Mass spectrometry-based draft of the mouse proteome.

The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo.

Molecular properties of epimutation hotspots.

Mistakes in the maintenance of CG methylation are a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harbouring localized 'epimutation hotspots'. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states that map to subregions of gene body methylation genes.

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.

Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data.

Background: Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells. These surveys can easily generate hundreds or even thousands of WGBS datasets in a single study.

A suppressor of axillary meristem maturation promotes longevity in flowering plants.

Post-embryonic development and longevity of flowering plants are, for a large part, determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs). The genes that are associated with AM maturation and underlie the differences between monocarpic (reproduce once and die) annual and the longer-lived polycarpic (reproduce more than once) perennial plants are still largely unknown. Here we identify a new role for the Arabidopsis AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation.

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation.

In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing in a species naturally lacking expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the transgene.

Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication.

The evolution of plants is characterized by whole-genome duplications, sometimes closely associated with the origin of large groups of species. The gamma (γ) genome triplication occurred at the origin of the core eudicots, which comprise ∼75% of flowering plants. To better understand the impact of whole-genome duplication, we studied the protein interaction network of MADS domain transcription factors, which are key regulators of reproductive development.

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana.

Several recent studies indicate that small Open Reading Frames (sORFs) embedded within multiple eukaryotic non-coding RNAs can be translated into bioactive peptides of up to 100 amino acids in size. However, the functional roles of the 607 Stress Induced Peptides (SIPs) previously identified from 189 Transcriptionally Active Regions (TARs) in Arabidopsis thaliana remain unclear. To provide a starting point for functional annotation of these plant-derived peptides, we performed a large-scale prediction of peptide binding sites on protein surfaces using coarse-grained peptide docking.

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

Background: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana.