HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C.; Yue, Feng; Li, Qunhua

doi:10.1101/101386

Cited by 74 publications

(115 citation statements)

References 42 publications

(85 reference statements)

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“…3f), showing that MksB and SMC are most likely not involved in the same process(es). Finally, we applied the software HiCRep on our various Hi-C map, a framework for assessing the reproducibility of Hi-C data 56 (Supplementary Fig. 2A).…”

Section: Resultsmentioning

confidence: 99%

Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

et al. 2020

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Higher-order chromosome folding and segregation are tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remain poorly characterized, especially in non-model species. Here, we investigate the role of DNApartitioning protein ParB and SMC condensin complexes in the actinobacterium Corynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated longrange interactions around ten centromere-like parS sites clustered at the replication origin (oriC). At least one oriC-proximal parS site is necessary for reliable chromosome segregation. We use chromatin immunoprecipitation and photoactivated single-molecule localization microscopy to show the formation of distinct, parS-dependent ParB-nucleoprotein subclusters. We further show that SMC/ScpAB complexes, loaded via ParB at parS sites, mediate chromosomal inter-arm contacts (as previously shown in Bacillus subtilis). However, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding; instead, this complex is involved in plasmid maintenance and interacts with the polar oriCtethering factor DivIVA. Our results complement current models of ParB-SMC/ScpAB crosstalk and show that some condensin complexes evolved functions that are apparently uncoupled from chromosome folding.

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Section: Resultsmentioning

confidence: 99%

Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

et al. 2020

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“…There is ongoing work to computationally assess and improve the quality of high‐throughput 3C‐based data. Recently, two new methods for measuring the reproducibility of Hi‐C data have been proposed (Yan, Yardimci, Yan, Noble, & Gerstein, ; Yang et al, ), with more methods for reproducibility and quality determination in development. Recent approaches to improve data quality at high resolutions involve imputing the high‐resolution matrix.…”

Section: Discussionmentioning

confidence: 99%

Computational methods for analyzing and modeling genome structure and organization

Lin

Bonora

Yardımcı

2018

WIREs Mechanisms of Disease

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Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.

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“…Hi‐C analysis were performed as previously described (Dong et al ). The reproducibility between biological replicates were calculated by HiCrep (Yang et al ) (Figure S1). For rice and foxtail millet domain calling, we used 20 kb bin size.…”

Section: Methodsmentioning

confidence: 99%

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

Dong

et al. 2019

JIPB

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Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains

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HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Cited by 74 publications

References 42 publications

Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

Computational methods for analyzing and modeling genome structure and organization

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

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