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Multiparameter functional diversity of human C2H2 zinc finger proteins

ABSTRACT: Multiparameter functional diversity of human C2H2 zinc finger proteins

PROVIDER: PRJEB14923 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1548614.fastq.gz	Fastqsanger.gz
	ERR1548615.fastq.gz	Fastqsanger.gz
	ERR1548616.fastq.gz	Fastqsanger.gz
	ERR1548617.fastq.gz	Fastqsanger.gz

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Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

2016-10-25 | GSE76495 | GEO

Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

2016-10-25 | E-GEOD-76495 | biostudies-arrayexpress

Multiparameter functional diversity of human C2H2 zinc finger proteins

Project description:Multiparameter functional diversity of human C2H2 zinc finger proteins

| PRJNA307565 | ENA

Multiparameter functional diversity of human C2H2 zinc finger proteins

Project description:We have identified protein protein interactions of 118 C2H2 zinc finger proteins by AP-MS using GFP-tagged constructs in order to understand their role in transcription regulation.

2016-12-09 | PXD003431 | Pride

Multiparameter functional diversity of human C2H2 zinc finger proteins.

Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions. Here, we report a multifaceted functional analysis of 131 human C2H2-ZF proteins, encompassing DNA binding sites, interacting proteins, and transcriptional response to genetic perturbation. We confirm the expected diversity in DNA binding motifs and genomic binding sites, and provide motif models for 78 previously uncharacterized C2H2-ZF proteins, most of which are unique. Surprisingly, the diversity in protein-protein interactions is nearly as high as diversity in DNA binding motifs: Most C2H2-ZF proteins interact with a unique spectrum of co-activators and co-repressors. Thus, multiparameter diversification likely underlies the evolutionary success of this large class of human proteins.

| S-EPMC5131825 | biostudies-literature

Multiparameter functional diversity of human C2H2 zinc finger proteins

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-10-25 | E-GEOD-76496 | biostudies-arrayexpress

HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

2021-01-05 | E-MTAB-9236 | biostudies-arrayexpress

Multiparameter functional diversity of human C2H2 zinc finger proteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-10-25 | GSE76496 | GEO

HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

Project description:To define the sequence preference of SALL4 C2H2 zinc finger domains, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified SALL4 ZFC1, ZFC2 and ZFC4 domains combined with no protein control experiment. We re-sequenced the libraries from E-MTAB-9236 with very high coverage to estimate the minimum number of reads required per sample for accurate results.

2022-03-01 | E-MTAB-11484 | biostudies-arrayexpress

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.

2015-02-17 | E-GEOD-52520 | biostudies-arrayexpress

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