DNA Methylation Dynamics in Male Germline Development in Brassica Rapa

Overview

Journal Mol Hortic

Date 2025 Mar 3

PMID 40033451

Authors

Jun Zhang

Di Wu

Yating Zhang

Xiaoqi Feng

Hongbo Gao

Affiliations

Soon will be listed here.

Abstract

Dynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants.

References

Long J, Walker J, She W, Aldridge B, Gao H, Deans S . Nurse cell--derived small RNAs define paternal epigenetic inheritance in . Science. 2021; 373(6550). DOI: 10.1126/science.abh0556. View

Pikaard C, Mittelsten Scheid O . Epigenetic regulation in plants. Cold Spring Harb Perspect Biol. 2014; 6(12):a019315. PMC: 4292151. DOI: 10.1101/cshperspect.a019315. View

Yang H, Lu P, Wang Y, Ma H . The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process. Plant J. 2011; 65(4):503-16. DOI: 10.1111/j.1365-313X.2010.04439.x. View

He Z, Ji R, Havlickova L, Wang L, Li Y, Lee H . Genome structural evolution in Brassica crops. Nat Plants. 2021; 7(6):757-765. DOI: 10.1038/s41477-021-00928-8. View

Danecek P, Bonfield J, Liddle J, Marshall J, Ohan V, Pollard M . Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2). PMC: 7931819. DOI: 10.1093/gigascience/giab008. View

Singh J, Mishra V, Wang F, Huang H, Pikaard C . Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway. Mol Cell. 2019; 75(3):576-589.e5. PMC: 6698059. DOI: 10.1016/j.molcel.2019.07.008. View

Lu Y, Song Y, Liu L, Wang T . DNA methylation dynamics of sperm cell lineage development in tomato. Plant J. 2020; 105(3):565-579. DOI: 10.1111/tpj.15098. View

Ooi C, Mantalas G, Koh W, Neff N, Fuchigami T, Wong D . High-throughput full-length single-cell mRNA-seq of rare cells. PLoS One. 2017; 12(11):e0188510. PMC: 5706670. DOI: 10.1371/journal.pone.0188510. View

Mosher R, Melnyk C, Kelly K, Dunn R, Studholme D, Baulcombe D . Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature. 2009; 460(7252):283-6. DOI: 10.1038/nature08084. View

10.

Slotkin R, Vaughn M, Borges F, Tanurdzic M, Becker J, Feijo J . Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009; 136(3):461-72. PMC: 2661848. DOI: 10.1016/j.cell.2008.12.038. View

11.

Ou S, Su W, Liao Y, Chougule K, Agda J, Hellinga A . Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019; 20(1):275. PMC: 6913007. DOI: 10.1186/s13059-019-1905-y. View

12.

Burgess D, Chow H, Grover J, Freeling M, Mosher R . Ovule siRNAs methylate protein-coding genes in trans. Plant Cell. 2022; 34(10):3647-3664. PMC: 9516104. DOI: 10.1093/plcell/koac197. View

13.

Jones P . Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012; 13(7):484-92. DOI: 10.1038/nrg3230. View

14.

Feng X, Zilberman D, Dickinson H . A conversation across generations: soma-germ cell crosstalk in plants. Dev Cell. 2013; 24(3):215-25. DOI: 10.1016/j.devcel.2013.01.014. View

15.

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

16.

Tang H, Lyons E . Unleashing the genome of brassica rapa. Front Plant Sci. 2012; 3:172. PMC: 3408644. DOI: 10.3389/fpls.2012.00172. View

17.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

18.

Cheng F, Liang J, Cai C, Cai X, Wu J, Wang X . Genome sequencing supports a multi-vertex model for Brassiceae species. Curr Opin Plant Biol. 2017; 36:79-87. DOI: 10.1016/j.pbi.2017.01.006. View

19.

Zhang J, Ahmad M, Gao H . Application of single-cell multi-omics approaches in horticulture research. Mol Hortic. 2023; 3(1):18. PMC: 10521458. DOI: 10.1186/s43897-023-00067-y. View

20.

Picelli S, Faridani O, Bjorklund A, Winberg G, Sagasser S, Sandberg R . Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014; 9(1):171-81. DOI: 10.1038/nprot.2014.006. View