CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers

Mei Zhang; Xuxu Ma; Chunyu Wang; Qing Li; Blake C. Meyers; Nathan M. Springer; Virginia Walbot

doi:10.1111/nph.17060

CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers

Mei Zhang, Xuxu Ma, Chunyu Wang, Qing Li, Blake C. Meyers, Nathan M. Springer, Virginia Walbot

Plant and Microbial Biology

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.

Original language	English (US)
Pages (from-to)	2984-2997
Number of pages	14
Journal	New Phytologist
Volume	229
Issue number	5
DOIs	https://doi.org/10.1111/nph.17060
State	Published - Dec 12 2020

Bibliographical note

Funding Information:
The seeds of dcl5-1 and ms23 mutants were generously provided by Han Zhang and Guo-ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite-sequencing libraries and Sandra Mathioni for sRNA-seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF-PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI-1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected]. Raw data were submitted to NCBI’s Short Read Archive under BioProject accession no. PRJNA639640.

Funding Information:
The seeds of and mutants were generously provided by Han Zhang and Guo‐ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite‐sequencing libraries and Sandra Mathioni for sRNA‐seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF‐PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI‐1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected] . Raw data were submitted to NCBI’s Short Read Archive under BioProject accession no. PRJNA639640. dcl5‐1 ms23

Publisher Copyright:
© 2020 The Authors New Phytologist © 2020 New Phytologist Trust

Keywords

DNA methylation
Dcl5
Ms23
Zea mays (maize)
phasiRNA

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10.1111/nph.17060

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title = "CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers",

abstract = "Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.",

keywords = "DNA methylation, Dcl5, Ms23, Zea mays (maize), phasiRNA",

author = "Mei Zhang and Xuxu Ma and Chunyu Wang and Qing Li and Meyers, {Blake C.} and Springer, {Nathan M.} and Virginia Walbot",

note = "Funding Information: The seeds of dcl5-1 and ms23 mutants were generously provided by Han Zhang and Guo-ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite-sequencing libraries and Sandra Mathioni for sRNA-seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF-PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI-1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected]. Raw data were submitted to NCBI{\textquoteright}s Short Read Archive under BioProject accession no. PRJNA639640. Funding Information: The seeds of and mutants were generously provided by Han Zhang and Guo‐ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite‐sequencing libraries and Sandra Mathioni for sRNA‐seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF‐PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI‐1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected] . Raw data were submitted to NCBI{\textquoteright}s Short Read Archive under BioProject accession no. PRJNA639640. dcl5‐1 ms23 Publisher Copyright: {\textcopyright} 2020 The Authors New Phytologist {\textcopyright} 2020 New Phytologist Trust",

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AU - Ma, Xuxu

AU - Wang, Chunyu

AU - Li, Qing

AU - Meyers, Blake C.

AU - Springer, Nathan M.

AU - Walbot, Virginia

N1 - Funding Information: The seeds of dcl5-1 and ms23 mutants were generously provided by Han Zhang and Guo-ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite-sequencing libraries and Sandra Mathioni for sRNA-seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF-PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI-1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected]. Raw data were submitted to NCBI’s Short Read Archive under BioProject accession no. PRJNA639640. Funding Information: The seeds of and mutants were generously provided by Han Zhang and Guo‐ling Nan, respectively. We thank Peter Hermanson for the preparation of sequence capture bisulfite‐sequencing libraries and Sandra Mathioni for sRNA‐seq libraries. This work was supported by US National Science Foundation Plant Genome Research Program (NSF‐PGRP) award #1649424 (BCM and VW), the International Postdoctoral Exchange Fellowship Program award #20140067 (MZ), US National Science Foundation grants DBI‐1237931 (NMS), and the Starting Funding of the Chinese Academy of Sciences (Y971RG1001 to MZ). Requests for materials should be addressed to [email protected] . Raw data were submitted to NCBI’s Short Read Archive under BioProject accession no. PRJNA639640. dcl5‐1 ms23 Publisher Copyright: © 2020 The Authors New Phytologist © 2020 New Phytologist Trust

PY - 2020/12/12

Y1 - 2020/12/12

N2 - Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.

AB - Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.

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KW - Ms23

KW - Zea mays (maize)

KW - phasiRNA

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CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers

Abstract

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