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BBA - Gene Structure and Expression (v.1769, #5-6)

Editorial Board (pp. ii).

Preface to special issue on plant chromatin: Structure and expression by Joe Ogas (pp. 267-268).

Vernalization: A model for investigating epigenetics and eukaryotic gene regulation in plants by Robert J. Schmitz; Richard M. Amasino (pp. 269-275).

The transition from vegetative to reproductive development is a highly regulated process that, in many plant species, is sensitive to environmental cues that provide seasonal information to initiate flowering during optimal times of the year. One environmental cue is the cold of winter. Winter annuals and biennials typically require prolonged exposure to the cold of winter to flower rapidly in the spring. This process by which flowering is promoted by cold exposure is known as vernalization. The winter-annual habit of Arabidopsis thaliana is established by the ability of FRIGIDA to promote high levels of expression of the potent floral repressor FLOWERING LOCUS C ( FLC) . In Arabidopsis, vernalization results in the silencing of FLC in a mitotically stable (i.e., epigenetic) manner that is maintained for the remainder of the plant life cycle. The repressed “off” state of FLC has features characteristic of facultative heterochromatin. Upon passing to the next generation, the “off” state of FLC is reset to the “on” state. The environmental induction and mitotic stability of vernalization-mediated FLC repression as well as the subsequent resetting in the next generation provides a system for studying several aspects of epigenetic control of gene expression.

Keywords: FLOWERING LOCUS C; Epigenetics; Vernalization

DNA methylation dynamics in plant genomes by Mary Gehring; Steven Henikoff (pp. 276-286).

Cytosine bases are extensively methylated in the DNA of plant genomes. DNA methylation has been implicated in the silencing of transposable elements and genes, and loss of methylation can have severe consequences for the organism. The recent methylation profiling of the entire Arabidopsis genome has provided insight into the extent of DNA methylation and its functions in silencing and gene transcription. Patterns of DNA methylation are faithfully maintained across generations, but some changes in DNA methylation are observed in terminally differentiated tissues. Demethylation by a DNA glycosylase is required for the expression of imprinted genes in the endosperm and de novo methylation might play a role in the selective silencing of certain self-incompatibility alleles in the tapetum. Because DNA methylation patterns are faithfully inherited, changes in DNA methylation that arise somatically during the plant life cycle have the possibility of being propagated. Therefore, epimutations might be an important source of variation during plant evolution.

Keywords: Methylation; Demethylation; Transcription; Transposons; Arabidopsis; Maize

Methyl-CpG-binding domain (MBD) proteins in plants by Gideon Grafi; Assaf Zemach; Letizia Pitto (pp. 287-294).

Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by which the methyl group is interpreted into a functional state has only recently begun to be explored with the isolation and characterization of methylated DNA binding proteins capable of binding 5-methylcytosine. These proteins belong to an evolutionary conserved protein family initially described in animals termed methyl-CpG-binding domain (MBD) proteins. Here, we highlight recent advances and present new prospects concerning plant MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.

Keywords: Cytosine methylation; Methyl-CpG-binding domain (MBD) protein; Heterochromatin; Decrease in DNA Methylation 1 (DDM1); Arginine methyltransferase (PRMT); Nucleolar organizing region (NOR); Plant

Roles of dynamic and reversible histone acetylation in plant development and polyploidy by Z. Jeffrey Chen; Lu Tian (pp. 295-307).

Transcriptional regulation in eukaryotes is not simply determined by the DNA sequence, but rather mediated through dynamic chromatin modifications and remodeling. Recent studies have shown that reversible and rapid changes in histone acetylation play an essential role in chromatin modification, induce genome-wide and specific changes in gene expression, and affect a variety of biological processes in response to internal and external signals, such as cell differentiation, growth, development, light, temperature, and abiotic and biotic stresses. Moreover, histone acetylation and deacetylation are associated with RNA interference and other chromatin modifications including DNA and histone methylation. The reversible changes in histone acetylation also contribute to cell cycle regulation and epigenetic silencing of rDNA and redundant genes in response to interspecific hybridization and polyploidy.

Keywords: Histone acetylation; Gene silencing; Epigenetics; Stress; Development; Hybrids; Polyploidy

Phosphorylation of histone H3 in plants—A dynamic affair by Andreas Houben; Dmitri Demidov; Ana D. Caperta; Raheleh Karimi; Francesco Agueci; Liudmila Vlasenko (pp. 308-315).

Histones are the main protein components of chromatin: they undergo extensive post-translational modifications, particularly acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation which modify the structural/functional properties of chromatin. Post-translational modifications of the N-terminal tails of the core histones within the nucleosome particle are thought to act as signals from the chromatin to the cell, for various processes. Thus, in many ways histone tails can be viewed as complex protein–protein interaction surfaces that are regulated by numerous post-translational modifications. Histone phosphorylation has been linked to chromosome condensation/segregation, activation of transcription, apoptosis and DNA damage repair. In plants, the cell cycle dependent phosphorylation of histone H3 has been described; it is hyperphosphorylated at serines 10/28 and at threonines 3/11 during both mitosis and meiosis in patterns that are specifically coordinated in both space and time. Although this post-translational modification is highly conserved, data show that the chromosomal distribution of individual modifications can differ between groups of eukaryotes. Initial results indicate that members of the plant Aurora kinase family have the capacity to control cell cycle regulated histone H3 phosphorylation, and in addition we describe other potential H3 kinases and discuss their functions.

Keywords: Histone phosphorylation; Chromosomes; Centromeres; Cell cycle; Aurora kinases

Plant SET domain-containing proteins: Structure, function and regulation by Danny W-K Ng; Tao Wang; Mahesh B. Chandrasekharan; Rodolfo Aramayo; Sunee Kertbundit; Timothy C. Hall (pp. 316-329).

Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/ interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein–protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense–antisense RNA.

Keywords: Arabidopsis; SET; genes; Alternative splicing; Epigenetics; Histone methylation; Rice; SET; genes; SET domain classes

SWI/SNF chromatin remodeling and linker histones in plants by Andrzej Jerzmanowski (pp. 330-345).

In yeast and mammals, ATP-dependent chromatin remodeling complexes belonging to the SWI/SNF family play critical roles in the regulation of transcription, cell proliferation, differentiation and development. Homologs of conserved subunits of SWI/SNF-type complexes, including several putative ATPases and other core subunits, have been identified in plants. Here I summarize recent insights in structural organization and functional diversification of putative plant SWI/SNF-type chromatin remodeling complexes and discuss in a broader evolutionary perspective the similarities and differences between plant and yeast/animal SWI/SNF remodeling. I also summarize the current view of localization in nucleosome and dynamic behaviour in chromatin of linker (H1) histones and discuss significance of recent findings indicating that in both plants and mammals histone H1 is involved in determining patterns of DNA methylation at selected loci.

Keywords: Plant SWI/SNF complexes; Plant linker histone

High mobility group proteins of the plant HMGB family: Dynamic chromatin modulators by Klaus D. Grasser; Dorte Launholt; Marion Grasser (pp. 346-357).

In plants, the chromosomal high mobility group (HMG) proteins of the HMGB family typically contain a central HMG-box DNA-binding domain that is flanked by a basic N-terminal and an acidic C-terminal domain. The HMGB proteins are abundant and highly mobile proteins in the cell nucleus that influence chromatin structure and enhance the accessibility of binding sites to regulatory factors. Due to their remarkable DNA bending activity, HMGB proteins can increase the structural flexibility of DNA, promoting the assembly of nucleoprotein complexes that control DNA-dependent processes including transcription. Therefore, members of the HMGB family act as versatile modulators of chromatin function.

Keywords: Plant chromatin; High mobility group (HMG) protein; Transcription; DNA-binding; Architectural factor; Nucleoprotein complex

RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile pathway for transcriptional gene silencing in plants by Bruno Huettel; Tatsuo Kanno; Lucia Daxinger; Etienne Bucher; Johannes van der Winden; Antonius J.M. Matzke; Marjori Matzke (pp. 358-374).

RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 ( defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.

Keywords: DNA demethylation; Heterochromatin; Pol IV; RNA-directed DNA methylation; RNAi; Transcriptional gene silencing

Polycomb group and trithorax group proteins in Arabidopsis by Stéphane Pien; Ueli Grossniklaus (pp. 375-382).

Polycomb group (PcG) and trithorax group (trxG) proteins form molecular modules of a cellular memory mechanism that maintains gene expression states established by other regulators. In general, PcG proteins are responsible for maintaining a repressed expression state, whereas trxG proteins act in opposition to maintain an active expression state. This mechanism, first discovered in Drosophila and subsequently in mammals, has more recently been studied in plants. The characterization of several Polycomb Repressive Complex 2 (PRC2) components in Arabidopsis thaliana constituted a first breakthrough, revealing key roles of PcG proteins in the control of crucial plant developmental processes. Interestingly, the recent identification of plant homologues of the Drosophila trithorax protein suggests a conservation of both the PcG and trxG gene regulatory system in plants. Here, we review the current evidence for the role of PcG and trxG proteins in the control of plant development, their biochemical functions, their interplay in maintaining stable expression states of their target genes, and point out future directions which may help our understanding of PcG and trxG function in plants.

Keywords: Arabidopsis; Chromatin; Epigenetics; Histone modification; Polycomb; trithorax

rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch by Sasha Preuss; Craig S. Pikaard (pp. 383-392).

Ribosomal RNA (rRNA) gene transcription accounts for most of the RNA in prokaryotic and eukaryotic cells. In eukaryotes, there are hundreds (to thousands) of rRNA genes tandemly repeated head-to-tail within nucleolus organizer regions (NORs) that span millions of basepairs. These nucleolar rRNA genes are transcribed by RNA Polymerase I (Pol I) and their expression is regulated according to the physiological need for ribosomes. Regulation occurs at several levels, one of which is an epigenetic on/off switch that controls the number of active rRNA genes. Additional mechanisms then fine-tune transcription initiation and elongation rates to dictate the total amount of rRNA produced per gene. In this review, we focus on the DNA and histone modifications that comprise the epigenetic on/off switch. In both plants and animals, this system is important for controlling the dosage of active rRNA genes. The dosage control system is also responsible for the chromatin-mediated silencing of one parental set of rRNA genes in genetic hybrids, a large-scale epigenetic phenomenon known as nucleolar dominance.

Keywords: Epigenetic phenomena; RNA polymerase I; DNA methylation; Cytosine methylation; Histone methylation; Histone deacetylation; Histone deacetylase; Transcription; Ribosomal RNA; Nucleolus; Nucleolus organizer region

Epigenetic transitions in plants not associated with changes in DNA or histone modification by Taisuke Nishimura; Jerzy Paszkowski (pp. 393-398).

Covalent modifications of DNA and histones correlate with chromatin compaction and with its transcriptional activity and contribute to mitotic and meiotic heritability of epigenetic traits. However, there are intriguing examples of the transition of epigenetic states in plants that appear to be uncoupled from the conventional mechanisms of chromatin-mediated regulation of transcription. Further study of the molecular mechanism and biological significance of such atypical epigenetic regulation may uncover novel aspects of epigenetic gene regulation and better define its role in plant development and environmental adaptation.

Keywords: BRU1/MGO3/TSK; Cytosine methylation; Epigenetic gene regulation; Histone modification; MOM1; RPA2

Composition of plant telomeres by Barbara Zellinger; Karel Riha (pp. 399-409).

Telomeres are essential elements of eukaryotic chromosomes that differentiate native chromosome ends from deleterious DNA double-strand breaks (DSBs). This is achieved by assembling chromosome termini in elaborate high-order nucleoprotein structures that in most organisms encompass telomeric DNA, specific telomere-associated proteins as well as general chromatin and DNA repair factors. Although the individual components of telomeric chromatin are evolutionary highly conserved, cross species comparisons have revealed a remarkable flexibility in their utilization at telomeres. This review outlines the strategies used for chromosome end protection and maintenance in mammals, yeast and flies and discusses current progress in deciphering telomere structure in plants.

Keywords: Telomerase; Telobox; Chromatin; Telomere-binding protein

Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression by Stanton B. Gelvin; Sang-Ic Kim (pp. 410-421).

Agrobacterium tumefaciens transfers DNA (T-DNA) to plant cells, where it integrates into the plant genome. Little is known about how T-DNA chooses sites within the plant chromosome for integration. Previous studies indicated that T-DNA preferentially integrates into transcriptionally active regions of the genome, especially in 5′-promoter regions. This would make sense, considering that chromatin structure surrounding active promoters may be more “open” and accessible to foreign DNA. However, recent results suggest that this seemingly non-random pattern of integration may be an artifact of selection bias, and that T-DNA may integrate more randomly than previously thought. In this chapter, I discuss the history of these observations and the role chromatin proteins may play in T-DNA integration and transgene expression. Understanding how chromatin conformation may influence T-DNA integration will be important in developing strategies for reproducible and stable transgene expression, and for gene targeting.

Keywords: Agrobacterium; Plant genetic engineering; T-DNA; Transgene; Chromatin; Methylation

Biological consequences of dosage dependent gene regulatory systems by James A. Birchler; Hong Yao; Siva Chudalayandi (pp. 422-428).

Chromatin and gene regulatory molecules tend to operate in multisubunit complexes in the process of controlling gene expression. Accumulating evidence suggests that varying the amount of any one member of such complexes will affect the function of the whole via the kinetics of assembly and other actions. In effect, they exhibit a “balance” among themselves in terms of the activity of the whole. When this fact is coupled with genetic and biological observations stretching back a century, a synthesis emerges that helps explain at least some aspects of a variety of phenomena including aneuploid syndromes, dosage compensation, quantitative trait genetics, regulatory gene evolution following polyploidization, the emergence of complexity in multicellular organisms, the genetic basis of evolutionary gradualism and potential implications for heterosis and co-evolving genes complexes involved with speciation. In this article we will summarize the evidence for this potential synthesis.

Keywords: Regulatory genes; Balance; Aneuploidy; Ploidy; Dosage compensation; QTL; Haploinsufficiency; Heterosis; Hybrid incompatibility

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BBA - Gene Structure and Expression (v.1769, #5-6)