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Identification of in vivo binding sites of human C2H2-ZF proteins

ABSTRACT: The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. We determined in vivo binding sites of 39 human C2H2-ZF proteins, and correlated them with potential functions for these proteins.

ORGANISM(S): synthetic construct

PROVIDER: GSE58341 | GEO | 2015/02/17

SECONDARY ACCESSION(S): PRJNA252040

REPOSITORIES: GEO

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Identification of in vivo binding sites of human GFP-tagged C2H2-ZF proteins

2016-10-25 | GSE76494 | GEO

Identification of in vivo binding sites of human C2H2-ZF proteins

Project description:The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. We determined in vivo binding sites of 39 human C2H2-ZF proteins, and correlated them with potential functions for these proteins. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Chromatin immunoprecipitation was performed as described before (Schmidt et al., Methods, 2009), and ChIP samples along with several control samples from different experimental batches were sequenced on Illumina HiSeq 2500. Reads were mapped to hg19 (GRCh37) assembly, and peaks were identified by MACS using an experiment-specific background that controls for various biases, such as the Sono-Seq effect as well as potential co-purification of targets of other (interacting) proteins.

2015-02-17 | E-GEOD-58341 | biostudies-arrayexpress

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Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay

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Evaluation of DNA-binding preferences of C2H2 zinc finger domains by PBM

Project description:The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. Using the bacterial 1-hybrid (B1H) system, we determined DNA-binding motifs for thousands of individual natural C2H2-ZFs, and correlated them with C2H2-ZF specificity residues. The data reported here includes results of protein-binding microarray (PBM) assays for 146 of these natural C2H2-ZFs, performed in order to validate B1H assays and to explore the DNA-binding specificity of C2H2-ZFs. Protein binding microarray (PBM) experiments were performed for a set of 185 variants of mouse Egr1 in which the third zinc finger was replaced by different C2H2-ZFs from different organisms. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006. Among the 185 variants examined, 146 variants yielded motifs in PBMs, which are included here.

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Project description:The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs). Here, we have explored the diversity of sequence preferences of C2H2-ZF proteins in non-metazoan organisms using PBM experiments.

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2016-07-11 | GSE83116 | GEO

Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay

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2015-02-17 | E-GEOD-52521 | biostudies-arrayexpress

Large-scale characterization of DNA binding landscape of eukaryotic C2H2 zinc fingers

Project description:This SuperSeries is composed of the SubSeries listed below. Cys2-His2 zinc finger (C2H2-ZF) proteins represent the largest class of putative human transcription factors (TFs). However, it is unknown whether most C2H2-ZFs even bind DNA, or what sequences they bind. Using a combination of bacterial one-hybrid (B1H) assays, protein-binding microarrays (PBMs), and ChIP-seq, we have found that most natural C2H2-ZFs bind DNA both in vitro and in vivo. This SuperSeries contains the data for identification of C2H2-ZF binding preferences using these three approaches. Refer to individual Series

2015-02-17 | E-GEOD-52523 | biostudies-arrayexpress

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