Athaliana_1001genomes

Genomics

A long-term focus of our laboratory has been to build genetic resources and tools in Arabidopsis thaliana. In collaboration with the Nordborg lab, we have established that A. thaliana has patterns of linkage disequilibrium well suited for GWAS mapping and have genotyped sets of accessions to allow mapping by members of the community.

We have made extensive collections of A. thaliana accessions, and made these available as well. We are currently collaborating on the 1001 Genome Project to sequence ~1100 A. thaliana accessions. These efforts have provided many opportunities to address questions in plant genomics and population structure.

We have recently published a paper profiling the transcriptome-wide patterns of m6A editing in two accessions of A. thaliana, in collaboration with Chuan He’s group in the department of Chemistry at the University of Chicago.  m6A mRNA editing is essential for plant development, but the role this editing mark plays in the cell is still unknown.   We found that m6A editing in plants is distinct from editing in yeast and mammals, enriched not only around the stop codon and within 3′-untranslated regions, but also around the start codon.

(a) Accumulation of m6A-IP reads along transcripts. Each transcript is divided into three parts: 5′ UTRs, CDs and 3′ UTRs. (b) The ​m6A peak distribution within different gene contexts. Left panel: total genes with ​m6A peaks; right panel: genes conserved in human and Arabidopsis.
(a) Accumulation of m6A-IP reads along transcripts. Each transcript is divided into three parts: 5′ UTRs, CDs and 3′ UTRs. (b) The ​m6A peak distribution within different gene contexts. Left panel: total genes with ​m6A peaks; right panel: genes conserved in human and Arabidopsis.

Deposition of this editing mark around the start codon was associated with chloroplast-specific genes and increased mRNA abundance, which suggests a regulatory role for m6A editing in plants distinct from other eukaryotes described to date.

University of Chicago, Dept. of Ecology & Evolution

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