CREMOFAC - a database of chromatin remodeling factors

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors. Results: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable

The CHROMEVALOA Database: A Resource for the Evaluation of Okadaic Acid Contamination in the Marine Environment Based on the Chromatin-Associated Transcriptome of the Mussel Mytilus galloprovincialis

Okadaic Acid (OA) constitutes the main active principle in Diarrhetic Shellfish Poisoning (DSP) toxins produced during Harmful Algal Blooms (HABs), representing a serious threat for human consumers of edible shellfish. Furthermore, OA conveys critical deleterious effects for marine organisms due to its genotoxic potential. Many efforts have been dedicated to OA biomonitoring during the last three decades. However, it is only now with the current availability of detailed molecular information on DNA organization and the mechanisms involved in the maintenance of genome integrity, that a new arena starts opening up for the study of OA contamination. In the present work we address the links between OA genotoxicity and chromatin by combining Next Generation Sequencing (NGS) technologies and bioinformatics. To this end, we introduce CHROMEVALOAdb, a public database containing the chromatin-associated transcriptome of the mussel Mytilus galloprovincialis (a sentinel model organism) in response to OA exposure. This resource constitutes a leap forward for the development of chromatin-based biomarkers, paving the road towards the generation of powerful and sensitive tests for the detection and evaluation of the genotoxic effects of OA in coastal areas

EpiFactors : a comprehensive database of human epigenetic factors and complexes

Altres ajuts: Russian Fund For Basic Research(RFFI)grant 14-04-0018 i grant 15-34-20423, Ake Olsson's foundation, Swedish Cancer foundation, Swedish Childhood cancer foundation, Dynasty Foundation Fellowship, RIKEN Omics Science Center, RIKEN Preventive Medicine and Diagnosis Innovation Program i RIKEN Center for Life Science Technologies.Abstract: Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians

Transcriptomic and Epigenetic Responses to Environmental Stress in Marine Bivalves with a Focus on Harmful Algal Blooms

Global change poses new threats for life in the oceans forcing marine organisms to respond through molecular acclimatory and adaptive strategies. Although bivalve molluscs are particularly tolerant and resilient to environmental stress, they must now face the challenge of more frequent and severe Harmful Algal Blooms (HABs) episodes. These massive outbreaks of microalgae produce toxins that accumulate in the tissues of these filter-feeder organisms, causing changes in their gene expression profiles, which in turn modify their phenotype in order to maintain homeostasis. Such modifications in gene expression are modulated by epigenetic mechanisms elicited by specific environmental stimuli, laying the foundations for long-term adaptations. The present work aims to examine the links between environmental stress in bivalve molluscs (with especial emphasis on Harmful Algal Blooms) and specific epigenetic marks triggering responses through modifications in gene expression patterns. Overall, a better understanding of the molecular strategies underlying the conspicuous stress tolerance observed in bivalve molluscs will provide a framework for developing a new generation of biomonitoring strategies. In addition, this strategy will represent a valuable contribution to our knowledge in acclimatization, adaptation and survival. With that goal in mind, the present work has generated transcriptomic data using RNA-Seq and microarray technologies, facilitating the characterization and investigation of the epigenetic mechanisms used by the Mediterranean mussel Mytilus galloprovincialis during responses to HAB exposure. That information was made publicly available through a specialized online resource (the Chromevaloa Database, chromevaloa.com) assessing the response of chromatin-associated transcripts to Okadaic Acid. Specific epigenetic marks have been assessed under lab-controlled exposure experiments simulating the natural development of the HAB Florida Red Tide (FRT). Results demonstrate a role for the phosphorylation of histone H2A.X and DNA methylation in the response to FRT in the Eastern oyster Crassostrea virginica. Lastly, the study of co-expression networks based on RNA-Seq data series from the Pacific oyster Crassostrea gigas reveals dynamic transcriptomic patterns that vary with time, stressor and tissue. However, consistent functional profiles support the existence of a core response to general conditions of environmental stress. Such response involves metabolic and transport processes, response to oxidative stress and protein repair or disposal, as well as the activation of immune mechanisms supporting a tightly intertwined neuroendocrine-immune regulatory system in bivalves

Histonas variantes en invertebrados marinos: puesta a punto de metodologías para el estudio de la cromatina y caracterización de las variantes macroH2A y H2A.Z.2 en moluscos bivalvos

[Resumen] En las células eucariotas el DNA se asocia con histonas y proteínas no histónicas formando un complejo conocido como cromatina que media en la organización y la regulación del material hereditario en el espacio del núcleo celular. Además del papel estructural de las histonas, la incorporación de variantes de estas proteínas a los nucleosomas es esencial para el correcto desarrollo de importantes procesos celulares como la regulación de la expresión génica, la replicación o la reparación del DNA. Aunque existe una gran cantidad de estudios sobre estas proteínas en organismos deuteróstomos, la presencia y características funcionales de histonas variantes, además de la especialización que imparten a la cromatina, son prácticamente desconocidas en el caso del linaje de animales protóstomos. Dentro de este grupo, los moluscos bivalvos presentan un interés especial debido a las condiciones ambientales a las que están expuestos que suscita una rápida y precisa regulación de la expresión génica. La caracterización de las histonas variantes macroH2A y H2A.Z.2 en especies de este grupo animal, así como el desarrollo de técnicas de estudio de su cromatina, aporta datos muy valiosos acerca de la especialización funcional impartida por estas proteínas a la cromatina de los diversos grupos de organismos eucariotas.[Resumo] Nas células eucarióticas o DNA asóciase con histonas e proteínas non histónicas formando un complexo coñecido como cromatina que media na organización e a regulación do material hereditario no espazo do núcleo celular. Ademais do papel estrutural das histonas, a incorporación de variantes destas proteínas aos nucleosomas é esencial para o correcto desenvolvemento de importantes procesos celulares como a regulación da expresión xénica, a replicación ou a reparación do DNA. Aínda que existe unha gran cantidade de estudos sobre estas proteínas en organismos deuteróstomos, a presenza e características funcionais de histonas variantes, ademais da especialización que imparten á cromatina, son practicamente descoñecidas no caso da liñaxe dos animais protóstomos. Dentro deste grupo, os moluscos bivalvos presentan un interese especial debido ás condicións ambientais ás que están expostos que suscita unha rápida e precisa regulación da expresión xénica. A caracterización das histonas variantes macroH2A e H2A.Z.2 en especies deste grupo animal, así como o desenvolvemento de técnicas de estudo da súa cromatina, achega datos moi valiosos acerca da especialización funcional impartida por estas proteínas á cromatina dos diversos grupos de organismos eucarióticas[Abstract] In eukaryotic cells DNA is associated with histone and non-histone proteins constituting a nucleoprotein structure known as chromatin, mediating the organization and regulation of the genetic material in the cell nucleus. Besides the structural role of histones, incorporation of variants of these proteins to nucleosomes is essential for the proper development of important cellular processes such as regulation of gene expression, replication, and DNA repair. Although several studies on these proteins are available in deuterostome organisms, the presence and functional characteristics of histone variants and the specialized functions imparted to the chromatin are virtually unknown in the case of the protostome lineage. Within this group, bivalve molluscs are of particular interest because of the environmental conditions to which they are exposed. The characterization of histone variants macroH2A and H2A.Z.2 in these organisms and the development of different techniques for studying their chromatin will provide valuable information about the functional specialization imparted by these proteins to the chromatin of eukaryotic organisms

CREMOFAC- a database of chromatin remodeling factors

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors.Results: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable