Biology subjects

Arneson, R.

Publications and source records attributed to Arneson, R..

3 recordsLinked to original sources

bioRxiv2026

Transcriptional Characterization of Nuclear-Integrated Organellar DNA in Populus

The continuous transfer of organellar DNA into the nuclear genome during eukaryotic evolution has resulted in the widespread occurrence of nuclear plastid DNA insertions (NUPTs) and nuclear mitochondrial DNA insertions (NUMTs). However, their functional significance in nuclear gene expression and genome evolution remains largely unresolved. In this study, we employed Oxford Nanopore Direct RNA Sequencing (DRS) to investigate the transcription of NUPTs and NUMTs in the Populus nuclear genome and compared their transcriptional characteristics with their genome-wide insertion patterns. Our analyses revealed that the majority of transcribed NUPTs and NUMTs are enriched within introns and are co-transcribed with their host or adjacent genes in polycistronic-like transcriptional units. In addition, NUPTs and NUMTs frequently generate intronless transcripts, features reminiscent of their prokaryotic ancestry. We further identified a putatively functional NUPT-derived psbH gene that is unique to P. trichocarpa, providing new insights into the evolution of nuclear-encoded organelle-targeted genes. In addition, we identified transcribed NUPT and NUMT insertion polymorphisms among alleles, suggesting that organellar DNA insertions contribute to allelic variation and may participate in environmental adaptation. Collectively, our findings reveal previously unrecognized roles of NUPT and NUMT transcription in gene regulation, allelic variation, genome evolution, and the emergence of novel genes.

genomics↗

bioRxiv2025

The Polycistronic Transcription Landscape of the Populus Genome

Transcripts spanning multiple gene loci are common in prokaryotes as a feature of polycistronic gene expression but have traditionally been considered rare in eukaryotic nuclear genomes. In this study, using Nanopore direct RNA sequencing (DRS), we identified widespread mRNA transcripts spanning two or more nuclear gene loci in two Populus species, Populus trichocarpa (Nisqually-1) and the hybrid poplar 717 (P. tremula x P. alba). These novel multi-gene-spanning transcripts structurally resemble polycistronic RNAs and are predicted to encode open reading frames (ORFs), including modified and fusion ORFs. Many of these transcripts exhibit tissue-specific, allele-specific, or drought-responsive expression pattern, suggesting potential roles in plant development and environmental adaptation. Functional enrichment and protein localization analyses revealed that genes associated with organelles and membranes are significantly overrepresented within these polycistronic-like (PC-like) transcriptional units. PC-like RNAs also undergo extensive alternative splicing and possess longer polyadenine [poly(A)] tails and fewer N-methyladenosine (mA) modification sites than their monocistronic counterparts. Under drought, dicistronic-like RNAs were more strongly coregulated with the corresponding 5' monocistronic gene than with the 3' monocistronic gene, whereas the two corresponding monocistronic genes exhibited a weaker positive correlation in expression. These findings indicate that transcription and RNA processing at PC-like loci are regulated through mechanisms distinct from those governing prokaryotic polycistronic operons. Collectively, our results reveal pervasive PC-like transcription in plant nuclear genomes and highlight its distinctive molecular features, complex regulation, and potential roles in plant growth and environmental adaptation.

genomics↗

bioRxiv2024

Efficient 3'-end tailing of RNA with modified adenosine for nanopore direct total RNA sequencing

Direct sequencing of total cellular RNA enables a better understanding of a broad spectrum of RNA species controlling cellular processes and organismal function. Current nanopore direct RNA sequencing method, however, only captures polyadenylated RNA for sequencing. To address this issue, we developed a unique 3-end RNA tailing method to capture total RNA for nanopore direct RNA sequencing. Due to the distinct electrical signature of the added tail on nanopore, this method allows simultaneous detection of both non-polyadenylated and polyadenylated RNAs. We demonstrated the effectiveness of this method in capturing the dynamics of transcription and polyadenylation of chloroplast RNAs in plant cell. With its high efficiency in retaining total RNA on nanopore, this method has the potential to be broadly applied to RNA metabolism and functional genomics studies.

genomics↗