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Series GSE44748 Query DataSets for GSE44748
Status Public on Oct 17, 2013
Title Genome-wide binding profiles of KLF3 and KLF3 mutants in MEF cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription factors are often regarded as being comprised of a DNA-binding domain and a functional domain. The two domains are considered separable and autonomous, with the DNA-binding domain directing the factor to its target genes and the functional domain imparting transcriptional regulation. We have examined a typical Zinc Finger (ZF) transcription factor from the Krüppel-like factor (KLF) family, KLF3. This factor has an N-terminal repression domain that binds the co-repressor C-terminal binding protein (CtBP), and a DNA-binding domain composed of three classical (ZFs) at its C-terminus. We established a system to compare the genomic occupancy profile of wildtype KLF3 with two mutants affecting the N-terminal functional domain: a mutant unable to contact its cofactor CtBP and a mutant lacking the entire N-terminal domain, but retaining the ZFs intact. We used chromatin immunoprecipitation followed by sequencing (ChIP-seq) to assess binding across the genome in murine embryonic fibroblasts. Our results define the in vivo recognition site for KLF3 and the two mutants as a typical CACCC-like element. Unexpectedly, we observe that mutations in the N-terminal functional domain severely affect DNA binding. In general, both mutations reduce binding but there are also instances where binding is retained or even increased. These results provide a clear demonstration that the correct localization of transcription factors to their target genes is not solely dependent on their DNA-contact domains. This informs our understanding of how transcription factors operate and is of relevance to the design of artificial ZF proteins.
Overall design ChIP-seq was performed on the three samples, KLF3, ΔDL and DBD in duplicate (biological replicates). Input samples were used as controls.
Contributor(s) Burdach J, Funnell AP, Artuz CM, Sin MK, Tan LY, Pearson RC, Crossley M
Citation(s) 24106088
Submission date Feb 28, 2013
Last update date May 15, 2019
Contact name Jon Burdach
Organization name University of New South Wales
Department BABS
Street address UNSW
City Sydney
State/province NSW
ZIP/Postal code 2052
Country Australia
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM1090064 KLF3, input
GSM1090065 KLF3, immunoprecipitation
GSM1090066 ΔDL, input
BioProject PRJNA191577
SRA SRP019227

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE44748_All_peaks.txt.gz 1.4 Mb (ftp)(http) TXT
GSE44748_DBD-1_peaks.txt.gz 754.0 Kb (ftp)(http) TXT
GSE44748_DBD-2_peaks.txt.gz 670.5 Kb (ftp)(http) TXT
GSE44748_DBD_merged_peaks.txt.gz 434.3 Kb (ftp)(http) TXT
GSE44748_DDL-1_peaks.txt.gz 1.4 Mb (ftp)(http) TXT
GSE44748_DDL-2_peaks.txt.gz 2.7 Mb (ftp)(http) TXT
GSE44748_DDL_merged_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE44748_KLF3-1_peaks.txt.gz 2.3 Mb (ftp)(http) TXT
GSE44748_KLF3-2_peaks.txt.gz 2.1 Mb (ftp)(http) TXT
GSE44748_KLF3_merged_peaks.txt.gz 1.3 Mb (ftp)(http) TXT
GSE44748_RAW.tar 1.9 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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