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Gene transcription may be regulated by remote enhancer or insulator regions through chromosome looping. Using a modification of chromosome conformation capture (3C) and fluorescence in situ hybridization, we found that one allele of the insulin-like growth factor 2 (Igf2)/H19 imprinting control region (ICR) on chromosome 7 colocalized with one allele of Wsb1/Nf1 on chromosome 11. Omission of CCCTC-binding factor (CTCF) or deletion of the maternal ICR abrogated this association and altered Wsb1/Nf1 gene expression. These findings demonstrate that CTCF mediates an interchromosomal association, perhaps by directing distant DNA segments to a common transcription factory, and the data provide a model for long-range allele-specific associations between gene regions on different chromosomes that suggest a framework for DNA recombination and RNA trans-splicing.

The number of structures of protein-protein complexes deposited to the Protein Data Bank is growing rapidly. These structures embed important information for predicting structures of new protein complexes. This motivated us to develop the PPISP method for predicting interface residues in protein-protein complexes. In PPISP, sequence profiles and solvent accessibility of spatially neighboring surface residues were used as input to a neural network. The network was trained on native interface residues collected from the Protein Data Bank. The prediction accuracy at the time was 70% with 47% coverage of native interface residues. Now we have extensively improved PPISP. The training set now consisted of 1156 nonhomologous protein chains. Test on a set of 100 nonhomologous protein chains showed that the prediction accuracy is now increased to 80% with 51% coverage. To solve the problem of over-prediction and under-prediction associated with individual neural network models, we developed a consensus method that combines predictions from multiple models with different levels of accuracy and coverage. Applied on a benchmark set of 68 proteins for protein-protein docking, the consensus approach outperformed the best individual models by 3-8 percentage points in accuracy. To demonstrate the predictive power of cons-PPISP, eight complex-forming proteins with interfaces characterized by NMR were tested. These proteins are nonhomologous to the training set and have a total of 144 interface residues identified by chemical shift perturbation. cons-PPISP predicted 174 interface residues with 69% accuracy and 47% coverage and promises to complement experimental techniques in characterizing protein-protein interfaces. .

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Hepatocellular carcinoma (HCC) is one of the most common potentially lethal human malignancies worldwide. Sorafenib, a tyrosine kinase inhibitor, was recently approved by the United States Food and Drug Administration for HCC. In this study, we established two sorafenib-resistant HCC cell lines from Huh7, a human HCC cell line, by long-term exposure of cells to sorafenib. Sorafenib induced significant apoptosis in Huh7 cells; however, Huh7-R1 and Huh7-R2 showed significant resistance to sorafenib-induced apoptosis at the clinical relevant concentrations (up to 10 M). Thorough comparisons of the molecular changes between Huh7 and resistant cells showed that the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway played a significant role in mediating acquired resistance to sorafenib in Huh7-R1 and Huh7-R2 cells. Phospho-Akt and p85 (a regulatory subunit of PI3K) were up-regulated, whereas tumor suppressor phosphatase and tensin homolog were down-regulated in these resistant cells. In addition, ectopic expression of constitutive Akt in Huh7 demonstrated similar resistance to sorafenib. The knockdown of Akt by RNA interference reversed resistance to sorafenib in Huh7-R1 cells, indicating the importance of Akt in drug sensitivity. Furthermore, the combination of 8-[4-(1-aminocyclobutyl)phenyl]-9-phenyl-1,2,4-triazolo[3,4-f][1,6]naphthyridin-3(2H)-one dihydrochloride (MK-2206), a novel allosteric Akt inhibitor, and sorafenib restored the sensitivity of resistant cells to sorafenib-induced apoptosis. In conclusion, activation of PI3K/Akt signaling pathway mediates acquired resistance to sorafenib in HCC, and the combination of sorafenib and MK-2206, an Akt inhibitor, overcomes the resistance at clinical achievable concentrations.

Early detection of SARS-CoV in throat wash and saliva suggests that these specimens are ideal for SARS diagnosis.

CTCF is a zinc finger DNA-binding protein that regulates the epigenetic states of numerous target genes. Using allelic regulation of mouse insulin-like growth factor II (Igf2) as a model, we demonstrate that CTCF binds to the unmethylated maternal allele of the imprinting control region (ICR) in the Igf2/H19 imprinting domain and forms a long-range intrachromosomal loop to interact with the three clustered Igf2 promoters. Polycomb repressive complex 2 is recruited through the interaction of CTCF with Suz12, leading to allelespecific methylation at lysine 27 of histone H3 (H3-K27) and to suppression of the maternal Igf2 promoters. Targeted mutation or deletion of the maternal ICR abolishes this chromatin loop, decreases allelic H3-K27 methylation, and causes loss of Igf2 imprinting. RNA interference knockdown of Suz12 also leads to reactivation of the maternal Igf2 allele and biallelic Igf2 expression. CTCF and Suz12 are coprecipitated from nuclear extracts with antibodies specific for either protein, and they interact with each other in a two-hybrid system. These findings offer insight into general epigenetic mechanisms by which CTCF governs gene expression by orchestrating chromatin loop structures and by serving as a DNA-binding protein scaffold to recruit and bind polycomb repressive complexes.The transcriptional regulator CCCTC-binding factor (CTCF) is a highly conserved 11-zinc-finger nuclear protein that controls the expression of a number of genes via chromatin insulation or enhancer blocking (for reviews, see references 5, 8, 23, and 28). CTCF silences genes by binding to sites within promoters, silencers, and insulators through the use of different combinations of zinc fingers (20). More than 15,000 CTCFbinding sites have been identified throughout the genome (16).The role of CTCF as an insulator regulating the imprinting of Igf2 and H19 has been extensively studied. Igf2 and H19 imprinting is directed by epigenetic modifications in the differentially methylated region (DMR) of the imprinting control region (ICR) located between these two adjacent genes (1,9,19,21,29,30). The binding of CTCF to the unmethylated maternal ICR creates a physical boundary, blocking the interaction of downstream enhancers with the remote Igf2 promoters and silencing the maternal allele (4,13,15). When this ICR is deleted (35) or mutated (32, 34), the maternal Igf2 allele is expressed, leading to biallelic expression. In addition, CTCF has recently been shown to act as a tethering protein, serving as a molecular glue to secure long-range intrachromosomal (17) and interchromosomal (18) interactions.By chromosome configuration capture (3C) methodology, it has been shown that CTCF participates in the formation of a long-range chromosomal loop to the upstream Igf2 DMRs when it is bound to the maternal ICR (17,42,21). This model suggests that CTCF may not only function as a physical insulator but also actively participate in the regulation of the imprinted Igf2 allele. We were interested in learning how CTCF mediates the suppressi...