DNA Splicing Research Articles

Multipart DNA Assembly Using Site-Specific Recombinases from the Large Serine Integrase Family.

Assembling multiple DNA fragments into functional plasmids is an important and often rate-limiting step in engineering new functions in living systems. Bacteriophage integrases are enzymes that carry out efficient recombination reactions between short,defined DNA sequences known as att sites. These DNA splicing reactions can be used to assemble large numbers of DNA fragments into a functional circular plasmid in a method termed serine integrase recombinational assembly (SIRA). The resulting DNA assemblies can easily be modified by further recombination reactions catalyzed by the same integrase in the presence of its recombination directionality factor (RDF). Here we present a set of protocols for the overexpression and purification of bacteriophage ϕC31 and Bxb1 integrase and RDF proteins, their use in DNA assembly reactions, and subsequent modification of the resulting DNA assemblies.

The Clonal Origins of Leukemic Progression of Myelodysplasia

IntroductionAcute myeloid leukemia (AML) that develops from pre-existing hematologic diseases, rather than developing de novo, is known as secondary AML (sAML). A number of hematologic malignancies can progress to sAML. However, the molecular and genetic characteristics behind the progression of hematologic malignancies to sAML remain unclear. To address this question and dissect the order of mutation acquisition throughout the course of the disease, we performed whole-exome sequencing and targeted deep sequencing on serial samples.Patients and MethodsThis study examined several cohorts with a combined total of 124 patients. This study was approved by research ethics boards at relevant institutions and samples were taken after informed consent. The discovery cohort (C1) consisted of 31 patients diagnosed with myelodysplasia who all progressed to sAML. Whole-exome sequencing (WXS) was performed for each case on bone marrow samples taken at the diagnosis of the antecedent malignancy and after sAML progression, as well as fractionated T-cell samples (CD3+). WXS (Agilent SureSelect v4) was performed on the 93 samples as per the manufacturer's protocol using an Illumina HiSeq 2000. The other cohorts included 72 non-progressed MDS patients (C2a, median follow-up of 3.5 years) and an additional 21 sAML patients (C2b) progressed to sAML from MDS, for whom samples from the MDS stage were not available. Targeted sequencing was performed using an Agilent custom probe set of the selected 92 genes. We multiplexed and sequenced the samples using an Illumina Hiseq 2000. Targeted deep sequencing was performed on all cohorts. Genomon-ITD was used to detect FLT3-ITD.ResultsThe mean read depth retrieved for target regions for WXS data was 73x. After calling and prioritizing variants, we found a mean and median of 7.7 and 6 significant variants per patient at the time of initial diagnosis, and 12.4 and 10 variants after sAML progression, respectively. We also detected that FLT3-ITD emerged in 2 patients after sAML progression.The presence of variants in T-cell samples in 5 C1 and 20 C2a patients provides evidence on the relative timing of early events for a subset of patients. Both cohorts notably lack activated signaling pathway variants at this stage (Figure A). The T-cell variants in 5 C1 patients with pathway associations were all in genes involved in DNA methylation (DNMT3A, IDH1/2, and TET2) or splicing machinery (SRSF2 and SF3B1). This pattern was verified in 20 C2a patients except for a single case that had an NRAS-G13D mutation. These patients showed evidence of having clonal hematopoiesis.At MDS, there were a significant number of cases with variants in genes involved in DNA methylation and/or splicing machinery (35.5% and 48.3%, respectively). However, the portion of cases with variants affecting these pathways increased significantly at the MDS stage, but did not change much by the sAML stage (Figure C-D). On the other hand, variants in genes involved in activated signaling pathways showed a distinctive pattern. The portion of cases with variants affecting activated signaling pathways noticeably increased at the sAML step (25.8% to 54.8%) (Figure B). The changes in VAF between stages within cases of these variants revealed a similar pattern.In summary, clonal evolution patterns can be postulated based on the acquisition/expansion of mutations related to the three signature pathways (Figure E). Forty-eight percent of patients showed growth or development of clones containing activated signaling pathway variants at the sAML stage. Sixteen percent of patients developed the MDS from preleukemic mutations associated with DNA methylation or splicing machinery, and 26% first developed clones of this category at the MDS stage (a total of 42%).ConclusionMutations in DNA methylation and splicing machinery genes are early disease events, expanding at the MDS stage but not during progression. On the other hand, activated signaling pathway mutations expand during progression, demonstrating that distinct categories of genetic lesions play roles at different stages of sAML in a generally fixed order. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections.

Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages. Immunohistochemistry and immunofluorescence are fundamental experimental approaches in clinical laboratories and are also widely used in basic research. However, the fixation procedure may generate artifacts and prevents monitoring of the dynamics of nuclear processes. Therefore, live-cell imaging is critical for studying the kinetics of basic nuclear events, such as DNA replication, transcription, splicing, and DNA repair. This review is focused on the advanced microscopy analyses of the cells, with a particular focus on live cells. We note some methodological innovations and new options for microscope systems that can also be used to study tissue sections. Cornerstone methods for the biophysical research of living cells, such as fluorescence recovery after photobleaching and fluorescence resonance energy transfer, are also discussed, as are studies on the effects of radiation at the individual cellular level.

Review on Nitric Oxide, Carbon Monoxide and Antisense Based Therapy towards Treatment of Restenosis

Balloon angioplasty has shown tremendous improvement in the treatment of atherosclerosis, but arterial renarrowing (restenosis) exists despite the benefits of intravascular devices called stents. Nitric Oxide (NO), carbon monoxide (CO) and Antisense therapy is some of the new potential treatment modalities. NO deficiency is associated with several vascular occlusive diseases, since NO regulates diverse aspects of blood vessel functions. More restricted human studies and several preclinical studies suggest that, NO supplement may solve the restenosis problem, although the data do not conclusively demonstrate this effect. CO, similar to NO, inhibits vascular smooth muscle cells (VSCM) proliferation and in turn relaxes blood vessels and inhibits platelet aggregation. Thus it is recently suggested that inhaling CO could address the restenosis problem. Recent advances in vascular gene transfer have shown positive results for cardiovascular diseases, particularly in the treatment of restenosis. Uncoiling the DNA, transcription of DNA, export of RNA, DNA splicing, RNA stability or RNA transcription involved in the synthesis of proteins in cellular proliferation are some of the process involving antisense based approach. This review focuses on discussing the recent advancements in the treatment of restenosis.

An alternative strategy to generate coding sequence of macrophage migration inhibitory factor-2 of Wuchereria bancrofti.

Background & objectives:Different developmental stages of Wuchereria bancrofti, the major causal organism of lymphatic filariasis (LF), are difficult to obtain. Beside this limitation, to obtain complete coding sequence (CDS) of a gene one has to isolate mRNA and perform subsequent cDNA synthesis which is laborious and not successful at times. In this study, an alternative strategy employing polymerase chain reaction (PCR) was optimized and validated, to generate CDS of Macrophage migration Inhibitory Factor-2 (wbMIF-2), a gene expressed in the transition stage between L3 to L4.Methods:The genomic DNA of W. bancrofti microfilariae was extracted and used to amplify the full length wbMIF-2 gene (4.275 kb). This amplified product was used as a template for amplifying the exons separately, using the overlapping primers, which were then assembled through another round of PCR.Results:A simple strategy was developed based on PCR, which is used routinely in molecular biology laboratories. The amplified CDS of 363 bp of wbMIF-2 generated using genomic DNA splicing technique was devoid of any intronic sequence.Interpretation & conclusions:The cDNA of wbMIF-2 gene was successfully amplified from genomic DNA of microfilarial stage of W. bancrofti thus circumventing the use of inaccessible L3-L4 transitional stage of this parasite. This strategy is useful for generating CDS of genes from parasites that have restricted availability.

MODELLING OF TWO STAGES DNA SPLICING LANGUAGES ON DE BRUIJN GRAPH

Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular. This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.

PERSISTENCY AND PERMANENCY OF TWO STAGES SPLICING LANGUAGES VIA YUSOF-GOODE APPROACH: TWO INITIAL STRINGS AND TWO RULES

The notation of representing restriction enzymes in the form of double-triple in order to formulate Yusof-Goode (Y-G) splicing system was mathematically proposed by Yusof in 2012. The aim of introducing Y-G splicing system was to study the process of recombinant deoxyribonucleic acid or DNA strand in a translucent way. In real situation, when the recombination action occurs, the recombinant DNA strands which will arise often contain the patterns of the restriction enzymes. Persistency and permanency are two properties of splicing system, which show whether the recombinant DNA strands will be split by the existence of restrictions enzymes or not if the reaction goes to the second stage. In this research, the persistency and permanency of two stages splicing languages according to the number of cutting sites of initial strings as well as crossing sites and context factors of splicing rules are investigated. Therefore, a Y-G splicing system consisting of two initial strings (with two cutting sites) and two rules is used to present the above properties of two stages DNA splicing languages.

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.

Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination, illustrating how the process of programmed genome rearrangement gives rise to evolutionary innovation.

Determination of the protein expression profiles of breast cancer cell lines by quantitative proteomics using iTRAQ labelling and tandem mass spectrometry

Breast cancer is the principal cancer in women worldwide. Although there are serum tumor markers such as CEA and HER2, they are detected in advanced stages of the disease and used as progression and recurrence markers. Therefore, there is a necessity for the identification of new markers that might lead to an early detection and also provide evidence of an effective treatment. The aim of this work was to determine the differential protein expression profiles of four breast cancer cell lines in comparison to a normal control cell line by iTRAQ labelling and tandem mass spectrometry, in order to identify putative biomarkers of the disease. We identified 1,020 iTRAQ-labelled polypeptides with at least one peptide identified with more than 95% in confidence. Overexpressed polypeptides in all cancer cell lines were 78, whilst the subexpressed were 128. We categorised them with PANTHER program into biological processes, being the metabolic pathways the most affected. We detected six groups of proteins with the STRING program involved in DNA topology, glycolysis, translation initiation, splicing, pentose pathway, and proteasome degradation. The main subexpressed protein network included mitochondrial proteins involved in oxidative phosphorylation. We propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. Biological significanceWe report a set of differentially expressed proteins in the MCF7 and T47D (Luminal A), MDA-MB-231 (Claudin low) and SK-BR-3 (HER2+) breast cancer cell lines that have not been previously reported in breast cancer disease. From these proteins, we propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. On the other hand, we propose sets of unique polypeptides in each breast cancer cell line that can be useful in the classification of different subtypes of breast cancer.

Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation.

Chemically engineered DNAs—in which global conformation can be modulated in response to specific stimuli—could be allosteric functional DNAs themselves or work as a modulator of the functional nucleic acids such as DNAzymes and aptamers. Here, we show that two terpyridines built in the DNA backbone form a stable intramolecular 1:2 complex, [M(terpy)2](2+), with divalent transition metal ions. Upon complexation, the DNA conjugates adopt a Ω-shape structure, in which two distal sequences located outside the terpyridines connect with each other to form a continuous segment with a specific structure or sequence. Such a DNA structure is globally controlled by local metal complexation events that can be rationally designed based on general coordination chemistry. This method is regarded as metal ion-directed dynamic sequence edition or DNA splicing. DNAzymes with peroxidase-like activity can thus be regulated by several transition metal ions through sequence edition techniques based on the Ω-motif.

Characterization of the Activity and Biological Function of Human Protein Arginine Methyltransferase 9 (PRMT9)

Protein arginine methyltransferases (PRMTs) make up a family of enzymes that transfer methyl groups onto arginine residues and play important roles in DNA repair, splicing, transcriptional control and signaling. In mammals, a family of nine PRMTs are known. PRMT1,2,3,4,6, and 8 catalyze the formation of asymmetric dimethylarginine (ADMA) and w‐monomethylarginine (MMA), PRMT5 catalyzes symmetric dimethylarginine (SDMA) and MMA formation, and PRMT7 catalyzes only MMA formation. The last member of this family, PRMT9 (also designated PRMT10), has not previously been characterized. In humans, it is encoded on a gene on chromosome 4 in position 4q31. We have now expressed human PRMT9 both as a GST‐fusion protein in bacterial cells and as a GFP‐fusion protein in human HEK293 cells. For both expression systems, we have also prepared catalytic mutants to serve as controls for possible contamination of other types of PRMTs. Using an in vitro methylation assay, we show that both forms of PRMT9 catalyze the methylation of myelin basic protein and a GST‐fusion protein of the N‐terminal domain of human fibrillarin. Studies are in progress to characterize the type of activity and physiological substrates for PRMT9.

An overview of the prediction of protein DNA-binding sites.

Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.

A New Relation of Second Order Limit Language in Simple and Semi-Simple Splicing System

Splicing system, which is an abstraction of operations on DNA molecules, can be modelled mathematically under the framework of formal language theory and informational macromolecules. The recombinant behavior of the set of double-stranded DNA molecules under the influence of restriction enzyme and ligase further lead to the cut and paste phenomenon in splicing system. The theoretical study of splicing language has contributed to a new type of splicing language known as a second order limit language, which is an extension of limit language. Some types of splicing system can produce second order limit language. Y-G splicing system is chosen among other models to model the DNA splicing process as this model preserves the biological traits and presents the transparent behavior of the DNA splicing process. In this paper, the relation between second order limit language with simple splicing and semi-simple splicing system are presented.

A Comparison of Second Order and Non-Second Order Limit Language Generated by Yusof-Goode Splicing System

DNA splicing process is a study on the recombinant behavior of double-stranded DNA molecules with the existence of restriction enzyme and ligase. Head introduced the first mathematical model of splicing systems by using the relation of informational macromolecules and formal language theory. In addition, a few laboratory experiments have been conducted in order to verify certain types of splicing language called inert/adult, transient and limit language. Previously, researchers have focused on those types of splicing languages. Recently, an extension of limit languages namely second order limit language has been introduced. In this paper, the difference between second order limit languages and non-second order limit languages is depicted in some examples. Then, the formations of second order limit language in Yusof-Goode splicing system are investigated.

Alternative forms of Y-box binding protein 1 and YB-1 mRNA.

The multifunctional eukaryotic protein YB-1 (Y-box binding protein 1) plays a role in DNA reparation, transcription regulation, splicing, and mRNA translation, thereby participating in many crucial events in cells. Its effect is dependent mostly on its amount, and hence, on regulation of its synthesis. Published data on regulation of synthesis of YB-1 mediated by its mRNA 5′ UTR, and specifically on the 5′ UTR length and the presence of TOP-like motifs in this region, are contradictory. Here we report that 5′ UTRs of major forms of human, rabbit, and mouse YB-1 mRNAs are about 140 nucleotides long and contain no TOP-like motifs mentioned in the literature. Also, we have found that YB-1 specifically interacts with the 5′ UTR of its own mRNA within a region of about 100 nucleotides upstream from the start codon. Apart from YB-1, translation of YB-1 mRNA in a cell free system gives an additional product with an extended N-terminus and lower electrophoretic mobility. The start codon for synthesis of the additional product is AUC at position –(60–58) of the same open reading frame as that for the major product. Also, in the cell there is an alternative YB-1 mRNA with exon 1 replaced by a part of intron 1; YB-1 synthesized in vitro from this mRNA contains, instead of its N-terminal A/P domain, 10–11 amino acids encoded by intron 1.

Mathematical Modelling of Some Null-Context and Uniform Splicing Systems

The mathematical modelling of splicing system which involves recombination of DNA molecules was first introduced by Head in 1987. Splicing of DNA involves cutting of DNA molecules using the restriction enzymes and re-associating different fragments of DNA molecules using the ligase under some specific chemical conditions. A splicing language, L is generated if there exists a splicing system S for which L = L(S). There are different types of splicing systems which have been discussed by various researchers. Among them are the persistent splicing system, null-context and uniform splicing system. In this paper, some molecular examples on null-context splicing system and uniform splicing systems with different initial strings and combination of restriction enzymes will be discussed. Applications of automata theory on some molecular examples of null-context and uniform splicing languages will also be presented in this paper.

Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

Integrating genetics and epigenetics in myelodysplastic syndromes: advances in pathogenesis and disease evolution.

The myelodysplastic syndromes (MDS) are a group of clonal diseases characterized by inefficient haematopoiesis, increased apoptosis and risk of evolution to acute myeloid leukaemia. Alterations in epigenetic processes, including DNA methylation, histone modifications, miRNA and splicing machinery, are well known pathogenical events in MDS. Although many advances have been made in determining the mutational frequency, distribution and association affecting these epigenomic regulators, functional integration to better understand pathogenesis of the disease is a challenging and expanding area. Recent studies are shedding light on the molecular basis of myelodysplasia and how mutations and epimutations can induce and promote this neoplastic process through aberrant transcription factor function (RUNX1, ETV6, TP53), kinase signalling (FLT3, NRAS, KIT, CBL) and epigenetic deregulation (TET2, IDH1/2, DNMT3A, EZH2, ASXL1, SF3B1, U2AF1, SRSF2, ZRSR2). In this review we will try to focus on the description of these mutations, their impact on prognosis, the functional connections between the different epigenetic pathways, and the existing and future therapies targeting these processes.

Gene mutations differently impact the prognosis of the myelodysplastic and myeloproliferative classes of chronic myelomonocytic leukemia

Initially classified in the myelodysplastic syndromes (MDSs), chronic myelomonocytic leukemia (CMML) is currently considered as a MDS/myeloproliferative neoplasm. Two classes-myelodysplastic and myeloproliferative-have been distinguished upon the level of the white blood cell count (threshold 13 G/L). We analyzed mutations in 19 genes reported in CMML to determine if and how these mutations impacted the respective prognosis of the two classes. We defined four major mutated pathways (DNA methylation, ASXL1, splicing, and signaling) and determined their prognostic impact. The number of mutated pathways impacted overall survival in the myelodysplastic class but not in the myeloproliferative class. The myeloproliferative class had a worse prognosis than the myelodysplastic class and was impacted by RUNX1 mutations only. Our results argue for a reclassification of CMML based on the myelodysplastic/myeloproliferative status.

Characterization of the activity and biological function of human protein arginine methyltransferase 9 (555.6)

Protein arginine methyltransferases (PRMTs) make up a family of enzymes that transfer methyl groups onto arginine residues and play important roles in DNA repair, splicing, transcriptional control and signaling. In mammals, a family of nine PRMTs are known. PRMT1,2,3,4,6, and 8 catalyze the formation of asymmetric dimethylarginine (ADMA) and ω‐monomethylarginine (MMA), PRMT5 catalyzes symmetric dimethylarginine (SDMA) and MMA formation, and PRMT7 catalyzes only MMA formation. The last member of this family, PRMT9 (also designated PRMT10), has not previously been characterized. In humans, it is encoded on a gene on chromosome 4 in position 4q31. We have now expressed human PRMT9 both as a GST‐fusion protein in bacterial cells and as a GFP‐fusion protein in human HEK293 cells. For both expression systems, we have also prepared catalytic mutants to serve as controls for possible contamination of other types of PRMTs. Using an in vitro methylation assay, we show that both forms of PRMT9 catalyze the methylation of myelin basic protein and a GST‐fusion protein of the N‐terminal domain of human fibrillarin. Studies are in progress to characterize the type of activity and physiological substrates for PRMT9.Grant Funding Source: Supported by Ruth L. Kirschstein National Research Service Award GM007185