to genome dynamics, evolution, gene structure, and regulation of gene expression. Once considered "junk DNA," TEs are now recognized for their significant roles in genome function and organization. TEs are epigenetically regulated through chromatin modifications, genomic imprinting, and the production of small RNAs and long non-coding RNAs (lncRNAs), which in turn can influence gene expression. Despite a wealth of data from sequencing projects advancing TE research, their large size—often exceeding the read lengths of many sequencing platforms—has limited comprehensive analysis. Moreover, the high copy number and sequence similarity (often >80%) within TE families can lead to misinterpretations and challenges in accurate annotation. Technologies like PacBio and Oxford Nanopore, which generate long reads, offer better coverage of transposons and high-quality genome assemblies. In this study, we utilize a PacBio RNA-seq dataset from Oryza sativa var. Nipponbare to investigate transcriptionally active, full-length transposons in the rice genome. We identify Genes Associated with Transposable Elements (GATEs) and correlate their distribution and expression with TE coverage. Our findings provide insights into the role of active TEs in the rice genome, with a focus on whether these element preferentially insert into housekeeping genes, inducible genes, or transcription factors.