We are analyzing https://link.springer.com/article/10.1186/s13059-015-0661-x.

Title:
Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization | Genome Biology
Description:
Background Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata. Results Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1. Conclusions We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies.
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Keywords {🔍}

cell, chromatin, features, types, figure, pubmed, boundaries, article, regions, models, google, scholar, compartment, additional, data, file, tad, cas, boundary, structure, genome, hkme, higherorder, domains, celltypespecific, organization, compartments, active, variable, ctcf, human, accuracy, type, central, locuslevel, model, nuclear, enrichments, hic, cells, peaks, modeling, random, hesc, binding, forest, analysis, transcription, patterns, show,

Topics {✒️}

adenovirus-e1-transformed cells due cell-type-specific enhancer activity cell-type-specific features responsible altered ap-1/atf complexes genome-wide chip-seq datasets constructed cell-type-specific models cell-type-specific features present fast gapped-read alignment higher-order structures vary representing higher-order organization explain higher-order structure showed cell-type-specific enrichments higher-order chromatin structure random forest approach cell-type-specific biology higher-order chromatin domains automating chromatin-state discovery cell-type-specific functions variable higher-order structure tailed mann–whitney test human higher-order domains cell-type-specific transitions long-distance dna interactions locus-level feature profiles higher-order domain dynamics possessing chip-seq peaks locus-level chromatin features multi-megabase-scale domains cell-type-specific transcription cell-type-specific structures solely compartment-level phenomena article download pdf cell-type-specific structure fine-grained tad structures higher-order structural variability orchestrates b-cell fate locus-level chromatin data undergoing compartment-level transitions cell-type-specific features locus-level encode data cell-type-specific regions cell-type-specific enhancers fold-change signal relative cell-type-specific models genome-wide location analysis c-derived eigenvector profiles megabase-sized genomic blocks maintaining b-cell identity genome-wide contact profiles predominantly short-range contacts

Schema {🗺️}

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         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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