DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development DOI Creative Commons
Li He, Huan Huang, Mariem Bradai

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 14, 2022

Abstract A contribution of DNA methylation to defense against invading nucleic acids and maintenance genome integrity is uncontested; however, our understanding the extent involvement this epigenetic mark in genome-wide gene regulation plant developmental control incomplete. Here, we knock out all five known methyltransferases Arabidopsis , generating methylation-free plants. This quintuple mutant exhibits a suite defects, unequivocally demonstrating that essential for multiple aspects development. We show CG non-CG are required plethora biological processes, including pavement cell shape, endoreduplication, death, flowering, trichome morphology, vasculature meristem development, root fate determination. Moreover, find has strong dose-dependent effect on expression repression transposable elements. Taken together, results demonstrate dispensable survival but proper processes.

Language: Английский

Shifting the limits in wheat research and breeding using a fully annotated reference genome DOI Open Access

R. Appels,

Kellye Eversole, Nils Stein

et al.

Science, Journal Year: 2018, Volume and Issue: 361(6403)

Published: Aug. 17, 2018

Insights from the annotated wheat genome Wheat is one of major sources food for much world. However, because bread wheat's a large hybrid mix three separate subgenomes, it has been difficult to produce high-quality reference sequence. Using recent advances in sequencing, International Genome Sequencing Consortium presents an with detailed analysis gene content among subgenomes and structural organization all chromosomes. Examples quantitative trait mapping CRISPR-based modification show potential using this agricultural research breeding. Ramírez-González et al. exploited fruits endeavor identify tissue-specific biased expression coexpression networks during development exposure stress. These resources will accelerate our understanding genetic basis wheat. Science , issue p. eaar7191 ; see also eaar6089

Language: Английский

Citations

2779
Dynamics and function of DNA methylation in plants DOI
Huiming Zhang,

Zhaobo Lang,

Jian‐Kang Zhu

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2018, Volume and Issue: 19(8), P. 489 - 506

Published: May 21, 2018

Language: Английский

Citations

1388
Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions DOI Creative Commons
Taiji Kawakatsu, Shao‐shan Carol Huang, Florian Jupe

et al.

Cell, Journal Year: 2016, Volume and Issue: 166(2), P. 492 - 505

Published: July 1, 2016

Language: Английский

Citations

678
Mass-spectrometry-based draft of the Arabidopsis proteome DOI
Julia Mergner, Martin Frejno, Markus List

et al.

Nature, Journal Year: 2020, Volume and Issue: 579(7799), P. 409 - 414

Published: March 11, 2020

Language: Английский

Citations

436
The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution DOI Open Access
Daniel Lang, Kristian K Ullrich, Florent Murat

et al.

The Plant Journal, Journal Year: 2017, Volume and Issue: 93(3), P. 515 - 533

Published: Dec. 13, 2017

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses structure and evolution we generated a chromosome-scale assembly using genetic linkage as well (end) sequencing long DNA fragments. We find that 57% comprises transposable elements (TEs), some which may be actively transposing during life cycle. Unlike in flowering plant genomes, gene- TE-rich regions show an overall even distribution along chromosomes. However, chromosomes are mono-centric with peaks class Copia potentially coinciding centromeres. Gene body methylation is evident 5.7% protein-coding genes, typically low GC expression. Some giant virus insertions transcriptionally active might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods evolved two rounds whole duplications (WGDs), apparently common mosses but not liverworts hornworts. Several hundred genes present colinear conserved since last ancestor plants. These syntenic enriched for functions related plant-specific cell growth tissue organization. P. patens lacks pericentromeric gene-rich distal typical most genomes. More non-seed genomes needed unravel how evolve, understand whether or bryophytes.

Language: Английский

Citations

417
Gene body DNA methylation in plants DOI Creative Commons
Adam J. Bewick, Robert J. Schmitz

Current Opinion in Plant Biology, Journal Year: 2017, Volume and Issue: 36, P. 103 - 110

Published: March 2, 2017

Language: Английский

Citations

360
Evolution of DNA Methylation across Insects DOI Creative Commons
Adam J. Bewick, Kevin J. Vogel, Allen J. Moore

et al.

Molecular Biology and Evolution, Journal Year: 2016, Volume and Issue: unknown, P. msw264 - msw264

Published: Nov. 19, 2016

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, therefore has been hypothesized facilitate the evolution of plastic traits such as sociality insects. However, is sparsely studied Therefore, we documented patterns across a wide diversity We predicted that underlying enzymatic machinery concordant with methylation. Finally, given suggestion facilitated social Hymenoptera, tested hypothesis system will be associated presence/absence among other insect orders. found widespread, detected all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed differed levels Hymenopteran (ants, bees, wasps sawflies) had some lowest levels, including several potential losses. Blattodea (cockroaches termites) show possible patterns, loss eusocial species whereas solitary highest levels. Species do not always possess typical machinery. identified duplication event maintenance methyltransferase 1 (DNMT1) shared by paralogs have experienced divergent, nonneutral evolution. This suggests alternative pathways may exist. Phylogenetically corrected comparisons revealed no evidence supports evolutionary association between Future functional studies required advance our understanding

Language: Английский

Citations

319
The prevalence, evolution and chromatin signatures of plant regulatory elements DOI
Zefu Lu, Alexandre P. Marand, William A. Ricci

et al.

Nature Plants, Journal Year: 2019, Volume and Issue: 5(12), P. 1250 - 1259

Published: Nov. 18, 2019

Language: Английский

Citations

314
Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward DOI Creative Commons
Christina L. Richards, Conchita Alonso, Claude Becker

et al.

Ecology Letters, Journal Year: 2017, Volume and Issue: 20(12), P. 1576 - 1590

Published: Oct. 12, 2017

Abstract Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted merge ecological experiments analyses elucidate the contribution epigenetics phenotypes, stress responses, adaptation habitat, and range distributions. While there has been some progress in revealing role processes, non‐model species so far limited describing broad patterns based on anonymous markers DNA methylation. contrast, model benefited from powerful genomic resources , which a more mechanistic understanding but realism. Understanding significance for ecology requires increased transfer knowledge methods research genomes evolutionarily divergent species, examination responses natural environments at level. This transforming genomics tools specifically studying is challenging given large often polyploid plants. Collaboration among molecular geneticists, ecologists bioinformaticians promises enhance our mutual links between genome function processes.

Language: Английский

Citations

301
On the origin and evolutionary consequences of gene body DNA methylation DOI Open Access
Adam J. Bewick, Lexiang Ji, Chad E. Niederhuth

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 113(32), P. 9111 - 9116

Published: July 25, 2016

Significance DNA methylation in plants is found at CG, CHG, and CHH sequence contexts. In plants, CG enriched the transcribed regions of many constitutively expressed genes (gene body methylation; gbM) shows correlations with several chromatin modifications. Contrary to other types methylation, evolution function gbM are largely unknown. Here we show two independent concomitant losses methyltransferase CHROMOMETHYLASE 3 (CMT3) without predicted disruption transcription modifications chromatin. This result suggests that CMT3 required for establishment actively genes, dispensable normal as well composition modification plant

Language: Английский

Citations

297