Biology subjects

Ramirez, F.

Publications and source records attributed to Ramirez, F..

4 recordsLinked to original sources

bioRxiv2018

Ultra-parallel ChIP-seq by barcoding of intact nuclei

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. However, sample preparation is still a largely individual and labor-intensive process that hinders assay throughput and comparability. Here, we present a novel method for ultra-parallelized high-throughput ChIP-seq that addresses the aforementioned problems. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), employs barcoding of chromatin within intact nuclei extracted from different sources (e.g. tissues, treatments, time points). Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and significant workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation large-scale clinical studies and scarce samples. RELACS can generate ChIP-seq libraries from hundreds of samples within three days and with less than 1000 cells per sample.

genomics↗

bioRxiv2018

Partially methylated domains are hallmarks of a cell specific epigenome topology

BackgroundPartially methylated domains, PMDs, are extended regions in the genome exhibiting a reduced average DNA-methylation level. PMDs cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. Here, we present a first comprehensive comparative analysis of PMDs across more than 190 WGBS methylomes of human and mouse cells providing a deep insight into structural and functional features associated with PMDs.\n\nResultsPMDs are ubiquitous signatures covering up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Additionally, each cell type comes with a distinct set of specific PMDs, and genes expressed in such PMDs show a strong cell type effect. Demethylation strength varies in PMDs with a tendency towards a more pronounced effect in differentiating and replicating cells. The strongest demethylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA-methylation within PMDs tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expressions. Characteristic combinations of heterochromatic signatures in PMDs are linked to domains of early, middle and late DNA-replication.\n\nConclusionPMDs are prominent signatures of long-range epigenomic organization. Integrative analysis identifies PMDs as important general, lineage- and cell-type specific topological features. PMD changes are hallmarks of cell differentiation. Demethylation of PMDs combined with increased heterochromatic marks is a feature linked to enhanced cell proliferation. In combination with broad histone marks PMDs demarcate distinct domains of late DNA-replication.

bioinformatics↗

bioRxiv2017

Community-driven data analysis training for biology

The primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.

bioinformatics↗

bioRxiv2017

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Eukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown that the DNA binding protein CTCF and cohesin contribute to a fraction of TAD boundaries. Apart from this, the molecular mechanisms governing this partitioning remain poorly understood. Using our new software, HiCExplorer, we annotated high-resolution (570 bp) TAD boundaries in flies and identified eight DNA motifs enriched at boundaries. Known insulator proteins bind five of these motifs while the remaining three motifs are novel. We find that boundaries are either at core promoters of active genes or at non-promoter regions of inactive chromatin and that these two groups are characterized by different sets of DNA motifs. Most boundaries are present at divergent promoters of constitutively expressed genes and the gene expression tends to be coordinated within TADs. In contrast to mammals, the CTCF motif is only present on 2% of boundaries in flies. We demonstrate that boundaries can be accurately predicted using only the motif sequences, along with open chromatin, suggesting that DNA sequence encodes the 3D genome architecture in flies. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogeome.ie-freiburg.mpg.de.

genomics↗