Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks

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dc.article.number112135
dc.contributor.authorMoyano, Tomas C.
dc.contributor.authorGutierrez, Rodrigo A.
dc.contributor.authorAlvarez, Jose M.
dc.contributor.authorMukhtar, S
dc.date.accessioned2025-05-01T10:32:23Z
dc.date.available2025-05-01T10:32:23Z
dc.date.issued2021
dc.description.abstractChromatin accessibility is directly linked with transcription in eukaryotes. Accessible regions associated with regulatory proteins are highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion, followed by high-throughput DNA sequencing (DNase-seq). The single-base-pair resolution digestion patterns from DNase-seq allows identifying transcription factor (TF) footprints of local DNA protection that predict TF-DNA binding. The identification of differential footprinting between two conditions allows mapping relevant TF regulatory interactions. Here, we provide step-by-step instructions to build gene regulatory networks from DNase-seq data. Our pipeline includes steps for DHSs calling, identification of differential TF footprints between treatment and control conditions, and construction of gene regulatory networks. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be adapted to work with DNase-seq data from any organism with a sequenced genome.
dc.description.funderFONDECYT
dc.description.funderANID -Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio)
dc.description.funderEvoNet project
dc.description.funderANID FONDECYT
dc.format.extent22 páginas
dc.fuente.origenWOS
dc.identifier.doi10.1007/978-1-0716-1534-8_3
dc.identifier.eisbn978-1-0716-1534-8
dc.identifier.eissn1940-6029
dc.identifier.isbn978-1-0716-1533-1
dc.identifier.issn1064-3745
dc.identifier.pubmedidMEDLINE:34251618
dc.identifier.scieloidS0718-69242020000300109
dc.identifier.scopusidSCOPUS_ID:85123021103
dc.identifier.urihttps://doi.org/10.1007/978-1-0716-1534-8_3
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/103842
dc.identifier.wosidWOS:000697783000004
dc.information.autorucFacultad de Ciencias Biológicas; Gutierrez Ilabaca Rodrigo Antonio; 0000-0002-5961-5005; 86782
dc.issue.numero1
dc.language.isoen
dc.nota.accesoSin adjunto
dc.pagina.final46
dc.pagina.inicio25
dc.publisherHUMANA PRESS INC
dc.relation.ispartofMODELING TRANSCRIPTIONAL REGULATION
dc.revistaMODELING TRANSCRIPTIONAL REGULATION
dc.rightsregistro bibliográfico
dc.subjectDNase-seq
dc.subjectChromatin
dc.subjectGenomic Footprinting
dc.subjectTranscription
dc.subjectGene Regulatory Networks
dc.subjectOPEN CHROMATIN
dc.subjectNUCLEOSOME
dc.subjectLANDSCAPE
dc.subjectDYNAMICS
dc.subjectELEMENTS
dc.subject.ddc610
dc.subject.deweyMedicina y saludes_ES
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleGenomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks
dc.typecapítulo de libro
dc.volumen2328
sipa.codpersvinculados86782
sipa.indexWOS
sipa.trazabilidadCarga WOS-SCOPUS;01-05-2025
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