Zinc-finger BED Research Articles

SILAC-Based Quantitative Proteomics Approach to Identify Transcription Factors Interacting with a Novel Cis-Regulatory Element

The motif TMTCGCGANR (M being C or A, R being A or G, and N any nucleotide) called M8 was discovered as a putative cis-regulatory element present in 368 human gene promoters. Of these, 236 (64%) are conserved within promoter sequences of four related organisms: human, mouse, rat and dog. However, transcription factors (TFs) interacting with the M8 motif has not yet been described. We previously reported the use of quantitative proteomics coupled to one-step DNA affinity purification as a means of screening for TFs associated with given functional DNA elements. The procedure is performed in-vitro employing SILAC-labeled nuclear extracts and making use of a well-characterized cis-regulatory motifs. Building on that, in this study we have combined our method with statistical analysis to filter out false positive hits from the one-step DNA affinity pull-down experiments. This resulted in the identification of zinc finger BED domain-containing protein 1 (ZBED1), alpha globin transcription factor CP2 (TFCP2), upstream binding protein 1 (UBP) and transcription factor CP2 like 1(TFCP2L1), as specific M8 interacting factors. We validated our screen demonstrating the in vivo binding of alpha globin transcription factor TFCP2 to selected genes harboring M8-containing promoters using ChIP (chromatin immuno-precipitation) assays. This not only implicates a functional role of the above proteins in regulating M8 motif containing genes, but also suggests the potential use of our approach to decipher protein-DNA interactions occurring in living cells.

Impact of benzo(a)pyrene, Cu and their mixture on the proteomic response of Mytilus galloprovincialis

In natural waters, chemical interactions between mixtures of contaminants can result in potential synergistic and/or antagonic effects in aquatic animals. Benzo(a)pyrene (BaP) and copper (Cu) are two widespread environmental contaminants with known toxicity towards mussels Mytilus spp.The effects of the individual and the interaction of BaP and Cu exposures were assessed in mussels Mytilus galloprovincialis using proteomic analysis. Mussels were exposed to BaP [10μgL−1 (0.396μM)], and Cu [10μgL−1 (0.16μM)], as well as to their binary mixture (mixture) for a period of 7 days. Proteomic analysis showed different protein expression profiles associated to each selected contaminant condition. A non-additive combined effect was observed in mixture in terms of new and suppressed proteins. Proteins more drastically altered (new, suppressed and 2-fold differentially expressed) were excised and analyzed by mass spectrometry, and eighteen putatively identified. Protein identification demonstrated the different accumulation, metabolism and chemical interactions of BaP, Cu and their mixture, resulting in different modes of action. Proteins associated with adhesion and motility (catchin, twitchin and twitchin-like protein), cytoskeleton and cell structure (α-tubulin and actin), stress response (heat shock cognate 71, heat shock protein 70, putative C1q domain containing protein), transcription regulation (zinc-finger BED domain-containing and nuclear receptor subfamily 1G) and energy metabolism (ATP synthase F0 subunit 6 protein and mannose-6-phosphate isomerase) were assigned to all three conditions. Cu exposure alone altered proteins associated with oxidative stress (glutathione-S-transferase) and digestion, growth and remodelling processes (chitin synthase), while the mixture affected only one protein (major vault protein) possibly related to multi drug resistance. Overall, new candidate biomarkers, namely zinc-finger BED domain-containing protein, chitin synthase and major vault protein, were also identified for BaP, Cu and mixture, respectively.

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells

We have investigated whether the recently discovered transcription factor, zinc finger BED domain-containing protein 6 (ZBED6), is expressed in insulin-producing cells and, if so, to what extent it affects beta cell function. ZBED6 was translated from a ZC3H11A transcript in which the ZBED6-containing intron was retained. ZBED6 was present in mouse βTC-6 cells and human islets as a double nuclear band at 115/120 kDa and as a single cytoplasmic band at 95-100 kDa, which lacked N-terminal nuclear localization signals. We propose that ZBED6 supports proliferation and survival of beta cells, possibly at the expense of specialized beta cell function-i.e., insulin production-because (i) the nuclear ZBED6 were the predominant forms in rapidly proliferating βTC-6 cells, but not in human islet cells; (ii) down-regulation of ZBED6 in βTC-6 cells resulted in altered morphology, decreased proliferation, a partial S/G2 cell-cycle arrest, increased expression of beta cell-specific genes, and higher rates of apoptosis; (iii) silencing of ZBED6 in the human PANC-1 duct cell line reduced proliferation rates; and (iv) ZBED6 binding was preferentially to genes that control transcription, macromolecule biosynthesis, and apoptosis. Furthermore, it is possible that beta cells, by switching from full length to a truncated form of ZBED6, can decide the subcellular localization of ZBED6, thereby achieving differential ZBED6-mediated transcriptional regulation.

Identification of Zinc-finger BED Domain-containing 3 (Zbed3) as a Novel Axin-interacting Protein That Activates Wnt/β-Catenin Signaling

Axin, a key modulator of the Wnt/beta-catenin pathway, acts as a scaffold protein in phosphorylating and degrading cytoplasmic beta-catenin. Canonical Wnt proteins appear to stabilize beta-catenin by inducing the interaction of LRP5/6 with Axin. This interaction requires the phosphorylation of the Ser or Thr residues in the PPPP(S/T)PX(T/S) motifs at the intracellular domain of LRP5/6. In this work, we identified a novel Axin-interacting protein, zinc-finger BED domain-containing 3 (Zbed3), by yeast two-hybrid screening. The interaction was confirmed in co-immunoprecipitation experiment in mammalian cells and in vitro pulldown assays. Moreover, we found Zbed3 also contains a PPPPSPT motif, which is crucial to its binding to Axin. The Ser and Thr residues in the motif appear to be also phosphorylated by glycogen synthase kinase 3beta (GSK3beta) and the CKI family kinases, as GSK3beta and CKIepsilon could enhance the interaction of Zbed3 with Axin. Mutation of the Ser (SA) or Thr (TA) residue to Ala in the motif markedly impaired its ability to interact with Axin. Expressing Zbed3, but not these mutants, led to inhibition of GSK3beta-mediated beta-catenin phosphorylation, cytoplasmic beta-catenin accumulation, and activation of lymphoid enhancer binding factor-1-dependent reporter gene transcription. Furthermore, knockdown of Zbed3 with RNA interference attenuated Wnt-induced beta-catenin accumulation, lymphoid enhancer binding factor-1-dependent luciferase reporter activity, and the Wnt target gene expression. These results together indicate that Zbed3 is a novel Axin-binding protein that is involved in Wnt/beta-catenin signaling modulation.