Biology subjects

Rose, A. B.

Publications and source records attributed to Rose, A. B..

3 recordsLinked to original sources

bioRxiv2025

Intron architecture predicts chromatin features in Arabidopsis thaliana

Introns are ubiquitous yet enigmatic features of eukaryotic genomes. They are reported to affect gene expression regulation but the mechanisms remain largely unresolved. Here we investigate the connections between intron architecture and chromatin features - histone marks, histone variants, DNA methylation, and gene expression patterns in Arabidopsis thaliana. We found that first intron positions predict active chromatin marks found near transcription start sites while the number of introns explains different chromatin marks enriched in the core of gene bodies in broadly expressed genes. Notably, gene body chromatin marks exhibit a positional gradient distribution across the ordinal position of exons and introns. We tested these relationships by comparing recent gene duplicates with diverged intron architectures, and confirmed that intron number is positively associated with H3K4me1, H3K36me3, H2A.X, meCG, and broad expression across tissues. Our results suggest two distinct mechanisms in which plant intron architecture may affect chromatin states and ultimately gene expression, motivating future experiments: intron positions early in genes may affect the establishment of activating histone marks around transcription start sites, while a greater total number of introns may increase the number of intronic motifs and gene length in general, allowing for the increased accumulation of gene-body-associated chromatin features. Short summaryHere we investigate the association between intron architecture and chromatin features in Arabidopsis thaliana. We found that the position of the first intron is negatively correlated with marks found near the transcription start site and associated with active expression. We also found that the number of introns within genes is correlated with marks found in gene bodies and are associated with actively transcribed genes.

genomics↗

bioRxiv2018

Intron-mediated enhancement is not limited to introns

Certain introns strongly increase mRNA accumulation by a poorly understood mechanism known as Intron-Mediated Enhancement (IME). Introns that boost expression by IME have no effect when located upstream of or more than ~1 Kb downstream from the start of transcription. The sequence TTNGATYTG, which is over-represented in promoter-proximal introns in Arabidopsis thaliana, can convert a non-stimulating intron into one that strongly increases mRNA accumulation. We tested the ability of an intron containing this motif to stimulate expression from different locations and found that it had the same positional requirements as naturally occurring IME introns. The motif also stimulated gene expression from within the 5-UTR and coding sequences of an intronless construct. Furthermore, the 5-UTR of another gene increased expression when inserted into an otherwise non-stimulating intron in coding sequences. These results demonstrate that splicing is not required for intron-mediated enhancement, and suggest that other sequences downstream of the transcription start site in addition to introns may stimulate expression by a similar mechanism.

molecular biology↗

bioRxiv2016

Intron-driven gene expression in the absence of a core promoter in Arabidopsis thaliana

In diverse eukaryotes, certain introns increase mRNA accumulation through the poorly understood mechanism of intron-mediated enhancement (IME). A distinguishing feature of IME is that these introns have no effect from upstream or more than 1 Kb downstream of the transcription start site (TSS). To more precisely define the intron position requirements for IME in Arabidopsis, we tested the effect of the UBQ10 intron on gene expression from 6 different positions surrounding the TSS of a TRP1:GUS fusion. The intron strongly increased expression from all transcribed positions, but had no effect when 204 nt or more upstream of the 5-most TSS. When the intron was located in the 5 UTR, the TSS unexpectedly changed, resulting in longer transcripts. Remarkably, deleting 303 nt of the core promoter, including all known TSSs and all but 18 nt of the 5 UTR, had virtually no effect on the level of gene expression as long as a stimulating intron was included in the gene. When the core promoter was deleted, transcription initiated in normally untranscribed sequences the same distance upstream of the intron as when the promoter was intact. Together, these results suggest that certain introns play unexpectedly large roles in directing transcription initiation and represent a previously unrecognized type of downstream regulatory elements for genes transcribed by RNA polymerase II. This study also demonstrates considerable flexibility in the sequences surrounding the TSS, indicating that the TSS is not determined by promoter sequences alone. These findings are relevant in practical applications where introns are used to increase gene expression and contribute to our general understanding of gene structure and regulation in eukaryotes.

molecular biology↗