Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation

Belaghzal, Houda; Dekker, Job

doi:10.1101/090001

Cited by 62 publications

(89 citation statements)

References 28 publications

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“…One gram of muscle tissue collected from the same fish was used for Hi‐C library construction. The Hi‐C experiment consisted of the following steps (Belaghzal, Dekker, & Gibcus, ): crosslinking, lysis, chromatin digestion, biotin marking, proximity ligations, crosslinking reversal and DNA purification. These were the same methods used in our previous study on G. maculatum (Liu et al, ).…”

Section: Methodsmentioning

confidence: 99%

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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Triplophysa is an endemic fish genus of the Tibetan Plateau in China. Triplophysa tibetana, which lives at a recorded altitude of ~4,000 m and plays an important role in the highland aquatic ecosystem, serves as an excellent model for investigating high‐altitude environmental adaptation. However, evolutionary and conservation studies of T. tibetana have been limited by scarce genomic resources for the genus Triplophysa. In the present study, we applied PacBio sequencing and the Hi‐C technique to assemble the T. tibetana genome. A 652‐Mb genome with 1,325 contigs with an N50 length of 3.1 Mb was obtained. The 1,137 contigs were further assembled into 25 chromosomes, representing 98.7% and 80.47% of all contigs at the base and sequence number level, respectively. Approximately 260 Mb of sequence, accounting for ~39.8% of the genome, was identified as repetitive elements. DNA transposons (16.3%), long interspersed nuclear elements (12.4%) and long terminal repeats (11.0%) were the most repetitive types. In total, 24,372 protein‐coding genes were predicted in the genome, and ~95% of the genes were functionally annotated via a search in public databases. Using whole genome sequence information, we found that T. tibetana diverged from its common ancestor with Danio rerio ~121.4 million years ago. The high‐quality genome assembled in this work not only provides a valuable genomic resource for future population and conservation studies of T. tibetana, but it also lays a solid foundation for further investigation into the mechanisms of environmental adaptation of endemic fishes in the Tibetan Plateau.

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Section: Methodsmentioning

confidence: 99%

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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“…However, some evidence suggests that it is better to err on the side of leaving larger DNA fragments rather than trying to achieve average sizes of 200 bp, as has sometimes been recommended [24,31]. Smaller fragments reduce the overall mappability of the Hi-C library after sequencing, in part because shorter sequences are less likely to be uniquely mappable, particularly in repetitive regions.…”

Section: Disadvantages Of Over-sonication To Short Dna Fragment Lengthmentioning

confidence: 99%

“…Recently, Belaghzal et al have developed an optimized protocol called Hi-C 2.0 which uses the DpnII enzyme and is designed for single aliquots of 5 million cells [24]. Some changes in the protocol from previously published approaches [17,31] might seem to be minor or just specific to the use of biotindATP and DpnII.…”

Section: Utility Of Hi-c 20 Conditions For Hindiii Librariesmentioning

confidence: 99%

“…Several excellent discussions of Hi-C theory and optimizations of Hi-C protocols have been published in recent years [17,[24][25][26], and numerous other insights about key steps of the Hi-C protocol have been discovered while researchers optimize this technique in various systems. Yet, Hi-C is still a technique that often requires troubleshooting and can sometimes unexpectedly result in low quality datasets even when the best current protocols are followed.…”

Section: Introductionmentioning

confidence: 99%

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Iteratively improving Hi-C experiments one step at a time

Golloshi

Sanders

McCord

2018

Preprint

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(250 words)The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases. Yet, the Hi-C protocol is still complex and subject to variations at numerous steps that can affect the resulting data. Thus, there is still a need for better understanding and control of factors that contribute to Hi-C experiment success and data quality. Here, we evaluate recently proposed Hi-C protocol modifications as well as often overlooked variables in sample preparation and examine their effects on Hi-C data quality. We examine artifacts that can occur during Hi-C library preparation, including microhomology-based artificial template copying and chimera formation that can add noise to the downstream data. Exploring the mechanisms underlying Hi-C artifacts pinpoints steps that should be further optimized in the future. To improve the utility of Hi-C in characterizing the 3D genome of specialized populations of cells or small samples of primary tissue, we identify steps prone to DNA loss which should be optimized to adapt Hi-C to lower cell numbers.Keywords: Hi-C; chromosome conformation capture; 3D genome structure; high throughput sequencing Highlights: 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point)  Variability in Hi-C libraries can arise from early steps of cell preparation  Hi-C 2.0 changes to interaction capture steps also benefit 6-cutter libraries  Artificial molecule fusions can arise during end repair and PCR, increasing noise 

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“…Hi-C has revealed different levels of genome organization, including the topologically associating domains (TADs [6,7], subTADs [8,9]), and chromatin compartments [5]. Yet, the potential for a more refined understanding of 3D genome organization remains largely untapped [10].…”

Section: Introductionmentioning

confidence: 99%

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

2020

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Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C's resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI's superiority to existing approaches. In addition, HIFI's restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.

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Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation

Cited by 62 publications

References 28 publications

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Iteratively improving Hi-C experiments one step at a time

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

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