DNA Methylation Dynamics during Fiber and Ovule Development

DNA methylation is essential for plant and animal development. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide methylcytosine-, mRNA-, and small RNA-sequencing analyses reveal distinct changes in CHH (H=A, T, or C) methylation among different tissues. In ovules CHH hypermethyaltion is associated with small RNA-directed DNA methylation (RdDM) and expression changes of nearby genes in euchromatin. However, the ovule-derived fiber cells not only maintain euchromatic CHH methylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM, which represses TEs and nearby genes. Furthermore, DNA methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. The CHH methylation in promoters mediated by RdDM-dependent and independent pathways could act as a double-lock feedback mechanism to regulate TE and gene expression during ovule and fiber development.