Journal ArticleDOI
Reconstructing de novo silencing of an active plant retrotransposon
Arturo Marí-Ordóñez,Antonin Marchais,Mathilde Etcheverry,Antoine Martin,Antoine Martin,Vincent Colot,Olivier Voinnet,Olivier Voinnet +7 more
Reads0
Chats0
TLDR
It is shown how this reconstructed TE burst causes widespread genome diversification and de novo epiallelism that could serve as sources for selectable and potentially adaptive traits.Abstract:
Transposable elements (TEs) contribute to genome size, organization and evolution. In plants, their activity is primarily controlled by transcriptional gene silencing (TGS), usually investigated at steady states, reflecting how long-established silent conditions are maintained, faithfully reiterated or temporarily modified. How active, invasive TEs are detected and silenced de novo in plants remains largely unknown. Using inbred lineages of hybrid Arabidopsis thaliana epigenomes combining wild-type and mutant chromosomes, we have deciphered the sequence of physiological and molecular events underlying the de novo invasion, proliferation and eventual demise of the single-copy endogenous retrotransposon Evade (EVD). We show how this reconstructed TE burst causes widespread genome diversification and de novo epiallelism that could serve as sources for selectable and potentially adaptive traits.read more
Citations
More filters
Journal ArticleDOI
Transgenerational Epigenetic Inheritance: myths and mechanisms
TL;DR: Although the inheritance of epigenetic characters can certainly occur-particularly in plants-how much is due to the environment and the extent to which it happens in humans remain unclear.
Journal ArticleDOI
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
Marjori Matzke,Rebecca A. Mosher +1 more
TL;DR: RNA-directed DNA methylation, the major small RNA-mediated epigenetic pathway in plants, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
Journal ArticleDOI
Dynamics and function of DNA methylation in plants.
TL;DR: DNA methylation in plants mediates gene expression, transposon silencing, chromosome interactions and genome stability, and the regulation of DNA methylation is important for plant development and for plant responses to biotic and abiotic stresses.
Journal ArticleDOI
The expanding world of small RNAs in plants
TL;DR: The biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNas, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation are discussed.
Identification of a Functional Transposon Insertion in the Maize Domestication Gene tb1
TL;DR: This paper showed that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
Steven J. Clough,Andrew F. Bent +1 more
TL;DR: The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.
Journal ArticleDOI
Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
TL;DR: Jalview 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
Related Papers (5)
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
Julie A. Law,Steven E. Jacobsen +1 more