TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets

This article has been accepted for publication in Bioinformatics Published by Oxford University PressThe identification of transcription factors (TFs) responsible for the co-regulation of specific sets of genes is a common problem in transcriptomics. Herein we describe TFEA.ChIP, a tool to estimate and visualize TF enrichment in gene lists representing transcriptional profiles. To generate the gene sets representing TF targets, we gathered ChIP-Seq experiments from the ENCODE Consortium and GEO datasets and used the correlation between Dnase Hypersensitive Sites across cell lines to generate a database linking TFs with the genes they interact with in each ChIP-Seq experiment. In its current state, TFEA.ChIP covers 327 different transcription factors from 1075 ChIP-Seq experiments, with over 150 cell types being represented. TFEA.ChIP accepts gene sets as well as sorted lists differentially expressed genes to compute enrichment scores for each of the datasets in its internal database using an Fisher's exact association test or a Gene Set Enrichment Analysis. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TF was correctly identified in 103 of a total of 144 analyzed datasets with a median area under the curve (AUC) of 0.86. In depth analysis of an RNAseq dataset, illustrates that the use of ChIP-Seq data instead of PWM-based provides key biological context to interpret the results of the analysis. To facilitate its integration into transcriptome analysis pipelines and allow easy expansion and customization of the TF-gene database, we implemented TFEA.ChIP as an R package that can be downloaded from Bioconductor: https://www.bioconductor.org/packages/devel/bioc/html/TFEA.ChIP.html and github: https://github.com/LauraPS1/TFEA-drafts In addition, make it available to a wide range of researches, we have also developed a web application that runs the package from the server side and enables easy exploratory analysis through interactive graphs: https://www.iib.uam.es/TFEA.ChIP/This work was supported by Ministerio de Ciencia e Innovación (Spanish Ministry of Science and Innovation, MICINN) [SAF2014-53819-R to Ldel P, SAF2017-88771-R to L del P] by Fundacion Caja Madrid (Beca de Movilidad para Profesores de las Universidades Publicas de Madrid 2011-2012 to LPO

ERK5 Is a Major Determinant of Chemical Sarcomagenesis: Implications in Human Pathology

Sarcomas are a heterogeneous group of tumors in which the role of ERK5 is poorly studied. To clarify the role of this MAPK in sarcomatous pathology, we used a murine 3-methyl-cholanthrene (3MC)-induced sarcoma model. Our data show that 3MC induces pleomorphic sarcomas with muscle differentiation, showing an increased expression of ERK5. Indeed, this upregulation was also observed in human sarcomas of muscular origin, such as leiomyosarcoma or rhabdomyosarcoma. Moreover, in cell lines derived from these 3MC-induced tumors, abrogation of Mapk7 expression by using specific shRNAs decreased in vitro growth and colony-forming capacity and led to a marked loss of tumor growth in vivo. In fact, transcriptomic profiling in ERK5 abrogated cell lines by RNAseq showed a deregulated gene expression pattern for key biological processes such as angiogenesis, migration, motility, etc., correlating with a better prognostic in human pathology. Finally, among the various differentially expressed genes, Klf2 is a key mediator of the biological effects of ERK5 as indicated by its specific interference, demonstrating that the ERK5–KLF2 axis is an important determinant of sarcoma biology that should be further studied in human pathology.This work has been supported with Grant RTI2018-094093-B-I00 funded by MCIN/AEI/10.13039/501100011033, “ERDF A way of making Europe” to RSP. Also supported with funds from Fundación Leticia Castillejo Castillo, Roche España and ACEPAIN to RSP and MJRH. RSP and MJRH’s Research Institute and the work carried out in their laboratory, received partial support from the European Community through the FEDER. JJ and EAL hold a predoctoral research contract cofounded by the European Social Fund and UCLM. OR holds a contract for accessing the Spanish System of Science, Technology, and Innovation (SECTI) funded by the University of Castilla-La Mancha (UCLM) and received partial support from the European Social Fund (FSE) through its Operative Program for Castilla-La Mancha (2007–2013

Los presupuestos participativos: dimensiones analíticas y líneas de debate en la experiencia española

Presidente: Francisco J. Vanaclocha Bellever; Vocal: Rafael Bañón Martínez; Secretaria: Blanca Olías de Lima Get

Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms

Hypoxia, or reduced oxygen availability, has been studied extensively for its ability to activate specific genes. Hypoxia induced gene expression is mediated by the HIF transcription factors, although not exclusively so. Despite the great knowledge on the mechanisms by which hypoxia activates genes, much less is known about how hypoxia promotes gene repression. In this review, we discuss the potential mechanisms underlying hypoxia-induced transcriptional repression responses. We highlight HIF-dependent and independent mechanisms, but also the potential roles of dioxygenases with functions at the nucleosome and DNA level. Finally, we discuss recent evidence regarding the involvement of transcriptional repressor complexes in hypoxia

Investigaciones e investigadores de la UAM

Continuamos en este número de la revista con la sección: Investigaciones en la Universidad Autónoma de Madrid, con la que se pretende dar a conocer investigaciones relacionadas con diversas disciplinas científicas que se han desarrollado o se están llevando a cabo en la UAM, con el fin de describir de una forma simple y didáctica tales trabajos, y con ello los contenidos de diversas ramas del conocimiento, y cumplir así con la finalidad inherente a esta revista de divulgar la ciencia así como de contribuir al surgimiento de posibles ideas o iniciativas para posteriores investigaciones por parte de los jóvenes científicos, o de estudiantes universitarios de grado o posgrado que están en disposición y voluntad de llegar a serlo. Se recogen a continuación algunos relatos de investigaciones realizadas por varios profesores de la UAM, los cuales se recogieron en una publicación conmemorativa del cumplimiento de los cuarenta años por parte de esta universidad y relativos a las siguientes disciplinas: Biomedicina, Historia Contemporánea, Química y alimentación, Matemáticas y Bioquímic

A yeast three-hybrid system that reconstitutes mammalian hypoxia inducible factor regulatory machinery

<p>Abstract</p> <p>Background</p> <p>Several human pathologies, including neoplasia and ischemic cardiovascular diseases, course with an unbalance between oxygen supply and demand (hypoxia). Cells within hypoxic regions respond with the induction of a specific genetic program, under the control of the Hypoxia Inducible Factor (HIF), that mediates their adaptation to the lack of oxygen. The activity of HIF is mainly regulated by the EGL-nine homolog (EGLN) enzymes that hydroxylate the alpha subunit of this transcription factor in an oxygen-dependent reaction. Hydroxylated HIF is then recognized and ubiquitinilated by the product of the tumor suppressor gene, pVHL, leading to its proteosomal degradation. Under hypoxia, the hydroxylation of HIF by the EGLNs is compromised due to the lack of oxygen, which is a reaction cosubstrate. Thus, HIF escapes degradation and drives the transcription of its target genes. Since the progression of the aforementioned pathologies might be influenced by activation of HIF-target genes, development of small molecules with the ability to interfere with the HIF-regulatory machinery is of great interest.</p> <p>Results</p> <p>Herein we describe a yeast three-hybrid system that reconstitutes mammalian HIF regulation by the EGLNs and VHL. In this system, yeast growth, under specific nutrient restrictions, is driven by the interaction between the β domain of VHL and a hydroxyproline-containing HIFα peptide. In turn, this interaction is strictly dependent on EGLN activity that hydroxylates the HIFα peptide. Importantly, this system accurately preserves the specificity of the hydroxylation reaction toward specific substrates. We propose that this system, in combination with a matched control, can be used as a simple and inexpensive assay to identify molecules that specifically modulate EGLN activity. As a proof of principle we show that two known EGLN inhibitors, dimethyloxaloylglycine (DMOG) and 6-chlor-3-hydroxychinolin-2-carbonic acid-N-carboxymethylamide (S956711), have a profound and specific effect on the yeast HIF/EGLN/VHL system.</p> <p>Conclusion</p> <p>The system described in this work accurately reconstitutes HIF regulation while preserving EGLN substrate specificity. Thus, it is a valuable tool to study HIF regulation, and particularly EGLN biochemistry, in a cellular context. In addition, we demonstrate that this system can be used to identify specific inhibitors of the EGLN enzymes.</p

Search for the Higgs boson decays H → ee and H → eμ in pp collisions at √s = 13 TeV with the ATLAS detector

Artículo escrito por un elevado número de autores, sólo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiera, y los autores pertenecientes a la UAMSearches for the Higgs boson decays H→eeand H→eμare performed using data corresponding to an integrated luminosity of 139 fb−1collected with the ATLAS detector in ppcollisions at √s=13 TeV at the LHC. No significant signals are observed, in agreement with the Standard Model expectation. For a Higgs boson mass of 125 GeV, the observed (expected) upper limit at the 95% confidence level on the branching fraction β(H→ee)is 3.6 ×10−4(3.5 ×10−4) and on β(H→eμ)is 6.2 ×10−5(5.9 ×10−5). These results represent improvements by factors of about five and six on the previous best limits on β(H→ee)and β(H→eμ)respectivelyWe acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF and DNSRC, Denmark; IN2P3-CNRS, CEA-DRF/IRFU, France; SRNSFG, Georgia; BMBF, HGF, and MPG, Germany; GSRT, Greece; RGC, Hong Kong SAR, China; ISF and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; NWO, Netherlands; RCN, Norway; MNiSW and NCN, Poland; FCT, Portugal; MNE/IFA, Romania; MES of Russia and NRC KI, Russian Federation; JINR; MESTD, Serbia; MSSR, Slovakia; ARRS and MIZŠ, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SERI, SNSF and Cantons of Bern and Geneva, Switzerland; MOST, Taiwan; TAEK, Turkey; STFC, United Kingdom; DOE and NSF, United States of America. In addition, individual groups and members have received support from BCKDF, CANARIE, CRC and Compute Canada, Canada; COST, ERC, ERDF, Horizon 2020, and Marie Skłodowska-Curie Actions, European Union; Investissements d' Avenir Labex and Idex, ANR, France; DFG and AvH Foundation, Germany; Herakleitos, Thales and Aristeia programmes co-financed by EU-ESF and the Greek NSRF, Greece; BSF-NSF and GIF, Israel; CERCA Programme Generalitat de Catalunya, Spain; The Royal Society and Leverhulme Trust, United Kingdo

Long-term implications of traditional forest regulation methods applied to Maritime pine (Pinus pinaster Ait.) forests in central Spain: a century of management plans

Producción CientíficaPinus pinaster stands in the northern Iberian range (Spain) have been under forest management plans for more than a century. The main goals have been sustainable yield and conservation and enhancement of forest conditions. In the study area, forest management plan implementation started to be effective in the late 19th and early 20th centuries and the plans have been evaluated every ten years. In these forests, a permanent forest compartment method has been applied as the management system. Different regeneration methods have been applied (uniform shelterwood and clear cutting in Soria, selective and uniform shelterwood and continuous cover forestry in Teruel). To analyse the evolution of each forest group, five management indicators have been tested in this study: number of merchantable trees, standing volume, resin production, allowable yield, and harvested volume. Forest situation improvement and maintenance of forest integrity are not only a consequence of the actions planed by foresters, they are also influenced by socio-economic transformations that have occurred during the last century such as the weakness of the resin market, decreasing demand for fire wood, restriction of pasture activities, and increasing recreation use.Ministerio de Educación y Ciencia (project AGL-2001-1780)Ministerio de Educación y Ciencia (project AGL2004-07094-C02-02)Ministerio de Educación y Ciencia (project AGL2007-65795-C02-01

miR-127 protects proximal tubule cells against ischemia/reperfusion : identification of Kinesin family member 3B as miR-127 target

Ischemia/reperfusion (I/R) is at the basis of renal transplantation and acute kidney injury. Molecular mechanisms underlying proximal tubule response to I/R will allow the identification of new therapeutic targets for both clinical settings. microRNAs have emerged as crucial and tight regulators of the cellular response to insults including hypoxia. Here, we have identified several miRNAs involved in the response of the proximal tubule cell to I/R. Microarrays and RT-PCR analysis of proximal tubule cells submitted to I/R mimicking conditions in vitro demonstrated that miR-127 is induced during ischemia and also during reperfusion. miR-127 is also modulated in a rat model of renal I/R. Interference approaches demonstrated that ischemic induction of miR-127 is mediated by Hypoxia Inducible Factor-1alpha (HIF-1α) stabilization. Moreover, miR-127 is involved in cell-matrix and cell-cell adhesion maintenance, since overexpression of miR-127 maintains focal adhesion complex assembly and the integrity of tight junctions. miR-127 also regulates intracellular trafficking since miR-127 interference promotes dextran-FITC uptake. In fact, we have identified the Kinesin Family Member 3B (KIF3B), involved in cell trafficking, as a target of miR-127 in rat proximal tubule cells. In summary, we have described a novel role of miR-127 in cell adhesion and its regulation by HIF-1α. We also identified for the first time KIF3B as a miR-127 target. Both, miR-127 and KIF3B appear as key mediators of proximal epithelial tubule cell response to I/R with potential al application in renal ischemic damage management

Vitamin D and Wnt3A have additive and partially overlapping modulatory effects on gene expression and phenotype in human colon fibroblasts

The Wnt/β-catenin signalling pathway is essential for intestinal epithelium homeostasis, but its aberrant activation is a hallmark of colorectal cancer (CRC). Several studies indicate that the bioactive vitamin D metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) inhibits proliferation and promotes epithelial differentiation of colon carcinoma cells in part through antagonism of the Wnt/β-catenin pathway. It is now accepted that stromal fibroblasts are crucial in healthy and pathologic intestine: pericryptal myofibroblasts are constituents of the stem cell niche and cancer-associated fibroblasts (CAFs) contribute to CRC progression. However, studies on the combined action of 1,25(OH)2D3 and Wnt factors in colon fibroblasts are lacking. Here we show by global transcriptomic studies that 1,25(OH)2D3 and Wnt3A have profound, additive, partially overlapping effects on the gene expression profile of CCD-18Co human colon myofibroblasts. Moreover, 1,25(OH)2D3 and Wnt3A inhibit CCD-18Co cell proliferation and migration, while 1,25(OH)2D3 reduces, but Wnt3A increases, their capacity to contract collagen gels (a marker of fibroblast activation). These data were largely confirmed in patient-derived primary colon normal fibroblasts and CAFs, and in fibroblasts from other origins. Our results indicate that 1,25(OH)2D3 and Wnt3A are strong regulators of colon fibroblast biology and contribute to a better knowledge of intestinal homeostasis and stromal fibroblast action in CRCThe work in the authors’ laboratories is supported by the Spanish Ministerio de Ciencia, Innovación y Universidades - Fondo Europeo de Desarrollo Regional (FEDER) (SAF2016-76377-R, SAF2017-90604-REDT), Consejo Superior de Investigaciones Científicas (201820I058), and Instituto de Salud Carlos III - FEDER (CIBERONC, CB16/12/00273; CIBERES, CB15/00037