Entries by Sunil Kumar

DNA methylation dynamics during early plant life

DNA methylation is extensively reprogrammed in the early embryo and germlines of mammals, whereas flowering plants do not show such extensive resetting except in the endosperm. Active DNA demethylation in the central cell and reduced activity of DNA methyltransferases leads to global hypomethylation of the maternal genome in the endosperm. On the paternal side, the […]

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

Understanding the complex regulatory mechanisms that contribute to germination and seedling establishment requires integration of gene-expression, transcription factors (TFs), DNA methylation, smallRNA data, and their interactions. Narsai et al. describe the first dynamic transcription factor network model of Arabidopsis seed germination over an extensive time-course, showing widespread alternative splicing and changes in known and novel […]

Comparison of the relative potential for epigenetic and genetic variation to contribute to trait stability

Epigenetic variation, both natural and induced, can influence heritable phenotypic variation of complex traits. Understanding the effect of epigenetic changes on trait variation is complicated by the confounding effects of DNA sequence polymorphisms. To overcome this complication, epigenetic recombinant inbred lines (epiRILs) have been developed from parental lines with little or no DNA sequence variation, […]

Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development

Different parts of the seed have distinct genetic origins and functions. The seed coat is maternally derived from ovule integuments, whereas the embryo descends from the fertilized egg and the endosperm from the central cell. Lin et al. profiled the methylome landscape during seed development and germination in Arabidopsis and soybean using laser capture microdissection […]

TET-mediated epimutagenesis of the Arabidopsis thaliana methylome

Natural and induced DNA methylation variations are known to alter gene expression changes that may ultimately be important for agronomically important traits. Epigenetically manipulating plant methylomes to create heritable changes can be invaluable in crop improvement programs. Ji et al. describe the expression of a human ten eleven translocation enzyme (TET) in Arabidopsis thaliana to […]

Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants

Plant DNA methylation in different sequence contexts is catalyzed by distinct types of methyltransferases. METHYLTRANSFERASE 1 (MET1) is responsible for CG methylation, CHROMOMETHYLASE (CMT1, 2, and 3) methylates CHG and CHH, while DOMAINS REARRANGED METHYLTRANSFERASE (DRM1 and 2) methylates in all three contexts through the RNA-directed DNA Methylation (RdDM) pathway. DECREASED DNA METHYLATION1 (DDM1) provides […]

What We’re Reading: April 20th

This week’s issue of What We’re Reading is guest edited by Sunil Kumar Kenchanmane Raju, a postdoc in Chad Niederhuth’s lab at Michigan State University. He is interested in understanding the epigenetic and epigenomic diversity across land plants. Sunil is a postdoc ambassador of ASPB and social media coordinator for the CSHL plant course. This […]

Maternal components of RdDM are required for seed development in Brassica rapa

RNA directed DNA methylation (RdDM) is an epigenetic process in which plant double-strand RNAs are processed into small RNAs (sRNA) that add repressive DNA methylation to homologous DNA sequences. RdDM primarily acts on repetitive DNA and transposable elements (TEs). Despite its important biological functions, loss of RdDM components in Arabidopsis does not show much phenotypic […]

A Kinesin-14 motor activates neocentromeres to promote meiotic drive in maize

Meiotic drive is essentially a subversion of meiosis such that particular regions or alleles are preferentially favored for transmission to the progeny. Abnormal chromosome 10 (Ab10) is a classic example of meiotic drive in maize that converts heterochromatic chromosomal knobs into motile ‘neocentromeres’. When Ab10 is present in the genome, all knobs move earlier and […]