Papers by Marco Antonio Mendoza
Single-tube linear DNA amplification for genome-wide studies using a few thousand cells
Nature Protocols, 2012
Analysis of protein-DNA interactions during meiosis by quantitative chromatin immunoprecipitation (qChIP)
Methods in Molecular Biology
During meiotic prophase a number of important events require recombination between maternal and p... more During meiotic prophase a number of important events require recombination between maternal and paternal chromosomes, which is initiated through the introduction of DNA double-strand breaks (DSBs). The majority of DSBs, which mostly occur at so-called hotspots, have been located between cohesin binding sites. qChIP (chromatin immunoprecipitation quantified by real-time PCR) is a sensitive, accurate, and cost-efficient alternative to ChIP-on-Chip for the analysis of noncovalent protein-DNA interactions at defined binding sites in vivo. Here we use qChIP to study Mre11 binding to three chromosomal loci during meiosis. We show that Mre11 interacts with a known hotspot region (UpsilonCR048) in the R-band of chromosome III, but not with a cold region in the G-band (UpsilonCR011). Interestingly Mre11 binds to a cohesin binding site (UpsilonCR067), 20 kb distal to UpsilonCR048, with similar intensity as to the hotspot, despite the absence of DSBs in this region.
Analysis of Protein–DNA Interactions During Meiosis by Quantitative Chromatin Immunoprecipitation (qChIP)
Methods in Molecular Biology, 2009
During meiotic prophase a number of important events require recombination between maternal and p... more During meiotic prophase a number of important events require recombination between maternal and paternal chromosomes, which is initiated through the introduction of DNA double-strand breaks (DSBs). The majority of DSBs, which mostly occur at so-called hotspots, have been located between cohesin binding sites. qChIP (chromatin immunoprecipitation quantified by real-time PCR) is a sensitive, accurate, and cost-efficient alternative to ChIP-on-Chip for the analysis of noncovalent protein-DNA interactions at defined binding sites in vivo. Here we use qChIP to study Mre11 binding to three chromosomal loci during meiosis. We show that Mre11 interacts with a known hotspot region (UpsilonCR048) in the R-band of chromosome III, but not with a cold region in the G-band (UpsilonCR011). Interestingly Mre11 binds to a cohesin binding site (UpsilonCR067), 20 kb distal to UpsilonCR048, with similar intensity as to the hotspot, despite the absence of DSBs in this region.
Journal of Medicinal Chemistry, 2009
Multinuclear platinum anticancer complexes are a proven option to overcome resistance of establis... more Multinuclear platinum anticancer complexes are a proven option to overcome resistance of established anticancer compounds. Transferring this concept to ruthenium complexes led to the synthesis of dinuclear Ru(II)-arene compounds containing a bis(pyridinone)alkane ligand linker. A pronounced influence of the spacer length on the in vitro anticancer activity was found, which is correlated to the lipophilicity of the complexes. IC 50 values in the same dimension as for established platinum drugs were found in human tumor cell lines. No cross-resistance to oxoplatin, a cisplatin prodrug, was observed for the most active complex in three resistant cell lines; in fact, a 10-fold reversal of sensitivity in two of the oxoplatin-resistant lines was found. (Bio)analytical characterization of the representative examples showed that the ruthenium complexes hydrolyze rapidly, forming predominantly diaqua species that exhibit affinity toward transferrin and DNA, indicating that both proteins and nucleobases are potential targets.
Genomics Data, 2014
Massive parallel DNA sequencing combined with chromatin immunoprecipitation and a large variety o... more Massive parallel DNA sequencing combined with chromatin immunoprecipitation and a large variety of DNA/ RNA-enrichment methodologies is at the origin of data resources of major importance. Indeed these resources, available for multiple genomes, represent the most comprehensive catalogue of (i) cell, development and signal transduction-specified patterns of binding sites for transcription factors ('cistromes') and for transcription and chromatin modifying machineries and (ii) the patterns of specific local post-translational modifications of histones and DNA ('epigenome') or of regulatory chromatin binding factors. In addition, (iii) the resources specifying chromatin structure alterations are emerging. Importantly, these types of "omics" datasets populate increasingly public repositories and provide highly valuable resources for the exploration of general principles of cell function in a multi-dimensional genome-transcriptome-epigenome-chromatin structure context. However, data mining is critically dependent on the data quality, an issue that, surprisingly, is still largely ignored by scientists and well-financed consortia, data repositories and scientific journals. So what determines the quality of ChIP-seq experiments and the datasets generated therefrom and what refrains scientists from associating quality criteria to their data? In this 'opinion' we trace the various parameters that influence the quality of this type of datasets, as well as the computational efforts that were made until now to qualify them. Moreover, we describe a universal quality control (QC) certification approach that provides a quality rating for ChIP-seq and enrichment-related assays. The corresponding QC tool and a regularly updated database, from which at present the quality parameters of more than 8000 datasets can be retrieved, are freely accessible at www.ngs-qc.org.
The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
Genome Research, 2015
Disappearance of the Barr body is considered a hallmark of cancer, although whether this correspo... more Disappearance of the Barr body is considered a hallmark of cancer, although whether this corresponds to genetic loss or to epigenetic instability and transcriptional reactivation is unclear. Here we show that breast tumors and cell lines frequently display major epigenetic instability of the inactive X chromosome, with highly abnormal 3D nuclear organization and global perturbations of heterochromatin, including gain of euchromatic marks and aberrant distributions of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells and a significant degree of aberrant gene activity from the inactive X chromosome, including several genes involved in cancer promotion. We demonstrate that many of these genes are aberrantly reactivated in primary breast tumors, and we further demonstrate that epigenetic instability of the inactive X can lead to perturbed dosage of X-linked factors. Taken together, our study provides the first integrated analysis of the inactive X chromosome in the context of breast cancer and establishes that epigenetic erosion of the inactive X can lead to the disappearance of the Barr body in breast cancer cells. This work offers new insights and opens up the possibility of exploiting the inactive X chromosome as an epigenetic biomarker at the molecular and cytological levels in cancer.
Integrative Genomics to Dissect Retinoid Functions
Subcellular Biochemistry, 2014
Retinoids and rexinoids, as all other ligands of the nuclear receptor (NR) family, act as ligand-... more Retinoids and rexinoids, as all other ligands of the nuclear receptor (NR) family, act as ligand-regulated trans-acting transcription factors that bind to cis-acting DNA regulatory elements in the promoter regions of target genes (for reviews see [12, 22, 23, 26, 36]). Ligand binding modulates the communication functions of the receptor with the intracellular environment, which essentially entails receptor-protein and receptor-DNA or receptor-chromatin interactions. In this communication network, the receptor simultaneously serves as both intracellular sensor and regulator of cell/organ functions. Receptors are "intelligent" mediators of the information encoded in the chemical structure of a nuclear receptor ligand, as they interpret this information in the context of cellular identity and cell-physiological status and convert it into a dynamic chain of receptor-protein and receptor-DNA interactions. To process input and output information, they are composed of a modular structure with several domains that have evolved to exert particular molecular recognition functions. As detailed in other chapters in this volume, the main functional domains are the DNA-binding (DBD) and ligand-binding (LBD) [5-7, 38, 56, 71]. The LBD serves as a dual input-output information processor. Inputs, such as ligand binding or receptor phosphorylations, induce allosteric changes in receptor surfaces that serve as docking sites for outputs, such as subunits of transcription and epigenetic machineries or enzyme complexes. The complexity of input and output signals and their interdependencies is far from being understood.
Sequential chromatin immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq)
Protocol Exchange, 2012
Aging Cell, 2014
Senescent cells secrete a plethora of factors with potent paracrine signaling capacity. Strikingl... more Senescent cells secrete a plethora of factors with potent paracrine signaling capacity. Strikingly, senescence, which acts as defense against cell transformation, exerts pro-tumorigenic activities through its secretome by promoting tumor-specific features, such as cellular proliferation, epithelial-mesenchymal transition and invasiveness. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has the unique activity of activating cell death exclusively in tumor cells. Given that the senescence-associated secretome (SAS) supports cell transformation, we asked whether SAS factor(s) would establish a program required for the acquisition of TRAIL sensitivity. We found that conditioned media from several types of senescent cells (CMS) efficiently sensitized pretransformed cells to TRAIL, while the same was not observed with normal or immortalized cells. Dynamic transcription profiling of CMS-exposed pretransformed cells indicated a paracrine autoregulatory loop of SAS factors and a dominant role of CMSinduced MYC. Sensitization to TRAIL coincided with and depended on MYC upregulation and massive changes in gene regulation. Senescent cell-induced MYC silenced its target gene CFLAR, encoding the apoptosis inhibitor FLIP L , thus leading to the acquisition of TRAIL sensitivity. Altogether, our results reveal that senescent cell-secreted factors exert a TRAIL-sensitizing effect on pretransformed cells by modulating the expression of MYC and CFLAR. Notably, CMS dose-dependent sensitization to TRAIL was observed with TRAIL-insensitive cancer cells and confirmed in co-culture experiments. Dissection and characterization of TRAILsensitizing CMS factors and the associated signaling pathway(s) will not only provide a mechanistic insight into the acquisition of TRAIL sensitivity but may lead to novel concepts for apoptogenic therapies of premalignant and TRAIL-resistant tumors.
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increas-ingl... more Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increas-ingly used to map protein–chromatin interactions at global scale. The comparison of ChIP-seq profiles for RNA polymerase II (PolII) established in different biological contexts, such as specific developmental stages or specific time-points during cell differenti-ation, provides not only information about the presence/accumulation of PolII at transcription start sites (TSSs) but also about functional features of transcription, including PolII stalling, pausing and transcript elongation. However, anno-tation and normalization tools for comparative studies of multiple samples are currently missing. Here, we describe the R-package POLYPHEMUS, which integrates TSS annotation with PolII enrich-ment over TSSs and coding regions, and normalizes signal intensity profiles. Thereby POLYPHEMUS fa-cilitates to extract information about global PolII action to reveal changes in the functional state of gene...
Characterising ChIP-seq binding patterns by model-based peak shape deconvolution
Seminars in cell & developmental biology, 2013
Nuclear receptors (NRs) are important mediators of the information encoded in the chemical struct... more Nuclear receptors (NRs) are important mediators of the information encoded in the chemical structure of its corresponding ligand, as they interpret such information in the context of the cell identity and physiological status and convert it into sequential transcription regulatory events. At the cell level this can result in temporally coordinated processes such as cell fate transitions, which comprise the regulation of a plethora of gene programs including among others regulation of cell proliferation, metabolism and specific functionalities that are acquired by the differentiated cell. While both the early steps of nuclear receptor function and their impact on animal/organ physiology is rather well understood, little is known about the dynamic gene networks that ultimately cause a particular (cell) physiological phenomenon induced by the cognate NR ligand/hormone. Thanks to advances in massive parallel sequencing and bioinformatics analyses of genome-wide data sets, time has come for the development of NR systems biology. Indeed it is now possible to integrate global transcription factor binding, epigenetic chromatin histone and DNA modification patterns with transcriptomes and 3-dimensional chromatin structures, extract decision points in temporal studies and decipher the temporal control of gene networks that are the ultimate genetic readouts of NR ligandinduced physiological phenomena. In this review we will summarize the chronology of the development of increasingly larger data sets for NR action, with a particular focus on studies performed with the RAR/RXR nuclear receptor family, and discuss the present attempts to integrate a multitude of genomewide data sets in the ultimate context of the temporal 3-dimensional chromatin structure.
Nucleic acids research, 2013
The absence of a quality control (QC) system is a major weakness for the comparative analysis of ... more The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin immunoprecipitation (ChIP-seq) but also related enrichment-based studies like methylated DNA immunoprecipitation/methylated DNA binding domain sequencing, global run on sequencing or RNA-seq. Importantly, QC assessment may significantly improve multidimensional comparisons that have great promise for extracting information from combinatorial analyses of the global profiles established for chromatin modifications, the bindings of epigenetic and chromatin-modifying enzymes/ machineries, RNA polymerases and transcription factors and total, nascent or ribosome-bound RNAs. Here we present an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. This QC system was used to certify >5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses.
Genome-wide studies of nuclear receptors in cell fate decisions
Nuclear receptors (NRs) are important mediators of the information encoded in the chemical struct... more Nuclear receptors (NRs) are important mediators of the information encoded in the chemical structure of its corresponding ligand, as they interpret such information in the context of the cell identity and physiological status and convert it into sequential transcription regulatory events. At the cell level this can result in temporally coordinated processes such as cell fate transitions, which comprise the regulation of a plethora of gene programs including among others regulation of cell proliferation, metabolism and specific functionalities that are acquired by the differentiated cell. While both the early steps of nuclear receptor function and their impact on animal/organ physiology is rather well understood, little is known about the dynamic gene networks that ultimately cause a particular (cell) physiological phenomenon induced by the cognate NR ligand/hormone.
Thanks to advances in massive parallel sequencing and bioinformatics analyses of genome-wide data sets, time has come for the development of NR systems biology. Indeed it is now possible to integrate global transcription factor binding, epigenetic chromatin histone and DNA modification patterns with transcriptomes and 3-dimensional chromatin structures, extract decision points in temporal studies and decipher the temporal control of gene networks that are the ultimate genetic readouts of NR ligand-induced physiological phenomena. In this review we will summarize the chronology of the development of increasingly larger data sets for NR action, with a particular focus on studies performed with the RAR/RXR nuclear receptor family, and discuss the present attempts to integrate a multitude of genome-wide data sets in the ultimate context of the temporal 3-dimensional chromatin structure.
Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generat... more Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generating sufficient amounts of DNA for genome-wide studies with minute amounts of cells. LinDA can be coupled to a great number of global profiling technologies. Indeed, chromatin immunoprecipitation coupled to massive parallel sequencing (ChIP-seq) has been achieved for transcription factors and epigenetic modification of chromatin histones with 1,000 to 5,000 cells. LinDA largely simplifies reChIP-seq experiments to monitor co-binding at chromatin target sites. The single-tube design of LinDA is ideal for handling ultrasmall amounts of DNA (<30 pg) and is compatible with automation. The actual hands-on working time is less than 6 h with one overnight reaction. The present protocol describes all materials and critical steps, and provides examples and controls for LinDA. Applications of LinDA for genome-wide analyses of biobank samples and for the study of chromatin conformation and nuclear architecture are in progress.
Cell, Jan 1, 2011
Meiotic recombination between homologous chromosomes initiates via programmed DNA doublestrand br... more Meiotic recombination between homologous chromosomes initiates via programmed DNA doublestrand breaks (DSBs), generated by complexes comprising Spo11 transesterase plus accessory proteins. DSBs arise concomitantly with the development of axial chromosome structures, where the coalescence of axis sites produces linear arrays of chromatin loops. Recombining DNA sequences map to loops, but are ultimately tethered to the underlying axis. How and when such tethering occurs is currently unclear. Using ChIPchip in yeast, we show that Spo11-accessory proteins Rec114, Mer2, and Mei4 stably interact with chromosome axis sequences, upon phosphorylation of Mer2 by S phase Cdk. This axis tethering requires meiotic axis components (Red1/Hop1) and is modulated in a domain-specific fashion by cohesin. Loss of Rec114, Mer2, and Mei4 binding correlates with loss of DSBs. Our results strongly suggest that hotspot sequences become tethered to axis sites by the DSB machinery prior to DSB formation.
Nature Methods, Jan 1, 2011
Molecular Systems …, Jan 1, 2011
Previously described ATRA-responsive genes characterised in this study as direct RXR α -RAR γ tar... more Previously described ATRA-responsive genes characterised in this study as direct RXR α -RAR γ targets, or as part of the functional co-citation network.
Nucleic Acids …, Jan 1, 2011
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increasingly... more Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increasingly used to map protein-chromatin interactions at global scale. The comparison of ChIP-seq profiles for RNA polymerase II (PolII) established in different biological contexts, such as specific developmental stages or specific time-points during cell differentiation, provides not only information about the presence/accumulation of PolII at transcription start sites (TSSs) but also about functional features of transcription, including PolII stalling, pausing and transcript elongation. However, annotation and normalization tools for comparative studies of multiple samples are currently missing. Here, we describe the R-package POLYPHEMUS, which integrates TSS annotation with PolII enrichment over TSSs and coding regions, and normalizes signal intensity profiles. Thereby POLYPHEMUS facilitates to extract information about global PolII action to reveal changes in the functional state of genes. We validated POLYPHEMUS using a kinetic study on retinoic acid-induced differentiation and a publicly available data set from a comparative PolII ChIP-seq profiling in Caenorhabditis elegans. We demonstrate that POLYPHEMUS corrects the data sets by normalizing for technical variation between samples and reveal the potential of the algorithm in comparing multiple data sets to infer features of transcription regulation from dynamic PolII binding profiles.
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Papers by Marco Antonio Mendoza
Thanks to advances in massive parallel sequencing and bioinformatics analyses of genome-wide data sets, time has come for the development of NR systems biology. Indeed it is now possible to integrate global transcription factor binding, epigenetic chromatin histone and DNA modification patterns with transcriptomes and 3-dimensional chromatin structures, extract decision points in temporal studies and decipher the temporal control of gene networks that are the ultimate genetic readouts of NR ligand-induced physiological phenomena. In this review we will summarize the chronology of the development of increasingly larger data sets for NR action, with a particular focus on studies performed with the RAR/RXR nuclear receptor family, and discuss the present attempts to integrate a multitude of genome-wide data sets in the ultimate context of the temporal 3-dimensional chromatin structure.