Rio DC THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
Nature Structural & Molecular Biology (Impact Factor: 13.31). 12/2009; 17(1):117-23. DOI: 10.1038/nsmb.1742
Source: PubMed


THAP-family C(2)CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by THAP proteins, we solved the crystal structure of the Drosophila melanogaster P element transposase THAP domain (DmTHAP) in complex with a natural 10-base-pair site. In contrast to C(2)H(2) zinc fingers, DmTHAP docks a conserved beta-sheet into the major groove and a basic C-terminal loop into the adjacent minor groove. We confirmed specific protein-DNA interactions by mutagenesis and DNA-binding assays. Sequence analysis of natural and in vitro-selected binding sites suggests that several THAPs (DmTHAP and human THAP1 and THAP9) recognize a bipartite TXXGGGX(A/T) consensus motif; homology suggests THAP proteins bind DNA through a bipartite interaction. These findings reveal the conserved mechanisms by which THAP-family proteins engage specific chromosomal target elements.

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    • "The bip1 gene functions in differentiating cells to regulate progenitor maintenance The bip1 gene was originally identified through a yeast two-hybrid screen that showed that its encoded protein binds the BTB/POZ domain of the transcription factor Bric à brac 1 (Bab1) (Pointud et al., 2001), a protein that has several developmental roles including the formation of ovarian terminal filament cells that are required for germline stem cell maintenance (Lin and Spradling, 1993; Sahut- Barnola et al., 1995; Couderc et al., 2002). Analysis of the predicted Bip1 amino acid sequence (InterPro) (Hunter et al., 2012) identifies a THAP domain containing a C2CH-type zinc finger motif that is known to bind DNA (Sabogal et al., 2010). "
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    ABSTRACT: Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the ‘equilibrium signal’ in order to distinguish it from the ‘niche signal’. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr. DOI:
    eLife Sciences 09/2014; 3:e03626. DOI:10.7554/eLife.03626 · 9.32 Impact Factor
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    • "THAP1 is widely expressed in brain and extraneural tissues including whole blood (Zhao et al. 2013). THAP1 binds to specific DNA sequences, regulating cell proliferation and the G1/S checkpoint through pRB/E2F cell-cycle target genes (Clouaire et al. 2005; Cayrol et al. 2007; Sabogal et al. 2010; LeDoux et al. 2012, 2013). For instance, RRM1 is a direct transcriptional target of THAP1 (Cayrol et al. 2007). "
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    ABSTRACT: Although coding variants in THAP1 have been causally associated with primary dystonia, the contribution of noncoding variants remains uncertain. Herein, we examine a previously identified Intron 1 variant (c.71+9C>A, rs200209986). Among 1672 subjects with mainly adult-onset primary dystonia, 12 harbored the variant in contrast to 1/1574 controls (P A variant was associated with an elevated ratio of Isoform 1 (NM_018105) to Isoform 2 (NM_199003) in leukocytes. In silico and minigene analyses indicated that c.71+9C>A alters THAP1 splicing. Lymphoblastoid cells harboring the c.71+9C>A variant showed extensive apoptosis with relatively fewer cells in the G2 phase of the cell cycle. Differentially expressed genes from lymphoblastoid cells revealed that the c.71+9C>A variant exerts effects on DNA synthesis, cell growth and proliferation, cell survival, and cytotoxicity. In aggregate, these data indicate that THAP1 c.71+9C>A is a risk factor for adult-onset primary dystonia.
    05/2014; 2(3). DOI:10.1002/mgg3.67
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    • "Other proteins are able to interact with both the minor and the major groove of the DNA e.g. MogR repressor of Listeria monocytogenes (49), Hin recombinase (50) and THAP proteins (51). HpFur, therefore, adds to this list of regulators able to readout specific determinants also in the minor groove. "
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    ABSTRACT: Most transcriptional regulators bind nucleotide motifs in the major groove, although some are able to recognize molecular determinants conferred by the minor groove of DNA. Here we report a transcriptional commutator switch that exploits the alternative readout of grooves to mediate opposite output regulation for the same input signal. This mechanism accounts for the ability of the Helicobacter pylori Fur regulator to repress the expression of both iron-inducible and iron-repressible genes. When iron is scarce, Fur binds to DNA as a dimer, through the readout of thymine pairs in the major groove, repressing iron-inducible transcription (FeON). Conversely, on iron-repressible elements the metal ion acts as corepressor, inducing Fur multimerization with consequent minor groove readout of AT-rich inverted repeats (FeOFF). Our results provide first evidence for a novel regulatory paradigm, in which the discriminative readout of DNA grooves enables to toggle between the repression of genes in a mutually exclusive manner.
    Nucleic Acids Research 12/2013; 42(5). DOI:10.1093/nar/gkt1258 · 9.11 Impact Factor
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