Alexandre Berr

Alexandre Berr
Institut de biologie moléculaire des plantes, Strasbourg

Dr. rer. Nat.

About

80
Publications
11,576
Reads
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1,904
Citations
Additional affiliations
November 2014 - present
University of Strasbourg
Position
  • CR1
February 2008 - present
French National Centre for Scientific Research
Position
  • CR2
February 2007 - present
University of Strasbourg
Position
  • CR

Publications

Publications (80)
Article
Full-text available
Previous studies in Arabidopsis thaliana have identified several histone methylation enzymes, including ARABIDOPSIS TRITHORAX1 (ATX1)/SET DOMAIN GROUP 27 (SDG27), ATX2/SDG30, LSD1-LIKE1 (LDL1), LDL2, SDG8, SDG25, and CURLY LEAF (CLF)/SDG1, as regulators of the key flowering repressor FLOWERING LOCUS C (FLC) and the florigen FLOWERING LOCUS T (FT)....
Article
Full-text available
The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb...
Article
Full-text available
Due to their sessile lifestyle, plants have to cope with an ever-changing environment and to defend themselves against a multitude of biotic aggressors that compromise their development and reproduction. Responses to various biotic stresses largely depend on the plant's capacity to modulate rapidly and specifically its transcriptome. In a stress ty...
Article
Full-text available
In plants, root nitrate uptake systems are under systemic feedback repression by the N satiety of the whole organism, thus adjusting the N acquisition capacity to the N demand for growth; however, the underlying molecular mechanisms are largely unknown. We previously isolated the Arabidopsis high nitrogen-insensitive 9-1 (hni9-1) mutant, impaired i...
Article
Full-text available
In eukaryotic cell nuclei, chromatin states dictated by different combinations of post-translational modifications of histones, such as acetylation, methylation and monoubiquitination of lysine residues, are part of the multitude of epigenomes involved in the fine-tuning of all genetic functions and in particular transcription. During the past deca...
Preprint
Full-text available
Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is Lysine 27 of H3 (H3K27), which trimethylation by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatio-temporal patterns of key developmental genes. H3K27...
Article
Full-text available
The maintenance of genetic information is important in eukaryotes notably through mechanisms occurring at the nuclear periphery where inner nuclear membrane proteins and nuclear pore-associated components are key factors regulating the DNA damage response (DDR). However, this aspect of DDR regulation is still poorly documented in plants. We address...
Preprint
Full-text available
Combinations of epigenetic modifications H3K4me3 and H3K27me3 implicate bistable feature which alternates between on and off state allowing rapid transcriptional changes upon external stimuli. Target of Rapamycin (TOR) functions as a central sensory hub to link a wide range of external stimuli to gene expression. However, the mechanisms underlying...
Article
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An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies...
Article
Full-text available
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant p...
Article
Full-text available
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant p...
Article
Full-text available
Post-translational covalent modifications of histones play important roles in modulating chromatin structure and are involved in the control of multiple developmental processes in plants. Here we provide insight into the contribution of the histone lysine methyltransferase SET DOMAIN GROUP 8 (SDG8), implicated in histone H3 lysine 36 trimethylation...
Preprint
Full-text available
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant p...
Preprint
Full-text available
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant p...
Article
Full-text available
Covalent modifications of histones are essential to control a wide range of processes during development and adaptation to environmental changes. With the establishment of reference epigenomes, patterns of histone modifications were correlated with transcriptionally active or silenced genes. These patterns imply the need for the precise and dynamic...
Article
Full-text available
Histone H2A monoubiquitination (H2Aub1), catalyzed by Polycomb Repressive Complex 1 (PRC1), is a key epigenetic mark in Polycomb silencing. However, little is known about how H2Aub1 is read to exert downstream physiological functions. The animal ZUOTIN RELATED FACTOR 1 (ZRF1) has been reported to bind H2Aub1 to promote or repress expression of vari...
Article
Full-text available
In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of t...
Chapter
Full-text available
Plants are sessile organisms and, as such, their survival relies on their ability to respond quickly all along their life cycle to any kind of environmental stimuli, including abiotic and biotic stresses. In this respect, plants have developed efficient mechanisms of protection and/or adaptation to minimize deleterious effects of stress on their gr...
Article
Full-text available
Centromeres are known as specific chromatin domains without which eukaryotic cells cannot divide properly during mitosis. Despite the considerable efforts to understand the centromere/kinetochore assembly during mitosis, until recently, comparatively few studies have dealt with the regulation of centromere during interphase. Here, we briefly review...
Article
Full-text available
In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an in...
Article
Full-text available
Centromeres play a pivotal role in maintaining genome integrity by facilitating the recruitment of kinetochore and sister-chromatid cohesion proteins, both required for correct chromosome segregation. Centromeres are epigenetically specified by the presence of the histone H3 variant (CENH3). In this study, we investigate the role of the highly cons...
Article
Full-text available
Histone lysine (K) methylation is a type of epigenetic modification involved in regulation of DNA-based processes, including transcription, replication and repair. It can either activate or repress transcription depending on the histone K residue on which methylation occurs and on chromatin context of additional other modifications. In both animals...
Article
Full-text available
Histone methylation is a major component in numerous processes such as flowering time, which is fine-tuned by multiple genetic pathways that integrate both endogenous and environmental signals. Previous studies have identified SET DOMAIN GROUP 26 (SDG26) as a histone methyltransferase involved in the activation of flowering since its loss-of-functi...
Article
Full-text available
Flowering at the right time is crucial to ensure successful plant reproduction and seed yield and is dependent on both environmental and endogenous parameters. Among the different pathways that impinge on flowering, the autonomous pathway promotes floral transition independently of day length through the repression of the central flowering represso...
Article
Full-text available
Protein ubiquitylation regulates a broad variety of biological processes in all eukaryotes. Recent work identified a novel class of cullin-containing ubiquitin ligases (E3s) composed of CUL4, DDB1, and one WD40 protein, believed to act as a substrate receptor. Strikingly, CUL4-based E3 ligases (CRL4s) have important functions at the chromatin level...
Article
Full-text available
As sessile organisms, plants have to endure a wide variety of biotic and abiotic stresses, and accordingly they have evolved intricate and rapidly inducible defense strategies associated with the activation of a battery of genes. Among other mechanisms, changes in chromatin structure are thought to provide a flexible, global, and stable means for t...
Article
Full-text available
Histone H3 lysine 4 trimethylation (H3K4me3) is abundant in euchromatin and is in general associated with transcriptional activation in eukaryotes. Although some Arabidopsis thaliana SET DOMAIN GROUP (SDG) genes have been previously shown to be involved in H3K4 methylation, they are unlikely to be responsible for global genome-wide deposition of H3...
Chapter
Full-text available
The extraordinary flexibility and plasticity of growth and development play a fundamental role in plant adaptation to environmental changes. Reversible epigenetic changes at the level of histone covalent modifications (e.g. methylation, acetylation and ubiquitylation), DNA methylation and ATP-dependent chromatin remodelling can rapidly establish a...
Article
Full-text available
The stress phytohormone ABA inhibits the developmental transition taking the mature embryo in the dry seed towards a young seedling. ABA also induces the accumulation of the basic leucine zipper (bZIP) transcription factor ABA-insensitive 5 (ABI5) which, apart from blocking endosperm rupture, also protects the embryo by stimulating the expression o...
Article
Full-text available
Covalent modifications of histone lysine residues by methylation play key roles in the regulation of chromatin structure and function. In contrast to H3K9 and H3K27 methylations that mark repressive states of transcription and are absent in some lower eukaryotes, H3K4 and H3K36 methylations are considered as active marks of transcription and are hi...
Article
Full-text available
Post-translational modifications of proteins by addition of ubiquitin can regulate protein degradation and localization, protein-protein interactions and transcriptional activation. In the ubiquitylation system, substrate specificity is primarily determined by the E2 ubiquitin-conjugating enzyme (UBC) and the E3 ubiquitin ligase. The Arabidopsis th...
Article
Full-text available
The chromosome arrangement in interphase nuclei is of growing interest, e.g., the spatial vicinity of homologous sequences is decisive for efficient repair of DNA damage by homologous recombination, and close alignment of sister chromatids is considered as a prerequisite for their bipolar orientation and subsequent segregation during nuclear divisi...
Article
Full-text available
Whole-mount fluorescence in situ hybridization (FISH) was applied to Arabidopsis thaliana seedlings to determine the three-dimensional (3D) interphase chromosome territory (CT) arrangement and heterochromatin location within the positional context of entire tissues or in particular cell types of morphologically well-preserved seedlings. The interph...
Article
Full-text available
In contrast to the situation described for mammals and Drosophila, chromosome territory (CT) arrangement and somatic homologous pairing in interphase nuclei of Arabidopsis thaliana (n = 5) are predominantly random except for a more frequent association of the chromosomes bearing a homologous nucleolus organizer region. To find out whether this chro...
Article
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Evolution of chromosome complements can be resolved by genome sequencing, comparative genetic mapping, and comparative chromosome painting. Previously, comparison of genetic maps and gene-based phylogenies suggested that the karyotypes of Arabidopsis thaliana (n = 5) and of related species with six or seven chromosome pairs were derived from an anc...
Article
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Efficient amplification and labelling of probes are crucial for successful sequence detection by fluorescent in situ hybridization (FISH). In particular, chromosome painting to visualize chromosome segments or entire chromosomes by FISH requires large amounts of probes derived from extended templates. There are a number of techniques for probe labe...
Thesis
Full-text available
Dissertation zur Erlangung des akademischen Grades doctor rerum naturalium (Dr.rer.nat.) vorgelegt der Mathematisch-Naturwissenschaftlich-Technischen Fakultät (matematisch-naturwissenschaftlicher Bereich) der Martin-Luther-Universität Halle-Wittenberg