Seed genome hypomethylated regions are enriched in transcription factor genes

The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from postfertilization through dormancy and germination for regions that contain <5% or <0.4% bulk methylation in CG, CHG, and CHH contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5-76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor (TF) genes and other developmental genes that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue, and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development, probably by the action of specific TFs and epigenetic events at the chromatin level.

Regulation of fertilization and early seed development

Plant reproduction meetings often deal either with pre-fertilization processes such as flowering and pollen biology or post-fertilization processes such as embryogenesis and seed development. The Biochemical Society Focused Meeting entitled 'Regulation of Fertilization and Early Seed Development' was organized to close this gap and to discuss mechanistic similarities and future research directions in the reproductive processes shortly before, during and after fertilization. As an outcome of the workshop, invited speakers and a few selected oral communication presenters contributed focused reviews and technical articles for this issue of Biochemical Society Transactions. We provide here a short overview of the contents and highlights of the various articles.

(Pro)cambium formation and proliferation: two sides of the same coin?

The body of higher plants is usually pervaded by the (pro)cambium, a reticulate system of meristematic cells harboring the potential for producing vascular tissues at critical times and places. The (pro)cambium thereby provides the basis for the differential modulation of long-distance transport capacities and plant body stability. Distinct regulatory networks responsible for the initiation and proliferation of (pro)cambium cells have been identified. However, although a tight interaction between these networks can be expected, connections have been established only sporadically. Here we highlight recent discoveries of how (pro)cambium development is regulated and discuss possible interfaces between networks regulating two processes: (pro)cambium formation and cambium proliferation.