DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.
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Acknowledgements We thank Penny Kianian and Nelson Garcia for critical reading and editing suggestions. We are also grateful for the comments from the reviewer. This work was supported by successive grants from the National Science Foundation (IOS: 1025881, IOS: 1546792) to Wojciech Pawlowski (Cornell University, NY), Shahr-yar Kianian (USDA-ARS Cereal Disease Laboratory), Joann Mudge [NCGR (National Center for Genome Resources, Santa Fe, New Mexico)], the late Ernest Retzel (NCGR), Jaroslaw Pillardy (Cornell University) and Changbin Chen (University of Minnesota).