Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis

Jaehoon Lee; Seunga Lee; Kyunghyuk Park; Sang-Yoon Shin; Jennifer M Frost; Ping-Hung Hsieh; Chanseok Shin; Robert L Fischer; Tzung-Fu Hsieh; Yeonhee Choi

doi:10.3389/fpls.2023.1204279

Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis

Front Plant Sci. 2023 Jun 8:14:1204279. doi: 10.3389/fpls.2023.1204279. eCollection 2023.

Authors

Jaehoon Lee^{1

2}, Seunga Lee^{1

2}, Kyunghyuk Park¹, Sang-Yoon Shin^{2

3}, Jennifer M Frost⁴, Ping-Hung Hsieh⁴, Chanseok Shin^{2

3}, Robert L Fischer⁴, Tzung-Fu Hsieh^{5

6}, Yeonhee Choi^{1

2}

Affiliations

¹ Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
² Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea.
³ Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
⁴ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States.
⁵ Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.
⁶ Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States.

Abstract

CHH methylation (mCHH) increases gradually during embryogenesis across dicotyledonous plants, indicating conserved mechanisms of targeting and conferral. Although it is suggested that methylation increase during embryogenesis enhances transposable element silencing, the detailed epigenetic pathways underlying this process remain unclear. In Arabidopsis, mCHH is regulated by both small RNA-dependent DNA methylation (RdDM) and RNA-independent Chromomethylase 2 (CMT2) pathways. Here, we conducted DNA methylome profiling at five stages of Arabidopsis embryogenesis, and classified mCHH regions into groups based on their dependency on different methylation pathways. Our analysis revealed that the gradual increase in mCHH in embryos coincided with the expansion of small RNA expression and regional mCHH spreading to nearby sites at numerous loci. We identified distinct methylation dynamics in different groups of mCHH targets, which vary according to transposon length, location, and cytosine frequency. Finally, we highlight the characteristics of transposable element loci that are targeted by different mCHH machinery, showing that short, heterochromatic TEs with lower mCHG levels are enriched in loci that switch from CMT2 regulation in leaves, to RdDM regulation during embryogenesis. Our findings highlight the interplay between the length, location, and cytosine frequency of transposons and the mCHH machinery in modulating mCHH dynamics during embryogenesis.

Keywords: CHH methylation; CMT2; DNA methylation; RdDM; embryogenesis; transposable elements.

Grants and funding

This work was funded by the National Research Foundation of Korea (NRF) Grant 2020R1A2C2009382 and 2021R1A5A1032428 to YC. This work was also supported by the Stadelmann-Lee Scholarship Fund, Seoul National University, to JL and SL and by the NSF Grant MCB-1715115 to T-FH.