Hi-C Sequencing

Hi-C sequencing is high‐throughput chromosome conformation capture technique to analyze spatial genome organization and map higher‐order chromosome folding and topological associated domains.

Hi-C is a high-throughput genomic and epigenomic technique designed to capture the three-dimensional (3D) conformation of chromatin within the nucleus. Chromatin, which packages long DNA strands in a confined nuclear volume, plays a crucial role in biological functions at both the gene and global nuclear levels. Understanding chromatin organization is essential for insights into gene regulation, chromosome morphogenesis, genome stability, and transmission, as well as the biophysics of chromatin and pathologies related to genome instability or nuclear morphology

Hi-C technology unveils the intricate three-dimensional structure of genomes, elucidating the hierarchical organization of chromatin from compartments (A/B Compartments) to topology-associated structural domains (TADs), and further to loops. This comprehensive understanding is crucial for studying spatial interactions among DNA sequences, constructing high-resolution chromosome 3D structures, deciphering gene regulation mechanisms, and facilitating the construction of trans-chromosomal genomes and chromosome-spanning haplotypes. Notably, genome 3D structures have been successfully reconstructed in various organisms including humans, Drosophila, yeast, Arabidopsis thaliana, rice, and cotton species. Comparative analysis of genome 3D structures across different samples has also been accomplished, shedding light on evolutionary and functional insights.

Applications of Hi-C Technology

 

  • Whole Genome Hi-C Maps: This includes comprehensive analysis of cis/trans interactions within the genome.
  • Compartment A/B Identification and Analysis: Hi-C facilitates the identification and analysis of genomic compartments, complemented by joint analyses with Chip-seq and RNA-seq data.
  • Gene/Repeat Sequence Interactions Analysis: Hi-C enables the investigation of interactions between genes and repetitive sequences, often integrated with RNA-seq data for comprehensive analysis.
  • TAD Identification and Analysis: Hi-C technology aids in the identification and analysis of Topologically Associated Domains (TADs), often coupled with Chip-seq and RNA-seq analyses.
  • Genome-Wide Loop Modeling: This aspect requires complementary data such as DNase-seq and is often analyzed jointly with Chip-seq and RNA-seq data.
  • Differential Analysis of 3D Structures: Hi-C allows for differential analysis of 3D structures among multiple samples, including differential analysis of compartment A/B, TADs, and loops

Specifications

  • Formaldehyde cross-linking
  • Lysis, restriction digest and biotinylation
  • Proximity ligation
  • Biotin removal, DNA shearing, size selection and end repair
  • Biotin pull-down
  • Library preparation and sequencing

Sample Requirements

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Unique DNBSEQ™ Sequencing Technology

BGI’s sequencing services are typically executed with proprietary DNBSEQ™ sequencing technology platforms, for great sequencing data at some of the lowest costs in the industry. DNBSEQ™ offers advantages in terms of lower amplification error rates and much lower duplication rates. In addition, studies have shown the lower index hopping rate in DNBSEQ™ platforms.