Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DNA binding activities of the C-clamp

ABSTRACT: Investigated the DNA binding specificity of the C-clamp of dnTCF1E Used a doxycycline inducible system to investigate the role of the C-clamp in the genome-wide binding of dnTCF1E. Induced dnTCF1EWT and dnTCF1Emut (C-clamp mutant that is null for C-clamp DNA binding) over 2 time points (2 hours and 9 hours). A 0 hour (no doxycycline, uninduced) control was also included.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Zeller

PROVIDER: E-GEOD-53536 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.

Hoverter Nate P NP Zeller Michael D MD McQuade Miriam M MM Garibaldi Angela A Busch Anke A Selwan Elizabeth M EM Hertel Klemens J KJ Baldi Pierre P Waterman Marian L ML

Nucleic acids research 20141120 22

LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, b ...[more]

PMID: 25414359

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Project description:The motor neuron (MN)–hexamer complex consisting of LIM homeobox 3, Islet-1, and nuclear LIM interactor is a key determinant of motor neuron specification and differentiation. To gain insights into the transcriptional network in motor neuron development, we performed a genome-wide ChIP-sequencing analysis and found that the MN–hexamer directly regulates a wide array of motor neuron genes by binding to the HxRE (hexamer response element) shared among the target genes. Interestingly, STAT3-binding motif is highly enriched in the MN–hexamer–bound peaks in addition to the HxRE. We also found that a transcriptionally active form of STAT3 is expressed in embryonic motor neurons and that STAT3 associates with the MN–hexamer, enhancing the transcriptional activity of the MN–hexamer in an upstream signal-dependent manner. Correspondingly, STAT3 was needed for motor neuron differentiation in the developing spinal cord. Together, our studies uncover crucial gene regulatory mechanisms that couple MN–hexamer and STAT-activating extracellular signals to promote motor neuron differentiation in vertebrate spinal cord. To explain our experimental scheme briefly, we are interested in finding target sites for the dimer of transcription factors Isl1 and Lhx3. To mimic the biological activity of Isl1/Lhx3 dimer, we made Isl1-Lhx3 fusion and found that Isl1-Lhx3 has a potent biological activity in multiple systems (i.e. generation of ectopic motor neurons). Then we made ES cell line that induces Flag-tagged Isl1-Lhx3 expression upon Dox treatment. These *mouse* ES cells differentiate to motor neurons (iMN-ESCs) when treated with Dox following EB formation. To identify genomic binding sites of Isl1-Lhx3 (Flag-tagged), we performed ChIP with Flag antibody (pull down of Flag-Isl1-Lhx3) in ES cells treated with Dox. ChIP with Flag antibody in ES cells treated with vehicle (no Dox) was done as a negative control in parallel, and sequenced along with +Dox sample. We have done these experiments twice (two sets).

Dataset Information

DNA binding activities of the C-clamp

Publications

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.

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