BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis

Chromatin modifiers that control plant development

The different cell types of a multicellular organism express different sets of genes. Although this is one of the oldest paradigms of developmental genetics, how different patterns of gene expression are established and maintained during subsequent cell division is an active topic of research. Chromatin modifiers play an essential role in controlling gene expression and in establishing epigenetic marks that can be inherited. During the past few years, large number of putative chromatin-associated proteins have been uncovered as controllers of meristem organization and activity, phase transition, and gametophyte and embryo development.

Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis

The SU(VAR)3-9 protein family was first identified in animals as heterochromatin-associated proteins and found to control establishment of heterochromatic chromatin domains by histone H3 lysine 9 methylation. In Arabidopsis ten SU(VAR)3-9 homologous SUVH genes are found where SUVH1, SUVH2 and SUVH4 represent different subgroups of genes. Also the SUVH1, SUVH2 and SUVH4 proteins represent heterochromatin-associated proteins and display differential effects on control of heterochromatic histone methylation marks. In Arabidopsis the heterochromatin specific histone methylation marks are mono- and dimethyl H3K9, mono- and dimethyl H3K27 and monomethyl H4K20. In contrast to animal systems trimethyl H3K9, trimethyl H3K27 and di- and trimethyl H4K20 do not index chromocenter heterochromatin in Arabidopsis. SUVH2 shows a central role in control of heterochromatin formation and heterochromatic gene silencing in Arabidopsis. Loss-of-function of SUVH2 results in significant reduction of all heterochromatin-specific histone methylation marks and causes DNA hypomethylation at chromocenter heterochromatin. SUVH2 overexpression leads to ectopic heterochromatisation accompanied with significant growth defects. SUVH2 shows strong dosage-dependent effects on transcriptional gene silencing. In Arabidopsis different experimental systems connected with transcriptional gene silencing have been used for genetic dissection of molecular mechanisms controlling epigenetic processes. Molecular analysis of the genes identified by the isolated modifier mutants suggests that transcriptional gene silencing in plants is caused by heterochromatisation. A new efficient experimental system for the analysis of transcriptional gene silencing has been established with the help of LUCIFERASE transgene repeats. The different lines established show either complete or partial silencing of the luciferase transgene repeats. These lines have been successfully used either for mutant isolation or for functional analysis of SUVH proteins in control of heterochromatic gene silencing.

Arabidopsis ribonucleotide reductases are critical for cell cycle progression, DNA damage repair, and plant development

Ribonucleotide reductase (RNR), comprising two large (R1) and two small (R2) subunits, catalyzes a rate-limiting step in the production of deoxyribonucleotides needed for DNA replication and repair. Previous studies in yeast and mammals indicated that defective RNR often led to cell cycle arrest, growth retardation, and p53-dependent apoptosis, whereas abnormally increased RNR activities led to higher mutation rates. Because plants are constantly exposed to environmental mutagens and plant cells are totipotent, an understanding of RNR function in plants is important. We isolated and characterized mutations in all three R2 genes (TSO2, RNR2A, and RNR2B) in Arabidopsis thaliana. tso2 mutants had reduced deoxyribonucleoside triphosphate (dNTP) levels and exhibited developmental defects, including callus-like floral organs and fasciated shoot apical meristems. tso2 single and tso2 rnr2a double mutants were more sensitive to UV-C light, and tso2 rnr2a seedlings exhibited increased DNA damage, massive programmed cell death, and release of transcriptional gene silencing. Analyses of single and double r2 mutants demonstrated that a normal dNTP pool and RNR function are critical for the plant response to mutagens and proper plant development. The correlation between DNA damage accumulation and the subsequent occurrence of apoptotic nuclei in tso2 rnr2a double mutants suggests that perhaps plants, like animals, can initiate programmed cell death upon sensing DNA damage.

Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana

Duplication of chromatin following DNA replication requires spatial reorganization of chromatin domains assisted by chromatin assembly factor CAF-1. Here, we tested the genomic consequences of CAF-1 loss and the function of chromatin assembly factor CAF-1 in heterochromatin formation. Genes located in heterochromatic regions are usually silent, and we found that this transcriptional repression persists in the absence of CAF-1 in Arabidopsis. However, using microarrays we observed that genes that are active during late S-phase, when heterochromatin is duplicated, were up-regulated in CAF-1 mutants. Arabidopsis CAF-1 mutants also have reduced cytological heterochromatin content; however, DNA methylation of pericentromeric repeats was normal, demonstrating that CAF-1 is not required for maintenance of DNA methylation. Instead, hypomethylation of the genome, which has only mild effects on the development of wild-type plants, completely arrested development of CAF-1 mutants. These results suggest that CAF-1 functions in heterochromatin formation. CAF-1 and DNA methylation, which is also needed for heterochromatin formation, have partially redundant functions that are essential for cell proliferation. Interestingly, transcriptional repression and heterochromatin compaction can be genetically separated, and CAF-1 is required only for the complete compaction of heterochromatin but not to maintain transcriptional repression of heterochromatic genes.

Replication, repair, and reactivation

In a recent issue of Current Biology, Kapoor et al. (2005) and Elmayan et al. (2005) illuminate the linkage between DNA replication and repair and transcriptional gene silencing in plants by showing that mutants in RPA2, a homolog of yeast and mammalian replication protein A, exhibit loss of silencing at transgene loci as well as some transposable elements. This is accompanied by a shift in histone H3 methylation modifications at these loci from a heterochromatic to a euchromatic pattern. Intriguingly, cytosine methylation is unaffected at the reactivated loci, indicating that transmission of DNA methylation and histone modification status can be uncoupled.

MGOUN3: evidence for chromatin-mediated regulation of FLC expression

The MGOUN3(MGO3)/BRUSHY1(BRU1)/TONSOKU(TSK) gene of Arabidopsis thaliana encodes a nuclear leucine-glycine-asparagine (LGN) domain protein that may be implicated in chromatin dynamics and genome maintenance. Mutants with defects in MGO3 display a fasciated stem and disorganized meristem structures. The transition to flowering was examined in mgo3 mutants and it was found that, under short days, the mutants flowered significantly earlier than the wild-type plants. Study of flowering-time associated gene expression showed that the floral transition inhibitor gene FLC was under-expressed in the mutant background. Ectopic expression of the flower-specific genes AGAMOUS (AG), PISTILLATA (PI), and SEPALLATA3 (SEP3) in mgo3 vegetative organs was also detected. Western blot and chromatin immunoprecipitation experiments suggested that histone H3 acetylation may be altered in the mgo3 background. Together, these data suggest that MGO3 is required for the correct transition to flowering and that this may be mediated by histone acetylation and associated changes in FLC expression.

ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis

We screened for suppressors of repressor of silencing1 (ros1) using the silenced 35S promoter-neomycin phosphotransferase II (Pro(35S):NPTII) gene as a marker and identified two allelic mutants, ror1-1 and ror1-2 (for suppressor of ros1). Map-based cloning revealed that ROR1 encodes a 31-kD protein similar to DNA replication protein A2 (RPA2A). Mutations in ROR1 reactivate the silenced Pro(35S):NPTII gene but not RD29A promoter-luciferase in the ros1 mutant. DNA methylation in rDNA, centromeric DNA, and RD29A promoter regions is not affected by ror1. However, chromatin immunoprecipitation data suggest that histone H3 acetylation is increased and histone H3K9 dimethylation is decreased in the 35S promoter in the ror1 ros1 mutant compared with ros1. These results indicate that release of silenced Pro(35S):NPTII by ror1 mutations is independent of DNA methylation. ROR1/RPA2A is strongly expressed in shoot and root meristems. Mutations in ROR1/RPA2A affect cell division in meristems but not final cell sizes. Our work suggests important roles of ROR1/RPA2A in epigenetic gene silencing and in the regulation of plant development.

Characterization of pollen tube development inPinus strobus (Eastern white pine) through proteomic analysis of differentially expressed proteins

The differentially expressed proteins in pollen tubes indicate their specific roles in this stage of male gametophyte development. To isolate these proteins, 2-DE was done using ungerminated pollen and 2-day-old pollen tubes of Pinus strobus. Results show that 645 and 647 protein spots were clearly resolved from pollen grains and pollen tubes, respectively. Thirty-eight protein spots were expressed only in pollen tubes, while 19 increased in intensity. MALDI-TOF MS was used to generate tryptic peptide masses that were submitted to Mascot for identification. Of the differentially expressed proteins, 12% matched with hypothetical proteins, 33% did not hit any protein, and for the 55%, a putative function was assigned based on similarity of sequences with previously characterized proteins. Therefore, pollen tube development can be characterized by the cellular activities that involve metabolism, stress/defense response, gene regulation, signal transduction, and cell wall formation. This study expands our understanding of the changes in protein expression associated with pollen tube development and provides insights into the molecular programs that separate the development of the pollen tubes from pollen grains. This is the first report that describes a global analysis of differentially expressed proteins from the pollen tube of any seed plant.

Stem cell regulation in the Arabidopsis shoot apical meristem

The aerial structure of higher plants is generated dynamically throughout the life cycle through the activity of stem cells that are located at the growing shoot tip, the apical meristem. The stem cells continuously divide to renew themselves and provide cells for leaf, stem and flower formation. Stem cell maintenance is governed by intercellular communication between the apical stem cells and the underlying organizing centre. Recent advances have been made in understanding the mechanisms that induce shoot stem cell identity, and that control the position and size of the organizing centre. Elements such as chromatin remodeling factors, transcription factors and microRNAs are newly implicated in these regulatory processes. These advances provide a framework for our understanding of how signals are integrated to specify and position the stem cell niche in the shoot apical meristem.

The yeast histone chaperone chromatin assembly factor 1 protects against double-strand DNA-damaging agents

The removal of histones from DNA and their subsequent replacement is likely to be necessary for all processes that require access to the DNA sequence in eukaryotic cells. The histone chaperone chromatin assembly factor 1 (CAF-1) mediates histone H3-H4 assembly during DNA replication and nucleotide excision repair in vitro. We have found that budding yeast deleted for the genes encoding CAF-1 are highly sensitive to double-strand DNA-damaging agents. Our genetic analyses indicate that CAF-1 plays a role in both homologous recombination and nonhomologous end-joining pathways and that the function of CAF-1 during double-strand repair is distinct from that of another histone H3-H4 chaperone, anti-silencing function 1 (ASF1). CAF-1 does not protect the genome by assembling it into a damage-resistant chromatin structure, because induction of CAF-1 after DNA damage is sufficient to restore viability. Furthermore, CAF-1 is not required for repair of the DNA per se or for DNA damage checkpoint function. CAF-1-mediated resistance to DNA damage is dependent on the ability of CAF-1 to bind PCNA, indicating that PCNA may recruit CAF-1 to sites of double-strand DNA repair. We propose that CAF-1 has an essential role in assembling chromatin during double-strand-DNA repair.

An Arabidopsis protein with a novel calcium-binding repeat sequence interacts with TONSOKU/MGOUN3/BRUSHY1 involved in meristem maintenance

TONSOKU(TSK)/MGOUN3/BRUSHY1 from Arabidopsis thaliana, which plays an important role in the maintenance of meristem organization, contains an LGN repeat motif similar to that found in animal proteins involved in asymmetric cell division. One protein that interacts with the LGN motif of TSK in a yeast two-hybrid screen, TSK-associating protein 1 (TSA1), contains a 10-fold repeat of a unique 41 amino acid sequence. The repeat sequence, with a glutamic acid-phenylalanine-glutamic acid (EFE) conserved core sequence, is enriched with acidic amino acids. TSA1 also contains an N-terminal putative signal peptide and it interacts with the LGN motif of TSK through a C-terminal region separated from the EFE repeats by a putative membrane-spanning region. The recombinant protein consisting of EFE repeats was rich in alpha-helical structure and possessed Ca2+-binding activity. Unlike nuclear localization of TSK, the TSA1 fused with green fluorescent protein (GFP) expressed in tobacco BY-2 cells was localized in small cytoplasmic vesicles during interphase. However, cellular localization of both TSA1-GFP and GFP-TSK changed dynamically during mitosis. In particular, both GFP-TSK and TSA1-GFP were concentrated in limited areas that are close to the ends of spindle microtubules ahead of separating chromatids. These results are discussed in terms of the possible involvement of TSK and TSA1 in mitosis.

Preventing transcriptional gene silencing by active DNA demethylation

DNA methylation is important for stable transcriptional gene silencing. DNA methyltransferases for de novo as well as maintenance methylation have been well characterized. However, enzymes responsible for active DNA demethylation have been elusive and several reported mechanisms of active demethylation have been controversial. There has been a critical need for genetic analysis in order to firmly establish an in vivo role for putative DNA demethylases. Mutations in the bifunctional DNA glycosylase/lyase ROS1 in Arabidopsis cause DNA hypermethylation and transcriptional silencing of specific genes. Recombinant ROS1 protein has DNA glycosylase/lyase activity on methylated but not unmethylated DNA substrates. Therefore, there is now strong genetic evidence supporting a base excision repair mechanism for active DNA demethylation. DNA demethylases may be critical factors for genome wide hypomethylation seen in cancers and possibly important for epigenetic reprogramming during somatic cell cloning and stem cell function.

High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene

Gene targeting, which is homologous recombination-mediated integration of an extra-chromosomal DNA segment into a chromosomal target sequence, enables the precise disruption or replacement of any gene. Despite its value as a molecular genetic tool, gene targeting remains an inefficient technology in most species. We report that expression of the yeast RAD54 gene, a member of the SWI2/SNF2 chromatin remodeling gene family, enhances gene targeting in Arabidopsis by one to two orders of magnitude, from 10(-4) to 10(-3) in WT plants to 10(-2) to 10(-1). We show that integration events, detected with an assay based on the use of a fluorescent seed marker, are precise and germinally transmitted. These findings suggest that chromatin remodeling is rate-limiting for gene targeting in plants and improves the prospects for using gene targeting for the precise modification of plant genomes.

Regulation of meristem activity by chromatin remodelling

The continuity and plasticity of plant development rely on the regulation of meristem activity in response to endogenous and environmental signals. Many plant development regulators involved in meristem function are transcription factors or signalling molecules. In the past few years, the role of chromatin remodelling in programming, maintaining or resetting specific gene expression profiles in subsequent cell generations has been shown to be crucial in plant development. Here, we summarize plant chromatin-remodelling factors required to regulate shoot apical meristem activity, particularly its maintenance during organogenesis and transitions between distinct developmental phases.

WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis

SNF2 chromatin-remodeling ATPases play an important role in ensuring proper development in higher eukaryotes by controlling accessibility of cis-regulatory DNA regions to transcription factors and to the transcriptional machinery. However, the biological targets controlled by these ATPases are largely unknown. Using genetic and molecular analyses we have identified WUSCHEL (WUS) as a biologically important target of the SNF2-class ATPase SPLAYED (SYD) in the shoot apical meristem of Arabidopsis. We present evidence that SYD is recruited to the WUS promoter and that it is involved in regulation of the stem cell pool maintenance via direct transcriptional control of this master regulator.

Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin

The fate of double-stranded RNA (dsRNA) in the cell depends on both its length and location . The expression of dsRNA in the nucleus leads to several distinct consequences. First, the promiscuous deamination of adenosines to inosines by dsRNA-specific adenosine deaminase (ADAR) can lead to the nuclear retention of edited transcripts . Second, dsRNAs might induce heterochromatic gene silencing through an RNAi-related mechanism . Is RNA editing also connected to heterochromatin? We report that members of the conserved Vigilin class of proteins have a high affinity for inosine-containing RNAs. In agreement with other work , we find that these proteins localize to heterochromatin and that mutation or depletion of the Drosophila Vigilin, DDP1, leads to altered nuclear morphology and defects in heterochromatin and chromosome segregation. Furthermore, nuclear Vigilin is found in complexes containing not only the editing enzyme ADAR1 but also RNA helicase A and Ku86/70. In the presence of RNA, the Vigilin complex recruits the DNA-PKcs enzyme, which appears to phosphorylate a discrete set of targets, some or all of which are known to participate in chromatin silencing. These results are consistent with a mechanistic link between components of the DNA-repair machinery and RNA-mediated gene silencing.

TONSOKU is expressed in S phase of the cell cycle and its defect delays cell cycle progression in Arabidopsis

TONSOKU(TSK)/MGOUN3/BRUSHY1 of Arabidopsis thaliana encodes a nuclear leucine-glycine-aspargine (LGN) domain protein implicated to be involved in genome maintenance, and mutants with defects in TSK show a fasciated stem with disorganized meristem structures. We identified a homolog of TSK from tobacco BY-2 cells (NtTSK), which showed high sequence conservation both in the LGN domain and in leucine-rich repeats with AtTSK. The NtTSK gene was expressed during S phase of the cell cycle in tobacco BY-2 cells highly synchronized for cell division. The tsk mutants of Arabidopsis contained an increased proportion of cells with 4C nuclei and cells expressing cyclin B1 compared with the wild type. These results suggest that TSK is required during the cell cycle and defects of TSK cause the arrest of cell cycle progression at G2/M phase.

ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis

The higher-plant shoot apical meristem is a dynamic structure continuously producing cells that become incorporated into new leaves, stems and flowers. The maintenance of a constant flow of cells through the meristem depends on coordination of two antagonistic processes: self-renewal of the stem cell population and initiation of the lateral organs. This coordination is stringently controlled by gene networks that contain both positive and negative components. We have previously defined the ULTRAPETALA1(ULT1) gene as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems, because mutations in ULT1 cause the enlargement of inflorescence and floral meristems, the production of supernumerary flowers and floral organs, and a delay in floral meristem termination. Here, we show that ULT1 negatively regulates the size of the WUSCHEL (WUS)-expressing organizing center in inflorescence meristems. We have cloned the ULT1 gene and find that it encodes a small protein containing a B-box-like motif and a SAND domain, a DNA-binding motif previously reported only in animal transcription factors. ULT1 and its Arabidopsis paralog ULT2 define a novel small gene family in plants. ULT1 and ULT2 are expressed coordinately in embryonic shoot apical meristems, in inflorescence and floral meristems, and in developing stamens, carpels and ovules. Additionally, ULT1 is expressed in vegetative meristems and leaf primordia. ULT2 protein can compensate for mutant ULT1 protein when overexpressed in an ult1 background, indicating that the two genes may regulate a common set of targets during plant development. Downregulation of both ULT genes can lead to shoot apical meristem arrest shortly after germination, revealing a requirement for ULT activity in early development.

Stepwise understanding of root development

Recent studies using Arabidopsis propose a framework of root development and pattern formation that can be divided to three processes. First, a positional signal that is delivered from neighboring cells controls the fate of undifferentiated cells. Then, cell fate is fixed through a protein-network that includes various transcription factors. Finally, the expression of a particular gene-set leads to fate-dependent cell differentiation, resulting in oriented cell division, cell specification and cell elongation. In addition, these processes could be modified by chromatin stabilization and protein degradation. We focus on three fundamental patterns of root development, circumferential pattern, radial pattern and proximo-distal pattern, and on novel approaches to identify genes that are responsible for the spatiotemporal regulation of root development.

Heterochromatin: On the ADAR Radar?

Vigilin proteins, the absence of which is known to cause abnormalities in heterochromatin, have been found to bind edited RNAs. Molecular complexes including vigilin comprise proteins involved with RNA editing and with DNA repair, making connections between these processes and RNA-based silencing mechanisms.

The INO80 protein controls homologous recombination in Arabidopsis thaliana

Homologous recombination (HR) serves a dual role in providing genetic flexibility and in maintaining genome integrity. Little is known about the regulation of HR and other repair pathways in the context of chromatin. We report on a mutant affected in the expression of the Arabidopsis INO80 ortholog of the SWI/SNF ATPase family, which shows a reduction of the HR frequency to 15% of that in wild-type plants. In contrast, sensitivity to genotoxic agents and efficiency of T-DNA integration remain unaffected, suggesting that INO80 is a positive regulator of HR, while not affecting other repair pathways. So far, INO80 function has only been reported in a lower eukaryote. Profiling studies on three ino80 allelic mutants show that INO80 regulates nearly 100 Arabidopsis genes. However, the transcriptional regulation of repair-related genes is unaffected in the mutant. This suggests a dual role for INO80 in transcription and DNA repair by HR.

Silencing of transposons in plant genomes: kick them when they're down

Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs.

Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it.