Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide sequences bound by the transcription factors BLUEJAY and JACKDAW in Arabidopsis thaliana roots

ABSTRACT: We report the genomic sequences bound by the C2H2 transcription factors BLUEJAY and JACKDAW as profiled by chromating immunoprecipitation experiments followed by Illumina high sequencing. Plants were carrying constructs of proteins (translational) fusions of these transcription factors to the yellow fluorescent protein. Gene fusions were expressed under all their genomic regulatory regions using recombineering. The recombineering technique was used to recombine the fluorecent protein at the 3' end of their genomic regions in a JATY clone carrying these genes. Subsequently the JATY clones carrying these translational fusions were introgressed into plants. We performed ChIP on roots grown under standard conditions and fixed with formaldehyde in PBS-EDTA. Sequences bound by BLUEJAY and JACKDAW were immunoprecipitated with a-GFP AbCam290 at 4 Â°C overnight. Biological replicate samples were make into libraries of ~100 bp insert size and 50 bp of single ends sequenced through Illumina High Sequencing. Two biological replicates of samples of plants expressing the C2H2 transcription factors fused to the yellow fluorescent protein; and of control wild type plants processed through the same protocol.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Miguel Moreno-Risueno

PROVIDER: E-GEOD-60011 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptional control of tissue formation throughout root development.

Moreno-Risueno Miguel A MA Sozzani Rosangela R Yardımcı Galip Gürkan GG Petricka Jalean J JJ Vernoux Teva T Blilou Ikram I Alonso Jose J Winter Cara M CM Ohler Uwe U Scheres Ben B Benfey Philip N PN

Science (New York, N.Y.) 20151001 6259

Tissue patterns are dynamically maintained. Continuous formation of plant tissues during postembryonic growth requires asymmetric divisions and the specification of cell lineages. We show that the BIRDs and SCARECROW regulate lineage identity, positional signals, patterning, and formative divisions throughout Arabidopsis root growth. These transcription factors are postembryonic determinants of the ground tissue stem cells and their lineage. Upon further activation by the positional signal SHORT ...[more]

PMID: 26494755

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Project description:Transcription factors are often regarded as having two distinct components: a DNA binding domain (DBD) to allow binding to the regulatory region of a target gene and a trans-acting functional domain (FD) to modulate gene expression. Recently, it is becoming clear that the DBDs of transcription factors alone are incapable of providing sufficient specificity to account for the highly complex genomic structures in eukaryotes. Other regions, outside of the DBD, may play a role in transcription factor DNA binding specificity in vivo. In order to test this hypothesis, we examined a model zinc finger transcription factor, KrÃ¼ppel-like factor 3 (KLF3) with a FD that recruits partner proteins for its repressive activity and a three zinc finger DBD. Previously, we showed that deletion of the entire KLF3 FD reduced DNA binding across the genome. This implied the importance of the FD for in vivo DNA binding specificity. In the current study, we fused the KLF3 FD onto an unrelated, but well characterised Artificial Zinc Finger (AZF) targeting a standard target gene, VEGF-A. We compared the genomic DNA binding profile of this chimeric KLF3 construct, termed KLF3FD-AZF, to that of the AZF alone. Chromatin Immunoprecipitation followed by next generation sequencing was used to assess genomic wide DNA-binding of these AZFs. Remarkably, in these gain-of-function experiments, we again observed that the KLF3 FD is critical for in vivo DNA binding specificity. The addition of KLF3 FD increased the number of binding sites by more than two fold compared to the AZF alone. KLF3 FD also directed more binding to the promoter regions. Further investigations of these acquired sites identified a substantial portion of these sites as the known endogenous KLF3 bound regions, whilst others contain sequences that are similar but not identical to the predicted AZF target sequence. These results clearly demonstrate that the specific localisation of this model transcription factor to target genes is not solely dependent on the DBD and that the regions outside of this domain may also play an important role. ChIP-Seq experiments were performed on four HEK293 cell lines, two each stably expressing AZF or KLF3FD.AZF or KLF3FD only (two biological replicates). Input samples were included as controls.

Dataset Information

Genome-wide sequences bound by the transcription factors BLUEJAY and JACKDAW in Arabidopsis thaliana roots

Publications

Transcriptional control of tissue formation throughout root development.

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