Chromatin and development: A special issue

Peer Reviewe

Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus

The genetic information is stored in the eukaryotic nucleus in the form of chromatin. This is a macromolecular entity that includes genomic DNA and histone proteins that form nucleosomes, plus a large variety of chromatin-associated non-histone proteins. Chromatin is structurally and functionally organised at various levels. One reveals the linear topography of DNA, histones and their post-translational modifications and non-histone proteins along each chromosome. This level provides regulatory information about the association of genomic elements with particular signatures that have been used to define chromatin states. Importantly, these chromatin states correlate with structural and functional genomic features. Another regulatory layer is established at the level of the 3D organisation of chromatin within the nucleus, which has been revealed clearly as non-random. Instead, a variety of intra- and inter-chromosomal genomic domains with specific epigenetic and functional properties has been identified. In this review, we discuss how the recent advances in genomic approaches have contributed to our understanding of these two levels of genome architecture. We have emphasised our analysis with the aim of integrating information available for yeast, Arabidopsis, Drosophila, and mammalian cells. We consider that this comparative study helps define common and unique features in each system, providing a basis to better understand the complexity of genome organisation.Ministerio de Economía y Competitividad (grant BFU2012–34821) and an institutional grant of Fundación Ramón Areces to the Centro de Biología Molecular Severo Ochoa.Peer Reviewe

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals.Weprofiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thaliana and found that the localization of these variants shows broad similarity in plants and animals, along with some unique features. H3.1 was enriched in silent areas of the genome, including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3′ end of genes, and correlated with histone modifications associated with gene activation, such as histone H3 lysine 4 methylation and H2B ubiquitylation, as well as RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin-disrupting processes like transcription.Ministry of Science and Education Grants; Fundación Ramón Areces; Junta de Ampliacion de Estudios Predoctoral Fellowship from the Consejo Superior de Investigaciones CientificasPeer Reviewe

Nuevos péptidos y proteínas así como los correspondientes ácidos nucleicos codificantes de los mismos, y sus aplicaciones en el control del ciclo de desarrollo de las células vegetales.

Fecha de solicitud:01.03.2003.- Titular: Consejo Superior de Investigaciones Científicas (CSIC).[EN]An isolated, enriched, cell free and/or recombinant nucleic acid (II) comprising a sequence encoding for expression of a protein or peptide (I) capable of altering E2F-dimerization partner (DP) activity in a plant cell is new. (P1) is characterized in that it has one or both DP activities in plants selected from: (1) the ability to dimerized with plant E2F protein; and (2) the ability to modulate, particularly enhance, E2F binding to E2F transcription factor binding sites in plant DNA or effect of it characterized in that the protein or peptide comprises a 261 amino acid sequence (S1) or a functionally active part of it or a sequence having at least 70% homology to so the sequence or part of it. Independent claims are also included for the following: (1) controlling one or more of plant growth, gene expression, cellular DNA replication, cell cycle progression, differentiation and development comprising increasing or decreasing DP protein activity in a plant cell through the expression of (P1); (2) isolated (I); (3) a nucleic acid probe (III) comprising a DNA sequence corresponding to an amino acid sequence comprising 261, 458, 52, or 51 amino acids fully defined in the specification; (4) a nucleic acid probe or primer (IV) comprising a double or single stranded DNA of sequence corresponding to 10 or more contiguous nucleotides taken from a sequence (S2) comprising 1089 base pairs fully defined in the specification, with the proviso that it is not selected from residues 70-136; (5) an oligonucleotides probe (V) comprising at least 18 contiguous bases of S2; (6) an antisense DNA (VI) to (II), (III), (IV) or (V); (7) a nucleic acid vector or construct (VII) comprising (II), (III), (IV), (V), or (VI) or its antisense nucleic acid; (8) a plant cell (IX) comprising (VIII); (9) a transgenic plant or its part (X) comprising (IX); (10) an antibody (XI) raised against (I); (11) identifying and/or isolating (M2) DNAs corresponding to complete or partial genes that are regulated in G1 passage, G1/S phase transition and/or S phase progression of the cell cycle, involves contacting sample of genomic DNA with binding material specific for binding such complete or partial genes, removing non-bound DNA from the specific binding material, and releasing and isolating the bound DNA, where the specific binding material comprises a peptide or protein including the DNA binding sequence of a protein that is capable of acting as a part of a plant hetero-oligomer transcription activator or repressor; ; and (12) a specific binding material (XII) which comprises a peptide or protein having DNA binding activity with respect to plant DNA transcription activator or repressor factor binding sites, particularly in genomic DNA, and having the ability to dimerize or oligomerize with a further such plant protein together with one or more of a further peptide or protein. [ES]Control del ciclo celular de las plantas. Se facilita un método de control del ciclo celular de las plantas, caracterizado por consistir en aumentar o disminuir la actividad de la proteína pareja de dimerización (DP) de E2F en una célula vegetal mediante la expresión de un péptido o proteína DP recombinante en esa célula.Peer reviewe

Intercambios entre cromátidas hermanas: mecanismos de formación y significación biológica

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 19-06-198

Links between genome replication and chromatin landscapes

© 2015 The Authors. Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication. Significance Statement The chromatin lanscape has a direct impact on genome replication at various levels including specification of replication origins, replication timing and the maintenance of genome integrity.MINECO and by an institutional grant from Fundación Ramón Areces to the Centro de Biologia Molecular Severo Ochoa.Peer Reviewe

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility. Current studies reinforce the idea of intimate crosstalk between chromatin features and processes involving DNA transactions.We thank members of the laboratory for discussions and E. Martinez-Salas for comments. Z.V. was the recipient of a Predoctoral Fellowship FPI from MINECO. This research was supported by grants BFU2012-34821 and BIO2013-50098-EXP from MINECO and BFU2015-68396-R from MINECO/FEDER, and by an institutional grant from Fundación Ramón Areces to the Centro de Biologia Molecular Severo Ochoa.Peer Reviewe

Structural and functional comparative study of the complexes formed by viral ø29, nf and GA-1 SSB proteins with DNA

Single-stranded DNA-binding proteins have in common their crucial roles in DNA metabolism, although they exhibit significant differences in their single-stranded DNA binding properties. To evaluate the correlation between the structure of different nucleoprotein complexes and their function, we have carried out a comparative study of the complexes that the single-stranded DNA-binding proteins of three related bacteriophages, ø29, Nf and GA-1, form with single-stranded DNA. Under the experimental conditions used, ø29 and Nf single-stranded DNA-binding proteins are stable monomers in solution, while GA-1 single-stranded DNA-binding protein presents a hexameric state, as determined in glycerol gradients. The thermodynamic parameters derived from quenching measurements of the intrinsic protein fluorescence upon single-stranded DNA binding revealed (i) that GA-1 single-stranded DNA-binding protein occludes a larger binding site (n=51 nt/oligomer) than ø29 and Nf SSBs (n=3.4 and 4.7 nt/monomer, respectively); and (ii) that it shows a higher global affinity for single-stranded DNA (GA-1 SSB, Keff=18.6 × 105 M−1; ø29 SSB, Keff=2.2 × 105 M−1; Nf SSB, Keff=2.9 × 105 M−1). Altogether, these parameters justify the differences displayed by the GA-1 single-stranded DNA-binding protein and single-stranded DNA complex under the electron microscope, and the requirement of higher amounts of ø29 and Nf single-stranded DNA-binding proteins than of GA-1 SSB in gel mobility shift assays to produce a similar effect. The structural differences of the nucleoprotein complexes formed by the three single-stranded DNA-binding proteins with single-stranded DNA correlate with their different functional stimulatory effects in ø29 DNA amplification.This investigation has been aided by research grant 2RO1 GM27242-20 from the National Institutes of Health, by grant PB93-0173 from the Dirección General de Investigación Cientı́fica y Técnica, by grant ERBFMRX CT97 0125 from the European Union and by an institutional grant from Fundación Ramón Areces. I. G. was holder of a pre-doctoral fellowship from Fundación Ramón Areces.Peer reviewe

Plantas transgénicas ATPSKP2D, su procedimiento de obtención y sus aplicaciones.

Fecha de presentación internacional: 30.09.2005.- Titular: Consejo Superior de Investigaciones Científicas (CSIC).[EN]The invention relates to AtPSKP2D transgenic plants, the production method thereof and uses of same. More specifically, the invention tackles the problem associated with obtaining novel transgenic plants that can adapt to restrictive environmental situations, preferably by developing lateral roots. In particular, the invention relates to AtPSKP2D transgenic plants which can respond to environmental situations and which contain a novel genetic material that can be used to control root development with the specific expression of genes of interest in the pericycle cells that form the lateral roots (RLs). The aforementioned techniques can be applied to plants of commercial interest, such that said transgenic plants can grow in media poor in nutrients or water and be fertilised with a smaller concentration of fertilisers. As such, the inventive plants represent a significant innovation in the agri-food sector.[ES]La presente invención se enfrenta al problema de proporcionar nuevas plantas transgénicas capaces de adaptarse a situaciones limitan tes del medio ambiente, preferentemente por su capacidad de desarrollar raíces laterales Se describen plantas transgénicas AtPSKP2D capaces de responder ante situaciones medioambientales que contienen un nuevo material genético que permite el control del desarrollo radicular mediante la expresión de forma específica de genes de interés en la células del periciclo formadoras de las raíces laterales (RLs). Estas técnicas pueden aplicarse a plantas de interés comercial de tal forma que estas pIantas transgénicas pueden crecer tanto en medios pobres en nutrientes o en agua, como fertilizadas con una menor concentración de fertilizantes, por lo que representan una importante innovación en el sector agroalimentario.Peer reviewe

Structural and functional comparative study of the complexes formed by viral ø29, nf and GA-1 SSB proteins with DNA

Single-stranded DNA-binding proteins have in common their crucial roles in DNA metabolism, although they exhibit significant differences in their single-stranded DNA binding properties. To evaluate the correlation between the structure of different nucleoprotein complexes and their function, we have carried out a comparative study of the complexes that the single-stranded DNA-binding proteins of three related bacteriophages, ø29, Nf and GA-1, form with single-stranded DNA. Under the experimental conditions used, ø29 and Nf single-stranded DNA-binding proteins are stable monomers in solution, while GA-1 single-stranded DNA-binding protein presents a hexameric state, as determined in glycerol gradients. The thermodynamic parameters derived from quenching measurements of the intrinsic protein fluorescence upon single-stranded DNA binding revealed (i) that GA-1 single-stranded DNA-binding protein occludes a larger binding site (n=51 nt/oligomer) than ø29 and Nf SSBs (n=3.4 and 4.7 nt/monomer, respectively); and (ii) that it shows a higher global affinity for single-stranded DNA (GA-1 SSB, Keff=18.6 × 105 M−1; ø29 SSB, Keff=2.2 × 105 M−1; Nf SSB, Keff=2.9 × 105 M−1). Altogether, these parameters justify the differences displayed by the GA-1 single-stranded DNA-binding protein and single-stranded DNA complex under the electron microscope, and the requirement of higher amounts of ø29 and Nf single-stranded DNA-binding proteins than of GA-1 SSB in gel mobility shift assays to produce a similar effect. The structural differences of the nucleoprotein complexes formed by the three single-stranded DNA-binding proteins with single-stranded DNA correlate with their different functional stimulatory effects in ø29 DNA amplification.This investigation has been aided by research grant 2RO1 GM27242-20 from the National Institutes of Health, by grant PB93-0173 from the Dirección General de Investigación Cientı́fica y Técnica, by grant ERBFMRX CT97 0125 from the European Union and by an institutional grant from Fundación Ramón Areces. I. G. was holder of a pre-doctoral fellowship from Fundación Ramón Areces.Peer reviewe