Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity

Previous studies have analyzed patterns of transcription, Transcription Factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression? With these in mind, following characterization of two states (before and after induction of a single TF of choice) we determined: (i) genomic binding sites of the TF, (ii) promoter nucleosome occupancy and (iii) transcriptome profiles. Results demonstrated that promoter-proximal TF binding influenced expression of the target gene when it was coupled to nucleosome repositioning at or close to its binding site in most cases. In contrast, only in few cases change in target gene expression was found when TF binding occurred without local nucleosome reorganization

Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals

Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14 500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001). Furthermore, analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter—remarkable difference in promoter activity in the ‘quadruplex-destabilized’ versus ‘quadruplex-intact’ promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals

Emerging trends in G-quadruplex biology - role in epigenetic and evolutionary events

G-quadruplex biology gained interest based on evidence supporting its widespread role as elements that can control or modulate gene regulation. This followed initial prediction based on computational analysis that found prevalence of quadruplex motifs in promoters of many bacterial and other organisms. In parallel, further evidence was found indicating the function of quadruplex motifs in replication, recombination and also DNA repair. In this review, we summarize recent findings that provide a new perspective by introducing quadruplex motifs in roles that support involvement during epigenetic events, in determining evolutionary selection and as possible determinants of quantitative expression traits (eQTL) across populations

Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide

Function of non-B DNA structures are poorly understood though several bioinformatics studies predict role of the G-quadruplex DNA structure in transcription. Earlier, using transcriptome profiling we found evidence of widespread G-quadruplex-mediated gene regulation. Herein, we asked whether Potential G-quadruplex (PG4) motifs associate with Transcription Factors (TF). This was analyzed using 220 position weight matrices [designated as Transcription Factor Binding Sites (TFBS)], representing 187 unique TF, in &#62;75 000 genes in human, chimpanzee, mouse and rat. Results show binding sites of nine TFs, including that of AP-2, SP1, MAZ and VDR, occurred significantly within 100 bases of the PG4 motif (P &#60; 1.24E-10). PG4–TFBS combinations were conserved in ‘orthologously’ related promoters across all four organisms and were associated with &#62;850 genes in each genome. Remarkably, seven of the nine TFs were zinc-finger binding proteins indicating a novel characteristic of PG4 motifs. To test these findings, transcriptome profiles from human cell lines treated with G-quadruplex-specific molecules were used; 66 genes were significantly differentially expressed across both cell-types, which also harbored conserved PG4 motifs along with one/more of the nine TFBS. In addition, genes regulated by PG4–TFBS combinations were found to be co-regulated in human tissues, further emphasizing the regulatory significance of the associations

Inhibition of endoglin-GIPC interaction inhibits pancreatic cancer cell growth

Endoglin, a 180-kDa disulfide-linked homodimeric transmembrane receptor protein mostly expressed in tumor-associated endothelial cells, is an endogenous binding partner of GAIP-interacting protein, C terminus (GIPC). Endoglin functions as a coreceptor of T&#946;RII that binds TGF&#946; and is important for vascular development and consequently has become a compelling target for antiangiogenic therapies. A few recent studies in Gastrointestinal Stromal Tumor (GIST), breast cancer and ovarian cancer, however, suggest that endoglin is upregulated in tumor cells and is associated with poor prognosis. These findings indicate a broader role of endoglin in tumor biology, beyond angiogenic effects. The goal of our current study is to evaluate the effects of targeting endoglin in pancreatic cancer both in vitro and in vivo. We analyzed the antiproliferative effect of both RNAi-based and peptide ligand-based inhibition of endoglin in pancreatic cancer cell lines, the latter yielding a GIPC PDZ domain-targeting lipopeptide with notable antiproliferative activity. We further demonstrated that endoglin inhibition induced a differentiation phenotype in the pancreatic cancer cells and sensitized them against conventional chemotherapeutic drug gemcitabine. Most importantly, we have demonstrated the antitumor effect of both RNAi-based and competitive inhibitor–based blocking of endoglin in pancreatic cancer xenograft models in vivo. To our knowledge, this is the first report exploring the effect of targeting endoglin in pancreatic cancer cells

Overall strategy of the association study.

<p>Overall strategy of the association study.</p

Basic characteristics of case and control data in discovery phase.

<p>Abbreviation: Con: Control, Can: Oral cancer, Leu: Leukoplakia.</p>a<p>P-values from Mann-Whitney test,</p>b<p>p-values from chi-square test.</p

Allelic association results among different comparison groups.

a<p>MAF: Minor Allele Frequency of reference population is listed;</p>b<p>Association tests abbreviations, CC: case (jointly oral cancer and leukoplakia) vs. control, CAC: cancer vs. control, CAL: cancer vs. leukoplakia and LC: leukoplakia vs. control;</p>c<p>P-values without any adjustment for age, sex and tobacco habits by logistic regression and without any multiple tests correction applied,</p>d<p>P-values without any adjustment for age, sex and tobacco habits by logistic regression but corrected for multiple testing by Benjamini-Hochberg False Discovery Rate method,</p>e<p>P-values after adjustment for age, sex and tobacco habits by logistic regression but no correction multiple testing was applied,</p>f<p>P-values after adjustment for age, sex and tobacco habits by logistic regression and corrected for multiple testing by Benjamini-Hochberg False Discovery Rate method.</p

Sequence and expression variations in 23 genes involved in mitochondrial and non-mitochondrial apoptotic pathways and risk of oral leukoplakia and cancer

Oral cancer is usually preceded by pre-cancerous lesion and related to tobacco abuse. Tobacco carcinogens damage DNA and cells harboring such damaged DNA normally undergo apoptotic death, but cancer cells are exceptionally resistant to apoptosis. Here we studied association between sequence and expression variations in apoptotic pathway genes and risk of oral cancer and precancer. Ninety nine tag SNPs in 23 genes, involved in mitochondrial and non-mitochondrial apoptotic pathways,were genotyped in 525 cancer and 253 leukoplakia patients and 538 healthy controls using Illumina Golden Gate assay. Six SNPs (rs1473418 at BCL2; rs1950252 at BCL2L2; rs8190315 at BID; rs511044 at CASP1; rs2227310 at CASP7 and rs13010627 at CASP10) significantlymodified risk of oral cancer but SNPs only at BCL2, CASP1and CASP10 modulated risk of leukoplakia. Combination of SNPs showed a steep increase in risk of cancerwith increase in “effective” number of risk alleles. In silico analysis of published data set and our unpublished RNAseq data suggest that change in expression of BID and CASP7 may have affected risk of cancer. In conclusion, three SNPs, rs1473418 in BCL2, rs1950252 in BCL2L2 and rs511044 in CASP1, are being implicated for the first time in oral cancer. Since SNPs at BCL2, CASP1 and CASP10modulated risk of both leukoplakia and cancer, so, they should be studied inmore details for possible biomarkers in transition of leukoplakia to cancer. This study also implies importance of mitochondrial apoptotic pathway gene (such as BCL2) in progression of leukoplakia to oral cancer

Allelic associations in with respect to tobacco exposure.

a<p>MAF: Minor allele frequency of the reference population is listed;</p>b<p>Association tests abbreviations, CC: case (jointly oral cancer and leukoplakia) vs. Control, CAC: cancer vs. Control, CAL: cancer vs. Leukoplakia, LC: leukoplakia vs. control, HD: High-dose and LD: Low-dose tobacco exposed group;</p>c<p>Benjamini-Hochberg False Discovery Rate corrected P-values for multiple tests.</p