Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria.

RNA editing in mitochondria and chloroplasts of land plants alters transcript sequences by site-specific conversions of cytidines into uridines. RNA editing frequencies vary extremely between land plant clades, ranging from zero in some liverworts to more than 2,000 sites in lycophytes. Unique pentatricopeptide repeat (PPR) proteins with variable domain extension (E/E+/DYW) have recently been identified as specific editing site recognition factors in model plants. The distinctive functions of these PPR protein domain additions have remained unclear, although deaminase function has been proposed for the DYW domain. To shed light on diversity of RNA editing and DYW proteins at the origin of land plant evolution, we investigated editing patterns of the mitochondrial nad5, nad4, and nad2 genes in a wide sampling of more than 100 liverworts and mosses using the recently developed PREPACT program (www.prepact.de) and exemplarily confirmed predicted RNA editing sites in selected taxa. Extreme variability in RNA editing frequency is seen both in liverworts and mosses. Only few editings exist in the liverwort Lejeunea cavifolia or the moss Pogonatum urnigerum whereas up to 20% of cytidines are edited in the liverwort Haplomitrium mnioides or the moss Takakia lepidozioides. Interestingly, the latter are taxa that branch very early within their respective clades. Amplicons targeting the E/E+/DYW domains and subsequent random clone sequencing show DYW domains among bryophytes to be highly conserved in comparison with their angiosperm counterparts and to correlate well with RNA editing frequencies regarding their diversities. We propose that DYW proteins are the key players of RNA editing at the origin of land plants.

DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients.

In addition to genetic predisposition, environmental and lifestyle factors contribute to the pathogenesis of type 2 diabetes (T2D). Epigenetic changes may provide the link for translating environmental exposures into pathological mechanisms. In this study, we performed the first comprehensive DNA methylation profiling in pancreatic islets from T2D and non-diabetic donors. We uncovered 276 CpG loci affiliated to promoters of 254 genes displaying significant differential DNA methylation in diabetic islets. These methylation changes were not present in blood cells from T2D individuals nor were they experimentally induced in non-diabetic islets by exposure to high glucose. For a subgroup of the differentially methylated genes, concordant transcriptional changes were present. Functional annotation of the aberrantly methylated genes and RNAi experiments highlighted pathways implicated in ß-cell survival and function; some are implicated in cellular dysfunction while others facilitate adaptation to stressors. Together, our findings offer new insights into the intricate mechanisms of T2D pathogenesis, underscore the important involvement of epigenetic dysregulation in diabetic islets and may advance our understanding of T2D aetiology.

Introducing intron locus cox1i624 for phylogenetic analyses in Bryophytes: on the issue of Takakia as sister genus to all other extant mosses.

Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), including the mosses. A final conclusion on the most basal lineages of mosses, for which genera such as Sphagnum and Takakia are the most likely candidates, is lacking. We have now investigated cox1i624, a mitochondrial group I intron conserved between the moss Physcomitrella patens and the liverwort Marchantia polymorpha. Focusing on a sampling of liverwort and moss genera, which had previously been identified as early branching taxa in their respective clades, we find that group I intron cox1i624 is universally conserved in all 33 mosses and 11 liverworts investigated. The group I intron core secondary structure is well conserved between the two ancient land plant clades. However, whereas dramatic size reductions are seen in the moss phylogeny, exactly the opposite is observed for liverworts. The cox1i624g1 locus was used for phylogenetic tree reconstruction also in combination with data sets of nad5i753g1 as well as chloroplast loci rbcL and rps4. The phylogenetic analyses revealed (i) very good support for the Treubiopsida as sister clade to all other liverworts, (ii) a sister group relationship of the nematodontous Tetraphidopsida and Polytrichopsida and (iii) two rivalling hypotheses about the basal-most moss genus with mitochondrial loci suggesting an isolated Takakia as sister to all other mosses and chloroplast loci indicating a Takakia-Sphagnum clade.

Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature.

Transcripts in mitochondria and chloroplasts of land plants are modified through RNA editing, the exchanges of pyrimidines-a post-transcriptional process that may affect more than 1,000 sites in the mitochondrial transcriptomes of some plant species. RNA editing mainly acts as a correcting mechanism to re-create evolutionary conserved coding sequences on mRNA level and can be reasonably well predicted in new plant organelle gene sequence data. Identification and annotation of RNA editing sites is cumbersome and error-prone for larger data sets or organelle sequences subject to highly frequent RNA editing. We here present PREPACT, WWW-accessible at http://www.prepact.de , which allows prediction, analysis, annotation and graphical display of RNA editing sites for both directions of pyrimidine exchanges, using the recently proposed RNA editing nomenclature. PREPACT offers prediction of RNA editing, analysis of partial editing in cDNA pools and a BLASTX mode for simultaneous prediction of genes and RNA editing sites in novel sequences. Output options include (i) lists and annotations of RNA editing sites, (ii) sequence alignments with user-controlled color highlighting of editings, (iii) graphical displays of RNA editing in sequences and alignments. Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses.