The recent discoveries of RNA interference and related RNA silencing pathways have revolutionized our understanding of gene regulation. RNA interference has been used as a research tool to control the expression of specific genes in numerous experimental organisms and has potential as a therapeutic strategy to reduce the expression of problem genes. At the heart of RNA interference lies a remarkable RNA processing mechanism that is now known to underlie many distinct biological phenomena.

Revealing the world of RNA interference

During the mid-twentieth century Conrad Waddington proposed his ontogenic concept of canalization, and suggested that epigenetic mechanisms might serve as a means of metastable memory imposed on the genetic material during differentiation. Subsequently, Waddington's theories have received substantial acknowledgment during the first decade of the twenty-first century, with numerous studies unraveling the important contributions of epigenetic mechanisms and the epigenomic control of differentiation. The early embryogenesis and primordial germ cell development have received much attention as developmental stages with extensive epigenomic reprogramming. In both developmental phases, the epigenomic landscape of chromosomes is rapidly and dramatically altered, and this goes along with a substantial change in the developmental potential of cells. In this chapter, a summary is provided of the current knowledge of epigenetic reprogramming mechanisms. These are discussed in line with biological concepts, and with the role of DNA methylation in particular.


Keywords:

Zygote;
Chromatin;
Epigenome;
Genomic imprints;
Epigenetic reprogramming

Epigenetic Reprogramming in Mammalian Development

https://www.cell.com/cell/pdf/S0092-8674(02)00807-3.pdf

DEMETER, a DNA Glycosylase Domain Protein, Is Required for Endosperm Gene Imprinting and Seed Viability in Arabidopsis

Active DNA demethylation is involved in many vital developmental and physiological processes of plants and animals. Recent genetic and biochemical studies in Arabidopsis have demonstrated that a subfamily of DNA glycosylases function to promote DNA demethylation through a base excision-repair pathway. These specialized bifunctional DNA glycosylases remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, resulting in a gap that is then filled with an unmethylated cytosine nucleotide by as yet unknown DNA polymerase and ligase enzymes. Evidence suggests that active DNA demethylation in mammalian cells is also mediated at least in part by a base excision repair pathway where the AID/Apobec family of deaminases convert 5-methylcytosine to thymine followed by G/T mismatch repair by the DNA glycosylase MBD4 or TDG. This review also discusses other possible mechanisms of active DNA demethylation, how genome DNA methylation status might be sensed to regulate the expression of demethylase genes, and the targeting of demethylases by small RNAs.

/pdf/active-dna-demethylation-mediated-by-dna-glycosylases-3xkvtv5wze.pdf

Active DNA demethylation mediated by DNA glycosylases.

http://fischerlab.berkeley.edu/sites/default/files/fischerlab/Gehring_2006.pdf

DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation

Higher plant reproduction is unique because two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, a tissue that supports embryo de- velopment. To understand mechanisms that initiate repro- duction, we isolated a mutation in Arabidopsis, f644, that allows for replication of the central cell and subsequent endosperm development without fertilization. When mutant f644 egg and central cells are fertilized by wild-type sperm, embryo development is inhibited, and endosperm is overpro- duced. By using a map-based strategy, we cloned and se- quenced the F644 gene and showed that it encodes a SET- domain polycomb protein. Subsequently, we found that F644 is identical to MEDEA (MEA), a gene whose maternal-derived allele is required for embryogenesis (Grossniklaus, U., Vielle- Calzada, J.-P., Hoeppner, M. A. & Gagliano, W. B. (1998) Science 280, 446-450). Together, these results reveal functions for plant polycomb proteins in the suppression of central cell proliferation and endosperm development. We discuss models to explain how polycomb proteins function to suppress en- dosperm and promote embryo development.

Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis (reproductionyembryoyseedyapomixis)

The present invention provides polynucleotides that control endosperm development in plants

Nucleic acids that control seed and fruit development in plants

Nucleic acids that control endosperm development in plants

Method of enhancing endosperm development in a plant

L'invention concerne des techniques qui permettent de reguler le developpement de l'endosperme chez les vegetaux.

Tomohiro Kiyosue

Papers

Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis (reproductionyembryoyseedyapomixis)

Nucleic acids that control seed and fruit development in plants

Nucleic acids that control endosperm development in plants

Method of enhancing endosperm development in a plant

Acides nucleiques regulant le developpement des graines et des fruits chez les vegetaux