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

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  • dc.contributor.author Sandoval Velasco, Marcela
  • dc.contributor.author Rodríguez, Juan Antonio
  • dc.contributor.author Pérez Estrada, Cynthia
  • dc.contributor.author Zhang, Guojie
  • dc.contributor.author Lieberman Aiden, Erez
  • dc.contributor.author Martí Renom, Marc A.
  • dc.contributor.author Gilbert, M Thomas
  • dc.contributor.author Smith, Oliver
  • dc.date.accessioned 2020-10-29T06:55:06Z
  • dc.date.available 2020-10-29T06:55:06Z
  • dc.date.issued 2020
  • dc.description.abstract 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 situHi-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.
  • dc.description.sponsorship This work was supported by ERC Consolidator Grant 681,396 “Extinction Genomics” to M.T.P.G. and the Marie-Skłodowska Curie Actions H2020-MSCA-IF-2015, project “EpiCDomestic,” grant number 704,254 to O.S. This research was partially funded by the European Union's Seventh Framework Programme ERC grant agreement 609,989 to M.A.M-R., European Union's Horizon 2020 research and innovation programme grant agreement 676,556 to M.A.M-R. We also acknowledge the support of Spanish Ministerio de Ciencia, Innovación y Universidades through BFU2017–85 926-P to M.A.M-R. and the Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-468 to M.A.M-R. C.R.G. acknowledges support from “Centro de Excelencia Severo Ochoa 2013–2017,” SEV-2012–0208 and the CERCA Programme/Generalitat de Catalunya.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Sandoval-Velasco M, Rodríguez JA, Perez Estrada C, Zhang G, Lieberman Aiden E, Marti-Renom MA, Gilbert MTP, Smith O. Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. Gigascience. 2020; 9(8):giaa087. DOI: 10.1093/gigascience/giaa087
  • dc.identifier.doi http://dx.doi.org/10.1093/gigascience/giaa087
  • dc.identifier.issn 2047-217X
  • dc.identifier.uri http://hdl.handle.net/10230/45610
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Gigascience. 2020; 9(8):giaa087
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/704254
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/609989
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676556
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017–85926-P
  • dc.rights © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword BGISEQ-500
  • dc.subject.keyword Hi-C
  • dc.subject.keyword Chromosome conformation capture
  • dc.subject.keyword Next-generation sequencing
  • dc.title Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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