Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.Fil: Chereji, Razvan V.. National Institutes of Health; Estados UnidosFil: Eriksson, Peter R.. National Institutes of Health; Estados UnidosFil: Ocampo, Josefina. National Institutes of Health; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Prajapati, Hemant Kumar. National Institutes of Health; Estados UnidosFil: Clark, David. National Institutes of Health; Estados Unido

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast

Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.Fil: Prajapati, Hemant K.. National Instituto of Child Health & Human Development; Estados UnidosFil: Ocampo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Clark, David J.. National Instituto of Child Health & Human Development; Estados Unido

Las barreras de la comunicación en las personas sordas. Ámbito de la ciudad

Los objetivos de este artículo son: dar a conocer los diferentes modelos de intervención aplicados a las personas que padecen de discapacidad auditiva; promover la sensibilización social, hacia la comprensión de las personas con discapacidad auditiva, y aumentar el conocimiento general de los medios y ayudas que favorecen la comunicación entre personas oyentes y sordas ;y, por último, desarrollar en las personas con discapacidad auditiva, estrategias comunicativas que les ayuden en la adquisición de competencias lingüísticas mediante el conocimiento y la intervención con las formas y técnicas de comunicación disponibles

Adaptaciones curriculares para alumnos con discapacidad

Estudio de caso sobre adaptaciones curriculares a un alumno con discapacidad motriz severa en la carrera de Arquitectura- FAU-UNT Tucumán (Argentina)

Situación de los derechos de las personas con discapacidad en la provincia de Tucumán. Políticas públicas de la última década

Realizar una evaluación de la situación de las personas con discapacidad en Argentina y en Tucumán, es tratar de encuadrar los derechos que establecen las normas sobre la igualdad de oportunidades para las personas con discapacidad. El análisis cuantitativo de la población con discapacidad resulta altamente complejo por la dispersión de las fuentes de datos y las múltiples dimensiones de las áreas que involucra; se podría mencionar a modo de ejemplo, la salud, la educación, el trabajo, la familia, los aspectos jurídicos, la condición de urbano o rural, el género, etc. Si bien la disgregación de las fuentes de datos es un hecho indiscutible en los países latinoamericanos, también existe un verdadero esfuerzo desde los diferentes sectores por “hacer visible” la problemática de las personas con situación de discapacidad, y poner de relieve la atención necesaria orientada a este grupo poblacional en particular, que involucra a su entorno cultural, físico, económico, político, social y educativo, donde se esperan respuestas desde una política de estado, enfocada particularmente hacia los derechos y donde resulten responsables los gobiernos y la sociedad civil

El turismo como actividad inclusiva: análisis de dos establecimientos hoteleros

El turismo accesible se orienta a posibilitar la inclusión de personas discapacitadas a la actividad turística y mejora las oportunidades del sector al contemplar este mercado potencial en crecimiento que actualmente alcanza casi al 10% de la población mundial. En este contexto surge esta investigación que indaga esta problemática en los establecimientos hoteleros de Tucumán: La residencia universitaria de Horco molle y la Hostería de Tafi del valle del Automóvil Club Argentino. La estrategia metodológica es de tipo cualitativa con componentes cuantitativos de nivel exploratorio descriptivo y se planteó como objetivos conocer las barreras en la oferta turística y la adecuación de los establecimientos y espacios en relación a las necesidades de personas discapacitadas y elaborar así una comparación entre las falencias que presentaran

Pomegranate transplant stress can be ameliorated by rhizophagus intraradices under nursery management

Arbuscular mycorrhizal fungi (AMF) establish an obligate mutualistic symbiosis with many plant species, increasing the uptake of phosphorous and other low-mobile nutrients by roots. In addition, AMF improve biotic and abiotic stress tolerance of host plants. Under these conditions, reactive oxygen species (ROS) increase occasional damage to proteins, lipids and DNA. Antioxidative enzymes in plants can play an important role in detoxifying ROS, thereby alleviating oxidative stress. In nursery practices, plants are subjected at least to two transplant conditions before being transplanted outside. It is important to achieve an optimal plant size to withstand environmental or other stresses when plants are transplanted into the field. The transplantation process can be considered a stress because plants have to adapt to new abiotic and biotic (rhizospheric) conditions. The aim of this study was to evaluate the effect of two Rhizophagus intraradices (N.C. Schenck & G.S. Sm.) C. Walker & A. Schüßler strains, GA5 and GC2, single and co-inoculated under two-transplant soil conditions, sterile and non-sterile, using cuttings of pomegranate (Punica granatum L.) as a model plant. These results showed that the GA5 single strain-inoculated plants improved growth and antioxidative enzyme responses to two transplant stress conditions. In conclusion, early mycorrhizal inoculation generates healthy plants that are more protected against environmental conditions, thereby improving plant transplant stress tolerance.Fil: Bompadre, Maria Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Colombo, Roxana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Silvani, Vanesa Analia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Fernandez Bidondo, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Pardo, Alejandro Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Micología Molecular; ArgentinaFil: Ocampo, Juan Antonio. Consejo Superior de Investigaciones Científicas. Estación Experimental del Zaidín; EspañaFil: Godeas, Alicia Margarita. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; Argentin

Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes

Background: The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM). Results: Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A–H2B dimer/H3–H4 tetramer interface, and H3 A110C, resides at the H3–H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed. Conclusions: Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.Fil: Marr, Luke T.. University of Rochester Medical Center; Estados UnidosFil: Ocampo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Clark, David J.. National Instituto of Child Health & Human Development; Estados UnidosFil: Hayes, Jeffrey J.. University of Rochester Medical Center; Estados Unido

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these \u27proto-chromatosomes\u27 are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1

Craniofacial Growth Analysis of Individuals With and Without Cleft Lip and Palate in Colombia

Introducción: El crecimiento craneofacial es un proceso dinámico e impredecible influenciado por factores genéticos y ambientales, presentando diferencias fenotípicas y de género. Objetivo: Evaluar las diferencias en el crecimiento y desarrollo craneofacial en un grupo de individuos colombianos con labio y paladar hendido (LPH) completo unilateral y bilateral y sin LPH, clasificados por género y edad. Entorno y población muestral: Quinientas cuarenta y una radiografías de perfil de 126 pacientes con CLP unilateral, 126 con CLP bilateral y 289 sin CLP. Todos los pacientes de los grupos afectados tenían antecedentes de cirugía de corrección del CLP sin moldeado nasoalveolar con tratamientos ortopédicos y ortodóncicos. Materiales y métodos: Este estudio transversal se realizó comparando 8 medidas cefalométricas en radiografías, 5 lineales/3 angulares. El análisis se realizó por mediana y rango intercuartílico para todas las medidas cefalométricas. La comparación entre los grupos se realizó mediante Kruskal-Wallis y U de Mann-Whitney, con una confianza del 95%. Resultados: Diferencias significativas entre los grupos de pacientes con y sin CLP, entre tipos de fisuras y géneros. Las estructuras esqueléticas de los pacientes con CLP eran más pequeñas que las de los controles, pero mejoraban con el crecimiento. Los pacientes con CLP unilateral presentaban perfiles planos y maloclusiones predominantemente de clase III, mientras que los pacientes con CLP bilateral, a edades tempranas, eran de clase II y en la etapa prepuberal, los valores eran progresivamente negativos hasta el final del periodo de crecimiento, sugiriendo clase III. Los pacientes con CLP presentaron rotación posteroinferior de la mandíbula, medidas verticales aumentadas y desviación de la base craneal. Conclusiones: Dadas sus alteraciones en el crecimiento, los pacientes con CLP se benefician del tratamiento ortopédico y ortodóncico.Introduction: Craniofacial growth is a dynamic and unpredictable process influenced by genetic and environmental factors, presenting phenotypic and gender differences. Objective: Evaluate the differences in craniofacial growth and development in a group of Colombian individuals with complete unilateral and bilateral cleft lip and palate (CLP) and without CLP, classified by gender and age. Setting and Sample Population: Five hundred forty-one profile radiographs of 126 patients with unilateral CLP, 126 with bilateral CLP, and 289 without CLP. All patients of affected groups had a history of CLP correction surgery without nasoalveolar molding with orthopedic and orthodontic treatments. Materials and Methods: This cross-sectional study was performed comparing 8 cephalometric measurements on radiographs, 5 linear/3 angular. Analysis was performed by median and interquartile range for all cephalometric measurements. Comparison between the groups was performed using Kruskal-Wallis and Mann-Whitney U, with a 95% confidence. Results: Significant differences between the groups of patients with and without CLP, between types of clefts and genders. The skeletal structures of patients with CLP were smaller than those of control but improved with growth. Patients with unilateral CLP presented flat profiles and predominant class III malocclusions, while patients with bilateral CLP, at early ages, were class II and in the prepubertal stage, the values were progressively negative until the end of the growth period, suggesting class III. Patients with CLP presented posteroinferior rotation of the mandible, vertical measurements increased, and deflection of the cranial base. Conclusion: Given their growth alterations, patients with CLP benefit from orthopedic and orthodontic treatment