2021
DOI: 10.1186/s13072-021-00389-5
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A cookbook for DNase Hi-C

Abstract: Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical s… Show more

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Cited by 22 publications
(31 citation statements)
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“…We assumed that this difference is because in the WGA-based protocol, there is no enrichment of proximity ligation products. In accord with the increase of intra-fragment reads, for WGA-based libraries, we observed more reads in FR-orientation, which often (although not always - Gridina et al, 2021) inversely correlate with the number of proximity ligation products (Fig. 2, A).…”
Section: Resultssupporting
confidence: 76%
“…We assumed that this difference is because in the WGA-based protocol, there is no enrichment of proximity ligation products. In accord with the increase of intra-fragment reads, for WGA-based libraries, we observed more reads in FR-orientation, which often (although not always - Gridina et al, 2021) inversely correlate with the number of proximity ligation products (Fig. 2, A).…”
Section: Resultssupporting
confidence: 76%
“…Even with the advent of new, high-resolution Hi-C methods such as DNAseI 78 and MNAse 79 , Hi-C detection of micro-TADs is challenging because, when sharing epigenetic status and located continuously, they are not insulated from each other. Evolutionary comparisons, such as identification of genome regulatory blocks 80 , may help to dissect these basic units of chromatin organization in future.…”
Section: Discussionmentioning
confidence: 99%
“…However, the literature lacks systematic analysis of how exactly the basic steps of the protocol work. At the same time, there are a lot of studies where individual selected steps were investigated ( Gavrilov and Razin, 2009 ; Comet et al, 2011 ; Gavrilov et al, 2013b , 2015 ; Nagano et al, 2015b ; Oksuz et al, 2020 ; Gridina et al, 2021 ). In this article, we try to fill this gap and explore in detail all the basic steps of the 3C protocol at once.…”
Section: Introductionmentioning
confidence: 99%