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Multiparameter functional diversity of human C2H2 zinc finger proteins

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: PRJNA307572PRJNA307565PRJNA307573

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Sadhna Phanse

LAB HEAD: Jack Greenblatt

PROVIDER: PXD003431 | Pride | 2016-12-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	FINV_uniprot_sprot_human_BSA_TRY_BCN_GFP_TEV_062911.fasta	Fasta
	GR_121206_35_OT3_ZNF136_1_HEK293.mzXML	Mzxml
	GR_121206_36_OT3_ZNF528_1_HEK293.mzXML	Mzxml
	GR_121206_58_OT3_ZNF514_1_HEK293.mzXML	Mzxml
	GR_130110_39_OT10_ZBTB12_GFP_1_HEK300.mzXML	Mzxml

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Publications

Multiparameter functional diversity of human C2H2 zinc finger proteins.

Schmitges Frank W FW Radovani Ernest E Najafabadi Hamed S HS Barazandeh Marjan M Campitelli Laura F LF Yin Yimeng Y Jolma Arttu A Zhong Guoqing G Guo Hongbo H Kanagalingam Tharsan T Dai Wei F WF Taipale Jussi J Emili Andrew A Greenblatt Jack F JF Hughes Timothy R TR

Genome research 20161116 12

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 ...[more]

PMID: 27852650

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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.

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Identification of in vivo binding sites of human GFP-tagged 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 2000. 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.

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