Biology subjects

Gilgenast, T. G.

Publications and source records attributed to Gilgenast, T. G..

3 recordsLinked to original sources

bioRxiv2018

3DeFDR: Identifying cell type-specific looping interactions with empirical false discovery rate guided thresholding

The mammalian genome is connected into tens of thousands of long-range looping interactions critically linked to spatiotemporal gene expression regulation. An important unanswered question is to what extent looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Although methods exist for calling loops in single biological conditions, there is a severe shortage of computational tools for rigorous assessment of cell type-specific looping interactions across multiple biological conditions. Here we present 3DeFDR, a simple and effective statistical tool for classifying dynamic looping interactions across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) data. 3DeFDR parses chromatin contacts into invariant and cell type-specific classes by thresholding on differences in modeled interaction strength signal across two or three cellular states. Thresholds are iteratively adjusted based on a target empirical false discovery rate computed between real and simulated 5C maps. 3DeFDR enables the sensitive detection of high-confidence looping interactions and markedly reduces false positives when benchmarked against a classic analysis of variance (ANOVA) test, our newly formulated parametric likelihood ratio test (3DLRT), and the leading Hi-C differential interaction caller diffHic. 3DeFDR also sensitively and specifically calls loops in Mb-scale genomic regions parsed from Hi-C data. Our work provides a statistical framework and an open-source coding library for identifying dynamic long-range looping interactions in high-resolution 5C data from multiple cellular conditions.

genomics↗

bioRxiv2017

Systematic evaluation of statistical methods for identifying looping interactions in 5C data

Chromosome-Conformation-Capture-Carbon-Copy (5C) is a molecular technology based on proximity ligation that enables high-resolution and high-coverage inquiry of long-range chromatin looping interactions. Computational pipelines for analyzing 5C data involve a series of inter-dependent normalization procedures and statistical methods that markedly influence downstream biological results. A detailed analysis of the trade-offs inherent to all stages of 5C analysis has not been reported, but is essential for understanding the biological basis of looping. Here, we provide a comparative assessment of method performance at each step in the 5C analysis pipeline, including sequencing depth and library complexity correction, bias mitigation, spatial noise reduction, distance-dependent expected and variance estimation, modeling, and loop detection. We present a detailed discussion of methodological advantages/disadvantages at each step and provide a full suite of algorithms, lib5C, to allow investigators to test the range of approaches on their own high-resolution 5C data. Principles learned from our comparative analyses will have broad impact on many other forms of Chromosome-Conformation-Capture-based data, including Hi-C, 4C, and Capture-C.

genomics↗

bioRxiv2017

Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries

More than 25 inherited neurological disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why specific STRs are susceptible to unstable expansion leading to severe pathology, whereas tens of thousands of normal-length repeat tracts across the human genome are relatively stable. Here, we unexpectedly discover that nearly all STRs associated with repeat expansion diseases are located at boundaries demarcating 3-D chromatin domains. We find that boundaries exhibit markedly higher CpG island density compared to loci internal to domains. Importantly, disease-associated STRs are specifically localized to ultra-dense CpG island-rich boundaries, suggesting that these loci might be hotspots for epigenetic instability and topological disruption upon unstable expansion. In Fragile X Syndrome, mutation-length expansion at the Fmr1 gene results in severe disruption of the boundary between TADs. Our data uncover higher-order chromatin architecture as a new dimension in understanding the mechanistic basis of repeat expansion disorders.

genomics↗