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DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent

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Molecular Plant 2016年第8期9卷 1142-1155页

作者： Zhenxing Wang rainer schwacke Reinhard Kunze institute of Biology - Applied Genetics Dahlem Centre of Plant Sciences - DCPS Freie Universit~t Berlin Albrecht-Thaler-Weg 6 14195 Berlin Germany Forschungszentrum JQlich GmbH Institute of Bio- and Geosciences Plant Sciences (IBG-2) 52425 JQlich Germany

Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs （IncRNAs）, many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and IncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild- type （WT） and ataxia telangiectasia mutated （atm） mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is 〉 2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cy- cle is largely lost. In contrast, only less than 0.6% of TEs and IncRNAs respond to DNA damage in WT plants, and the regulation of 〉95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and IncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and IncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and IncRNAs located close to genes commonly function as controlling elements.

关键词： Arabidopsis thaliana ataxia telangiectasia mutated DNA damage response transposable element,long non-coding RNA

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MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

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Molecular Plant 2019年第6期12卷 879-892页

作者： rainer schwacke Gabriel Y.Ponce-Soto Kirsten Krause Anthony M.Bolger Borjana Arsova Asis Hallab Kristina Gruden Mark Stitt Marie E.Bolger Bjorn Usadel Institute for Bio- and Geosciences (IBG-2: Plant Sciences) Forschungszentrum Julich Wilhelm Johnen StraBe Jiilich Germany Department of Arctic and Marine Biology The Arctic University of Norway Biology Building 9037 Tromso Norway Institute for Botany and Molecular Genetics BioEconomy Science Center Worringer Weg RWTH Aachen University 52074 Aachen Germany National Institute of Biology Department of Biotechnology and Systems Biology Vedna Pot 111 1000 Ljubljana Slovenia Max Planck Institute for Molecular Plant Physiology Department of Systems Regulation 14476 Potsdam-Golm Germany

Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

关键词： Plant genomes Functional annotation MapMan Mercator Transcriptomes

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