Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide identification of bZIP29 target genes in Arabidopsis cell cultures

ABSTRACT: The Arabidopsis basic leucine zipper transcription factor bZIP29 of the bZIP group I TF family, expressed mainly in proliferative tissues, is functionally characterized in this study. Genes bound by bZIP29 were mapped genome-wide using a tandem ChIP procedure (TChAP) on cell cultures expressing the TF fused to the His-Bio-His tag. The generated data suggests that bZIP29 might be an important player in the reorganization of cell walls during cell proliferation.

INSTRUMENT(S): Illumina Genome Analyzer II, Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-3754 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.

Van Leene Jelle J Blomme Jonas J Kulkarni Shubhada R SR Cannoot Bernard B De Winne Nancy N Eeckhout Dominique D Persiau Geert G Van De Slijke Eveline E Vercruysse Leen L Vanden Bossche Robin R Heyndrickx Ken S KS Vanneste Steffen S Goossens Alain A Gevaert Kris K Vandepoele Klaas K Gonzalez Nathalie N Inzé Dirk D De Jaeger Geert G

Journal of experimental botany 20160922 19

Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes conf ...[more]

PMID: 27660483

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Project description:In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in mammalian genomes the information controlling nucleosome assembly may partially coincide with the information that enables TFs to recognize cognate sites in cis-regulatory elements while ignoring the myriad of non-functional, randomly occurring consensus binding sites. This way, nucleosome-mediated masking would be coupled to TF binding site functionality. The hematopoietic master regulator Pu.1 maintained nucleosome depletion at macrophage-specific enhancers that were otherwise occupied by nucleosomes in other cell types and in reconstituted chromatin. We identified a minimal set of DNA sequence and shape features that predicted Pu.1 binding with 78% accuracy. The same features predicted nucleosome occupancy in cells where Pu.1 was not expressed with higher accuracy than specifically designed models. Control of nucleosome deposition by DNA sequence and shape features that also specify TF consensus site functionality may allow maintaining the gatekeeper function of nucleosomes during evolution of cis-regulatory elements. Chromatin immuno-precipitations of the transcription factor Pu.1 followed by multiparallel sequencing performed in murine bone marrow-derived macrophages. Experiments carried out in cells infected either with a retroviral vector containing a short hairpin targeting Pu.1 or with the empty vector as control. The shPU.1 hairpin (sequence available upon request) was selected among five designed using a publicly available software (http://katahdin.mssm.edu/siRNA) and was cloned in a modified version of TtRMPVIR inducible retroviral vector (Genbank HQ456318) in which the puromycin resistance gene was inserted. The empty vector, containing an sh-Renilla sequence, was used as control. Chromatin immuno-precipitations of the transcription factor PU.1 binding to in vitro reconstituted chromatin followed by multiparallel sequencing Micrococcal nuclease digestion of chromatin extracted from bone marrow derived macrophages followed by multiparallel sequencing . Experiments were carried out in untreated cells (4 replicates) and cells infected either with a retroviral vector containing a short hairpin targeting Pu.1 or with the empty vector as control (2 replicates). The shPU.1 hairpin (sequence available upon request) was selected among five designed using a publicly available software (http://katahdin.mssm.edu/siRNA) and was cloned in a modified version of TtRMPVIR inducible retroviral vector (Genbank HQ456318) in which the puromycin resistance gene was inserted. The empty vector, containing an sh-Renilla sequence, was used as control. Micrococcal nuclease digestion of in vitro reconstituted chromatin followed by multiparallel sequencing

Dataset Information

Genome-wide identification of bZIP29 target genes in Arabidopsis cell cultures

Publications

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.

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