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

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 su...

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Authors: Sandoval Velasco, Marcela, Rodríguez, Juan Antonio, Pérez Estrada, Cynthia, Zhang, Guojie, Lieberman Aiden, Erez, Marti-Renom, Marc A., Gilbert, M Thomas, Smith, Oliver
Format: article
Status:Published version
Publication Date:2020
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/45610
Online Access:http://hdl.handle.net/10230/45610
http://dx.doi.org/10.1093/gigascience/giaa087
Access Level:Open access
Keyword:BGISEQ-500
Hi-C
Chromosome conformation capture
Next-generation sequencing
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spelling Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platformSandoval Velasco, MarcelaRodríguez, Juan AntonioPérez Estrada, CynthiaZhang, GuojieLieberman Aiden, ErezMarti-Renom, Marc A.Gilbert, M ThomasSmith, OliverBGISEQ-500Hi-CChromosome conformation captureNext-generation sequencingBackground: 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.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.Oxford University Press202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/45610http://dx.doi.org/10.1093/gigascience/giaa087reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésGigascience. 2020; 9(8):giaa087info:eu-repo/grantAgreement/EC/H2020/681396info:eu-repo/grantAgreement/EC/H2020/704254info:eu-repo/grantAgreement/EC/FP7/609989info:eu-repo/grantAgreement/EC/H2020/676556info:eu-repo/grantAgreement/ES/2PE/BFU2017–85926-P© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/456102026-06-12T07:21:37Z
dc.title.none.fl_str_mv Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
title Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
spellingShingle Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
Sandoval Velasco, Marcela
BGISEQ-500
Hi-C
Chromosome conformation capture
Next-generation sequencing
title_short Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
title_full Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
title_fullStr Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
title_full_unstemmed Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
title_sort Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform
dc.creator.none.fl_str_mv Sandoval Velasco, Marcela
Rodríguez, Juan Antonio
Pérez Estrada, Cynthia
Zhang, Guojie
Lieberman Aiden, Erez
Marti-Renom, Marc A.
Gilbert, M Thomas
Smith, Oliver
author Sandoval Velasco, Marcela
author_facet Sandoval Velasco, Marcela
Rodríguez, Juan Antonio
Pérez Estrada, Cynthia
Zhang, Guojie
Lieberman Aiden, Erez
Marti-Renom, Marc A.
Gilbert, M Thomas
Smith, Oliver
author_role author
author2 Rodríguez, Juan Antonio
Pérez Estrada, Cynthia
Zhang, Guojie
Lieberman Aiden, Erez
Marti-Renom, Marc A.
Gilbert, M Thomas
Smith, Oliver
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv BGISEQ-500
Hi-C
Chromosome conformation capture
Next-generation sequencing
topic BGISEQ-500
Hi-C
Chromosome conformation capture
Next-generation sequencing
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/45610
http://dx.doi.org/10.1093/gigascience/giaa087
url http://hdl.handle.net/10230/45610
http://dx.doi.org/10.1093/gigascience/giaa087
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Gigascience. 2020; 9(8):giaa087
info:eu-repo/grantAgreement/EC/H2020/681396
info:eu-repo/grantAgreement/EC/H2020/704254
info:eu-repo/grantAgreement/EC/FP7/609989
info:eu-repo/grantAgreement/EC/H2020/676556
info:eu-repo/grantAgreement/ES/2PE/BFU2017–85926-P
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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