TY - JOUR

T1 - Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform

AU - Sandoval-Velasco, Marcela

AU - Antonio Rodriguez, Juan

AU - Estrada, Cynthia Perez

AU - Zhang, Guojie

AU - Aiden, Erez Lieberman

AU - Marti-Renom, Marc A.

AU - Gilbert, M. Thomas P.

AU - Smith, Oliver

PY - 2020

Y1 - 2020

N2 - Background: Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. Results: We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. Conclusions: Our straightforward modification to an Illumina-compatible in situ Hi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.

AB - Background: Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. Results: We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. Conclusions: Our straightforward modification to an Illumina-compatible in situ Hi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.

KW - Hi-C

KW - BGISEQ-500

KW - next-generation sequencing

KW - chromosome conformation capture

KW - ORGANIZATION

KW - PRINCIPLES

KW - REGIONS

KW - 5C

U2 - 10.1093/gigascience/giaa087

DO - 10.1093/gigascience/giaa087

M3 - Journal article

C2 - 32845983

VL - 9

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 8

M1 - giaa087

ER -