Human Gene Sequences Research Articles

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly.

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

DNA Mutations via Chern\u2013Simons Currents

We test the validity of a possible schematization of DNA structure and dynamics based on the Chern–Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern–Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern–Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.

Application of the yeast comet assay in Testing some food additives for genotoxicity by comet assay in yeast

Food additives of various types are frequently used in the food sector. Their use is justified by the need to preserve, color, or sweeten a variety of foods. Despite the fact that some additives have been demonstrated to be cytotoxic, they are nevertheless utilized in practice. The effects of monosodium glutamate (MSG), sodium benzoate (SB), and saffron on several yeast haploid knockout strains were studied in this study (YKO). We used the Comet test method to find the optimum amounts at which this set of dietary additives could cause DNA damage. Three regularly used dietary additives were found to efficiently damage DNA. We also evaluated the sensitivity of higher eukaryotic cells to the genotoxic effects of these chemicals with yeast. The comet assay exhibited a better sensitivity of yeast cells, which was undeniably confirmed. The genotypes of haploid (knockout) yeast strains were chosen based on the (Clustal Omega Multiple Sequence Alignment EMBL-EBI) alignment of human and yeast gene sequence homology.

Use of signals of positive and negative selection to distinguish cancer genes and passenger genes.

A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. We have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations, oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.

V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.

The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that these nonamers explain the vast majority of tandem fusions in human repertoires. We further reveal large clonal lineages formed by tandem fusions in antigen-stimulated immunosequencing data sets, suggesting that such data sets contain many more tandem fusions than previously thought and that about a quarter of large clonal lineages with unusually long CDR3s are generated through tandem fusions. Finally, we developed the SEARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently completed Vertebrate Genomes Project assemblies, nearly doubling the number of mammalian species with known D genes. Our analysis revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J recombination is not a “bug” but an important feature preserved throughout mammalian evolution.

AncesTree: An interactive immunoglobulin lineage tree visualizer.

High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.

O-GlcNAcylation Dampens Dpp/BMP Signaling to Ensure Proper Drosophila Embryonic Development.

BMP (bone morphogenetic protein) signaling activity is precisely controlled by both pathway agonists andantagonists. Here, we identify a previously unrecognized BMP signaling antagonist. We demonstrate that the Drosophila BMP type I receptor Sax(Saxophone) functions as a Dpp (Decapentaplegic) receptor in Drosophila embryos, but that its activity is normally inhibited by the O-linked glycosyltransferase Sxc (Super sex combs). In wild-type embryos, Sax activity is inhibited, and the BMP type I receptor Tkv (Thickveins) is the sole conduit for Dpp. In contrast, in sxc mutants, the Dpp signal istransduced by both Tkv and Sax, and elevated Dpp signaling results in embryonic lethality. We also demonstrate that Sxc O-glycosylates Sax andobserve elevated Dpp signaling in response to maternal restriction of dietary sugar. These findings link fertility to nutritive environment and point to Sax signaling as the nutrient-sensitive branch of BMP signaling.

Enhanced Chondrogenic Differentiation Activities in Human Bone Marrow Aspirates via sox9 Overexpression Mediated by pNaSS-Grafted PCL Film-Guided rAAV Gene Transfer.

Background: The delivery of therapeutic genes in sites of articular cartilage lesions using non-invasive, scaffold-guided gene therapy procedures is a promising approach to stimulate cartilage repair while protecting the cargos from detrimental immune responses, particularly when targeting chondroreparative bone marrow-derived mesenchymal stromal cells in a natural microenvironment like marrow aspirates. Methods: Here, we evaluated the benefits of providing a sequence for the cartilage-specific sex-determining region Y-type high-mobility group box 9 (SOX9) transcription factor to human marrow aspirates via recombinant adeno-associated virus (rAAV) vectors delivered by poly(ε-caprolactone) (PCL) films functionalized via grafting with poly(sodium styrene sulfonate) (pNaSS) to enhance the marrow chondrogenic potential over time. Results: Effective sox9 overexpression was observed in aspirates treated with pNaSS-grafted or ungrafted PCL films coated with the candidate rAAV-FLAG-hsox9 (FLAG-tagged rAAV vector carrying a human sox9 gene sequence) vector for at least 21 days relative to other conditions (pNaSS-grafted and ungrafted PCL films without vector coating). Overexpression of sox9 via rAAV sox9/pNaSS-grafted or ungrafted PCL films led to increased biological and chondrogenic differentiation activities (matrix deposition) in the aspirates while containing premature osteogenesis and hypertrophy without impacting cell proliferation, with more potent effects noted when using pNaSS-grafted films. Conclusions: These findings show the benefits of targeting patients’ bone marrow via PCL film-guided therapeutic rAAV (sox9) delivery as an off-the-shelf system for future strategies to enhance cartilage repair in translational applications.

Cloning, expression and purification of human PDGF-BB gene in Escherichia coli: New approach in PDGF-BB protein production

IntroductionPlatelet-derived growth factor (PDGF) is a potent mitogen and chemoattractant for many cells of mesenchymal origin, such as fibroblasts, activated macrophages, and smooth muscle cells. PDGF plays critical roles in angiogenesis, embryogenesis, inflammation, and cell differentiation; therefore, it can be beneficial in wound healing. It has three dimer forms: PDGF-AA, AB, and BB, produced by platelets, activated macrophages, activated fibroblasts, keratinocytes, and some other cells in the body. The therapeutic potential of recombinant human PDGF-BB in wound healing and diabetic ulcers has been proven. The objective of this study was to produce recombinant human PDGF-BB protein in E. coli and its purification. MethodsIn this research study, the human PDGF-B gene sequence was obtained and synthesized after optimization. Using a prokaryotic expression vector, pET-15b, pET-15b-PDGF-B was constructed. The expression and purification of the recombinant human PDGF-B in a prokaryotic host, Escherichia coli BL21 (DE3), under T7 promoter was performed. Protein purification was done on Ni2+ affinity chromatography (NTA) column. ResultsThe recombinant human PDGF-BB protein, as a potential therapeutic target, was produced by cloning and protein expression of human PDGF-B gene in E. coli, then was purified. The purified recombinant human protein, pET-PDGF-B, revealed a sharp band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with a molecular weight of about 12 kDa. ConclusionThe recombinant construction of prokaryotic expression vector, pET15b-PDGF-B, and the production of PDGF-BB protein provide a foundation for further studies about the function of PDGF-BB and production of biologically active PDGF-BB protein.

Different Approaches to Unveil Biomolecule Configurations and Their Mutual Interactions

A novel technique was demonstrated that overcomes important drawbacks to crosslink cells by irradiation with ultrashort ultraviolet laser pulses (L-crosslinking). To use this technique coupled to Chromatin ImmunoPrecipitation (ChIP) in a high throughput context, a prescreening fast method needs to be implemented to set up suitable irradiation conditions of the cell sample for efficient L-crosslinking with no final and long ChIP analysis. Here a fast method is reported where living human cells have been first transfected with a vector coding for Estrogen Receptor α (ERα), linked to Green Florescent protein (ERα-GFP), so that the well-known interaction between the Estrogen Receptor Elements (ERE) region of the cell DNA and the ERα protein can be detected by studying the fluorometric response of the irradiated cells. The damage induced to cells by ultraviolet irradiation is characterized by looking at the DNA integrity, protein stability, and cellular viability. A second novel approach is presented to analyze or re-visit DNA and RNA sequences and their molecular configurations. This approach is based on methods derived from Chern-Simons super-gravity adapted to describe mutations in DNA/RNA strings, as well as interactions between nucleic acids. As a preliminary case, we analyze the KRAS human gene sequence and some of its mutations. Interestingly, our model shows how the Chern-Simons currents are able to characterize the mutations within a sequence, in particular giving a quantitative indication of the mutation likelihood.

Synthesis, G-Quadruplex DNA binding and cytotoxic properties of naphthalimide substituted styryl dyes

G-Quadruplex DNAs, formed by G-rich DNA sequences in human genes, are promising targets for design of cancer drugs. In this study, two naphthalimide substituted styryl dyes with different sizes of aromatic groups were synthesized. The spectral analysis showed that the dye X-2 with a large aromatic group formed aggregates in buffer solution displaying very weak fluorescence intensity, and disaggregated in the presence of G-Quadruplex DNAs with large intensity enhancements (up to ~1800 fold). Moreover, X-2 displayed good selectivity to G-Quadruplex DNAs. In contrast, dye X-3 with the smaller aromatic group had much lower fluorescence enhancements and poor selectivity to G-Quadruplex DNAs, suggesting that the suitably sized aromatic ring was essential for the interaction with G-Quadruplex. Further binding studies suggested that X-2 mainly bound on G-quartet surface through end-stacking mode. Cytotoxicity assay showed that both of the two dyes showed good anti-proliferative activities against the cancer cell lines and less cytotoxicity in non-malignant cell lines, which were better than a standard drug 5-fluorouracil. In addition, living cell imaging was also studied and demonstrated the potential applications of the new dye X-2 in bioassays and cell imaging.

Loss-of-Function Mutations in Human Regulator of G Protein Signaling RGS2 Differentially Regulate Pharmacological Reactivity of Resistance Vasculature.

Regulator of G protein signaling 2 (RGS2) plays a role in reducing vascular contraction and promoting relaxation due to its GTPase accelerating protein activity toward Gαq. Previously, we identified four human loss-of-function (LOF) mutations in RGS2 (Q2L, D40Y, R44H, and R188H). This study aimed to investigate whether those RGS2 LOF mutations disrupt the ability of RGS2 to regulate vascular reactivity. Isolated mesenteric arteries (MAs) from RGS2-/- mice showed an elevated contractile response to 5 nM angiotensin II and a loss of acetylcholine (ACh)-mediated vasodilation. Reintroduction of a wild-type (WT) RGS2-GFP plasmid into RGS2-/- MAs suppressed the vasoconstrictor response to angiotensin II. RGS2 LOF mutants failed to suppress the angiotensin II constriction response compared with RGS2 WT. In contrast, ACh-mediated vasoconstriction was restored by expression of RGS2 WT, D40Y, and R44H but not by RGS2 Q2L or R188H. Phosphorylation of RGS2 D40Y and R44H by protein kinase G (PKG) may explain their maintained function to support relaxation in MAs. This is supported by phosphomimetic mutants and suppression of vasorelaxation mediated by RGS2 D40Y by a PKG inhibitor. These results demonstrate that RGS2 attenuates vasoconstriction in MAs and that RGS2 LOF mutations cannot carry out this effect. Among them, the Q2L and R188H mutants supported less relaxation to ACh, whereas relaxation mediated by the D40Y and R44H mutant proteins was equal to that with WT protein. Phosphorylation of RGS2 by PKG appears to contribute to this vasorelaxation. These results provide insights for precision medicine targeting the rare individuals carrying these RGS2 mutations. SIGNIFICANCE STATEMENT: Regulator of G protein signaling 2 (RGS2) has been implicated in the control of blood pressure; rare mutations in the RGS2 gene have been identified in large-scale human gene sequencing studies. Four human mutations in RGS2 that cause loss of function (LOF) in cell-based assays were examined in isolated mouse arteries for effects on both vasoconstriction and vasodilation. All mutants showed the expected LOF effects in suppressing vasoconstriction. Surprisingly, the D40Y and R44H mutant RGS2 showed normal control of vasodilation. We propose that this is due to rescue of the mislocalization phenotype of these two mutants by nitric oxide-mediated/protein kinase G-dependent phosphorylation. These mechanisms may guide drug discovery or drug repurposing efforts for hypertension by enhancing RGS2 function.

Regulation of PLPP3 gene expression by NF-κB family transcription factors

Lipid phosphate phosphatase 3 (LPP3), encoded by the PLPP3 gene, is an integral membrane enzyme that dephosphorylates phosphate esters of glycero- and sphingophospholipids. Cell surface LPP3 can terminate the signaling actions of bioactive lysophosphatidic acid (LPA) and sphingosine 1 phosphate, which likely explains its role in developmental angiogenesis, vascular injury responses, and cell migration. Heritable variants in the final intron PLPP3 associate with interindividual variability in coronary artery disease risk that may result from disruption of enhancer sequences that normally act in cis to increase expression of the gene. However, the mechanisms regulating PLPP3 expression are not well understood. We show that the human PLPP3 promoter contains three functional NF-κB response elements. All of these are required for maximal induction of PLPP3 promoter activity in reporter assays. The identified sequences recruit RelA and RelB components of the NF-κB transcription complex to chromatin, and these transcription factors bind to the identified target sequences in two different cell types. LPA promotes binding of Rel family transcription factors to the PLPP3 promoter and increases PLPP3 gene expression through mechanisms that are attenuated by an NF-κB inhibitor, LPA receptor antagonists, and inhibitors of phosphoinositide 3 kinase. These findings indicate that up-regulation of PLPP3 during inflammation and atherosclerosis results from canonical activation of the NF-κB signaling cascade to increase PLPP3 expression through nuclear import and binding of RelA and RelB transcription factors to the PLPP3 promoter and suggest a mechanism by which the LPP3 substrate, LPA, can regulate PLPP3 expression.

The Identification of Metallothionein Gene in Human Plasma: Molecular analysis of Kadmium and Lead Pollution in Gas Station Environment

Metallothionein (MTs) is a protein that binds to metals, cysteine-rich and has low molecular weights. Metallothionein binds metals and has some essential cellular functions, such as transportation, storage, and metal detoxification. When metallic lead (Pb) and cadmium (Cd) are absorbed, it will immediately be bounded by metallothionein and transported by the blood to the liver. Metallothionein gene is encoded by MTs. This study aimed to identify the MTs gene in blood of fuel station workers which can further be used as a biomarker of the vulnerability of the body as a result of exposure to heavy metals like Pb and Cd in humans. This study was a cross-sectional study, conducted for 8 months and took place in Fuel Stations in the city of Semarang. Samples were fuel station workers who met the study criteria, they sought to fulfill as much as 52 samples. Blood of samples was taken approximately 5 ml and then the MT2 gene was analyzed using Polymerase Chain Reaction (PCR). The data were analyzed descriptively. The results showed that 96% of MT2 gene expression had a resemblance to normal human gene sequences by Blast GenBank. MT2 gene expression does not always reflect the accumulation of lead and cadmium in the blood of fuel station workers. The MT2 gene is likely to have a limitation when used as a biomarker for early detection of the heavy metals exposure in humans to determine the susceptibility of heavy metals exposure.

Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis.

It is increasingly recognized that gut microbiota play a pivotal role in the development of atherosclerotic cardiovascular disease. Previously, we have reported that the abundance of genus Bacteroides is lower in patients with coronary artery disease (CAD) than in patients without CAD with coronary risk factors or in healthy volunteers. However, it remains unclear which and how specific gut bacteria contribute to the progression of atherosclerosis. We recruited patients with CAD patients and controls without CAD with coronary risk factors. We then compared gut microbial composition using 16S ribosomal RNA gene sequencing in fecal samples to detect species with differential abundance between 2 groups. Subsequently, we used atherosclerosis-prone mice to study the mechanisms underlying the relationship between such species and atherosclerosis. Human fecal 16S ribosomal RNA gene sequencing revealed a significantly lower abundance of Bacteroides vulgatus and Bacteroides dorei in patients with CAD. This significant differential abundance was confirmed by quantitative polymerase chain reaction. Gavage with live B. vulgatus and B. dorei attenuated atherosclerotic lesion formation in atherosclerosis-prone mice, markedly ameliorating endotoxemia followed by decreasing gut microbial lipopolysaccharide production, effectively suppressing proinflammatory immune responses. Furthermore, fecal lipopolysaccharide levels in patients with CAD were significantly higher and negatively correlated with the abundance of B. vulgatus and B. dorei. Our translational research findings identify a previously unknown link between specific gut bacteria and atherosclerosis. Treatment with live B. vulgatus and B. dorei may help prevent CAD. URL: https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000018051 . Unique identifier: UMIN000015703.

Polymorphisms in protamine 1 and 2 genes in asthenozoospermic men: A case-control study

Asthenozoospermia is one of the etiologies for male factor infertility. It was shown that any abnormality in protamines genes, reduction of protamines transcript and protamines deficiency may play a key role in asthenozoospermia. The aim of the current study was the evaluation of protamine-1 and 2 genes (PRM1 and PRM2) polymorphisms in asthenozoospermic men. In this case-control study, the samples were corresponded to asthenozoospermic specimens of infertile men. The normozoospermic samples were considered as the control group. DNA sequence amplification was performed using four PRM1 and PRM2 primers, designed from 5' to 3' flank regions. The human PRM1 and PRM2 gene sequences were screened in search of potential mutations in highly prevalent polymorphism regions in asthenozoospermia versus normozoospermia. Totally, nine highly prevalent polymorphism regions between the forward and reverse primers were screened. Three of them corresponded to PRM1 and six to PRM2. The most prevalent polymorphism regions in PRM1 were related to 102G>T (rs35576928), 49C>T (rs140477029) and 139C>A (rs737008). In the PRM2, 6 highly prevalent polymorphisms regions were screened, including 248C>T (rs779337774), 401G>A (rs545828790), 288C>T (rs115686767), 288G>C (rs201933708), 373C>A (rs2070923), and 298G>C (rs1646022). The allele frequencies of three upper mentioned single nucleotide polymorphisms in asthenozoospermic men including 373C>A, 298G>C and 139C>A was higher than the control group. Our findings indicated that the frequency of some altered genotypes in asthenozospermia was slightly higher than control group. We proposed more extensive studies to be sure that; these genotypes can precisely be related to diagnosis of asthenozoospermia, as the molecular markers.

MiRNA regulates OCT4 expression in breast cancer cells.

Breast cancer cell infiltration, migration, and proliferation significantly affect its curative effect. Stemness gene octamer-binding transcription factor 4 (OCT4) upregulated in breast cancer tissue compared with normal control. MiRNA exhibits regulatory role in gene expression. This study adopted bioinformatics to predict the miRNA to regulate OCT4 gene and investigated its impact on breast cancer cell infiltration, migration, and proliferation. MirBase database was analyzed to explore the potential miRNA in regulating OCT4 based on human OCT4 gene sequence. MiRNA mimics and inhibitor were synthetized and transfected to BS524 cells. qRT-PCR was applied to test miRNA and OCT4 mRNA expressions in cells at 12 h, 24 h, and 48 h after transfection. Western blot was selected to detect OCT4 protein expression. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was selected to determine cell proliferation. Scratch assay was adopted to evaluate cell migration. Transwell assay was used to analyze cell infiltration. MiR-145 may regulate OCT4 gene with score 82. OCT4 mRNA and protein increased at 12 h after transfection (p > 0.05). OCR4 gene significantly upregulated, cell proliferation, migration, and infiltration enhanced by miR-145 transfection compared with control (p < 0.05). OCT4 gene downregulated, while cell proliferation, infiltration, and migration markedly weakened in miR-145 inhibitor group compared with control (p < 0.05). MiR-145 affects breast cancer BS524 cell proliferation, infiltration, and migration via positively regulating OCT4 gene expression.

Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries.

The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque (Macaca mulatta) using oligonucleotide primers based on human IG gene sequences. Our previous screening relied on Sanger sequencing, which was inefficient and generated only a few dozen sequences. Here, we re-analyzed this library using single molecule, real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform to generate thousands of highly accurate circular consensus sequencing (CCS) reads corresponding to full length single chain fragment variable. CCS data were then analyzed through the international ImMunoGeneTics information system® (IMGT®)/HighV-QUEST (www.imgt.org) to identify variable genes and perform statistical analyses. Overall the library was very diverse, with 2,569 different IMGT clonotypes called for the 5,238 IGHV sequences assigned to an IMGT clonotype. Within the library, SIV-specific antibodies represented a relatively limited number of clones, with only 135 different IMGT clonotypes called from 4,594 IGHV-assigned sequences. Our data did confirm that the IGHV4 and IGHV3 gene usage was the most abundant within the rhesus antibodies screened, and that these genes were even more enriched among SIV gp140-specific antibodies. Although a broad range of VH CDR3 amino acid (AA) lengths was observed in the unpanned library, the vast majority of SIV gp140-specific antibodies demonstrated a more uniform VH CDR3 length (20 AA). This uniformity was far less apparent when VH CDR3 were classified according to their clonotype (range: 9–25 AA), which we believe is more relevant for specific antibody identification. Only 174 IGKV and 588 IGLV clonotypes were identified within the VL sequences associated with SIV gp140-specific VH. Together, these data strongly suggest that the combination of SMRT sequencing with the IMGT/HighV-QUEST querying tool will facilitate and expedite our understanding of polyclonal antibody responses during SIV infection and may serve to rapidly expand the known scope of macaque V genes utilized during these responses.

Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus.

Triplexes are noncanonical DNA structures, which are functionally associated with regulation of gene expression through ncRNA targeting to chromatin. Based on the rules of Hoogsteen base-pairing, polypurine sequences of a duplex can potentially form triplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyses have revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers, suggesting a potential function of RNA–DNA triplexes in transcriptional regulation. Here, we have quantitatively evaluated the potential of different sequences of human and mouse ribosomal RNA genes (rDNA) to form triplexes at different salt and pH conditions. We show by biochemical and biophysical approaches that some of these predicted sequences form triplexes with high affinity, following the canonical rules for triplex formation. We further show that RNA triplex-forming oligos (TFOs) are more stable than their DNA counterpart, and point mutations strongly affect triplex formation. We further show differential sequence requirements of pyrimidine and purine TFO sequences for efficient binding, depending on the G–C content of the TTS. The unexpected sequence specificity, revealing distinct sequence requirements for purine and pyrimidine TFOs, shows that in addition to the Hoogsteen pairing rules, a sequence code and mutations have to be taken into account to predict genomic TTS.

Prediction of miRNA regulating the potential cancer-promoting gene CCL18 in cutaneous malig-nant melanoma and correlation analysis between CCL18 mRNA and miRNA expression

Objective To explore the miRNA regulating the potential cancer-promoting gene CCL18 in cutaneous malignant melanoma. Methods Bioinformatics analysis was conducted by using online software miRanda and TargetScan, so as to predict the miRNA targeting CCL18 gene. Three kinds of CCL18 3′UTR dual-luciferase reporter vectors, including mutant 3′UTR vector (mutant 3′UTR group) , wild-type 3′UTR vector (wild-type 3′UTR group) and empty vector (blank control group) , as well as miRNA vectors carring selected miRNAs were constructed according to human gene sequence analysis, and then were used to co-transfect 293T cells. After 48-hour treatment, the cells were lysed for detection of luciferase activity. Real-time fluorescence-based quantitative PCR was performed to measure the expression of CCL18 and selected miRNA in 14 fresh malignant melanoma tissue specimens and 14 paracancerous normal skin tissue specimens (control tissues) , and their correlations were analyzed. Results Online software analysis showed that some miRNAs were identified to target the 3′UTR of CCL18 gene, including miR-183, miR-128 and miR-33a. Luciferase reporter vectors and miRNA vectors were constructed successfully. As luciferase activity assay showed, when miR-183 and miR-128 were bound to the CCL18 3′UTR, the luciferase activities were significantly higher in their mutant 3′UTR groups (11.63 ± 0.42; 8.80 ± 0.49) than in their wild-type 3′UTR groups (4.86 ± 0.39; 5.01 ± 0.54; both P 0.05) . Real-time fluorescence-based quantitative PCR revealed higher mRNA expression of the CCL18 gene (3.52 ± 1.68) , but lower expression of miR-183 (0.49 ± 0.32) , miR-128 (0.30 ± 0.20) and miR-33a (0.46 ± 0.40) in the malignant melanoma tissues compared with the control tissues. The mRNA expression of the CCL18 gene was negatively correlated with the expression of miR-128 (rs=-0.548, P 0.05) . Conclusion miR-128 may play a role in regulating the potential malignant melanoma-promoting gene CCL18. Key words: Melanoma; MicroRNAs; RNA, small interfering; Chemokine CCL18