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1.
BMC Evol Biol ; 19(1): 162, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375061

RESUMO

BACKGROUND: Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. RESULTS: We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to 'long' G. lamblia introns, RNA secondary structural potential is evident for 'long' (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S. salmonicida; cumulatively, illustrating significant snRNA differences within some diplomonads. Finally, we studied spliceosomal protein complements and find protein sets in Giardia, Spironucleus and Trepomonas sp. PC1 highly- reduced but well conserved across the clade, with between 44 and 62 out of 174 studied spliceosomal proteins detectable. Comparison with more distant relatives revealed a highly nested pattern, with the more intron-rich fornicate Kipferlia bialata retaining 87 total proteins including nearly all those observed in the diplomonad representatives, and the oxymonad Monocercomonoides retaining 115 total proteins including nearly all those observed in K. bialata. CONCLUSIONS: Comparisons in diplomonad representatives and species of other closely-related metamonad groups indicates similar patterns of intron structural conservation and spliceosomal protein composition but significant divergence of snRNA structure in genomically-reduced species. Relative to other eukaryotes, loss of evolutionarily-conserved snRNA domains and common sets of spliceosomal proteins point to a more streamlined splicing mechanism, where intron sequences and structures may be functionally compensating for the minimalization of spliceosome components.


Assuntos
Sequência Conservada , Diplomonadida/genética , Íntrons/genética , Parabasalídeos/genética , Filogenia , Spliceossomos/genética , Regiões 5' não Traduzidas/genética , Pareamento de Bases/genética , Sequência de Bases , Genoma , Conformação de Ácido Nucleico , Processamento de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Nuclear Pequeno/química , RNA Nuclear Pequeno/genética , Proteínas Ribossômicas/genética
2.
BMC Evol Biol ; 19(1): 166, 2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31434566

RESUMO

BACKGROUND: The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. RESULTS: We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. CONCLUSIONS: Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution.


Assuntos
Quirópteros/classificação , Quirópteros/genética , Filogenia , África , Animais , Núcleo Celular/genética , Citocromos b/genética , DNA Mitocondrial/genética , Íntrons , Simpatria
3.
DNA Cell Biol ; 38(10): 1100-1111, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418589

RESUMO

Members of the Sox gene family play crucial roles during reproduction and development, but their genome-wide identification has not yet been performed in large yellow croaker, Larimichthys crocea. In this study, a total of 26 members of the Sox gene family were identified from the genome of large yellow croaker and classified into seven subgroups based on the conserved HMG-box domain they contain. Among the identified Sox gene family members, eight belonged to the SoxB subgroup (five in B1 and three in B2), four belonged to the SoxC subgroup, four belonged to the SoxD subgroup, six belonged to the SoxE subgroup, three belonged to the SoxF subgroup, and one belonged to the SoxK subgroup. During evolution, members of the SoxE subgroup (Sox8, Sox9, Sox10), Sox1, Sox4, Sox6, and Sox11 evolved into two copies, which may be a result of teleost-specific whole-genome duplication. Sox genes were distributed unevenly across 15 chromosomes. The number of introns in large yellow croaker Sox genes varied from 0 to 14. Results of the expression profile during embryogenesis revealed that most of the members of the Sox gene family had lower expression, except several Sox genes, and expression patterns also differed among each Sox gene group and duplicated gene. This study systematically characterized and analyzed the Sox gene family in large yellow croaker and provided new insights into its function during embryogenesis.


Assuntos
Proteínas de Peixes/genética , Regulação da Expressão Gênica no Desenvolvimento , Genoma , Perciformes/genética , Filogenia , Fatores de Transcrição SOXB1/genética , Sequência de Aminoácidos , Animais , Evolução Biológica , Mapeamento Cromossômico , Biologia Computacional , Embrião não Mamífero , Desenvolvimento Embrionário , Éxons , Proteínas de Peixes/classificação , Duplicação Gênica , Íntrons , Família Multigênica , Perciformes/classificação , Isoformas de Proteínas/classificação , Isoformas de Proteínas/genética , Fatores de Transcrição SOXB1/classificação , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
4.
Gene ; 716: 144036, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31381952

RESUMO

Nebulin is a 770 kDa protein that is localized along the thin filaments of skeletal muscles in vertebrates. It is also present in the striated muscles of Amphioxus, an invertebrate cephalochordate that is phylogenetically close to vertebrates. However, the nebulin of urochordate ascidians or its expression in invertebrate hearts has not been investigated. In this study, we investigated the structure and cardiac expression of the nebulin gene in Ciona intestinalis, a urochordate whose phylogeny lies between cephalochordates and vertebrates. As a result of the gene structure analysis, we found that the Ciona nebulin gene predicted to be 62 kb and consists of 143 exons. The nebulin was expected to consist of a unique N-terminal region, followed by 155 nebulin repeats, another unique region, a Ser-rich region and a C-terminal SH3 domain. Whole-mount in situ hybridization experiments showed that the Ciona nebulin gene was expressed in a variety of muscles, including hearts. However, Western blot analysis using antibody to Ciona nebulin did not detect the presence of full-length nebulin. Alternatively, RT-PCR experiments on samples of Ciona heart detected the expression of nebulette-like and nrap-like isoforms from the Ciona nebulin gene. These results indicate that, similarly to vertebrate hearts, Ciona hearts do not express nebulin, but rather nrap- and nebulette-like isoforms. These results also imply that the nebulin, nebulette and nrap genes in vertebrates were separated from an ancestral invertebrate nebulin gene during vertebrate evolution.


Assuntos
Ciona intestinalis/genética , Família Multigênica , Proteínas Musculares/genética , Miocárdio/metabolismo , Animais , Ciona intestinalis/metabolismo , Evolução Molecular , Éxons , Íntrons , Proteínas Musculares/química , Proteínas Musculares/metabolismo , Domínios Proteicos , RNA Mensageiro/metabolismo
5.
J Agric Food Chem ; 67(35): 9727-9737, 2019 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-31398034

RESUMO

The present study aimed to search for chicken abdominal fat deposition-related polymorphisms within RB1 and to provide functional evidence for significantly associated genetic variants. Association analyses showed that 11 single nucleotide polymorphisms (SNPs) in intron 17 of RB1, were significantly associated with both abdominal fat weight (P < 0.05) and abdominal fat percentage (P < 0.05). Functional analysis revealed that the A allele of g.32828A>G repressed the transcriptional efficiency of RB1 in vitro, through binding nuclear factor-kappa B (NF-KB) and SRY-related HMG box protein 2 (SOX2). Furthermore, RB1 mRNA expression levels in the abdominal fat tissue of individuals with the A/A genotype of g.32828A>G were lower than those of individuals with the G/G genotype. Collectively, we propose that the intronic SNP g.32828A>G of RB1 is an obesity-associated variant that directly affects binding with NF-KB and SOX2, leading to changes in RB1 expression which in turn may influence chicken abdominal fat deposition.


Assuntos
Adiposidade , Proteínas Aviárias/metabolismo , Galinhas/metabolismo , NF-kappa B/metabolismo , Proteína do Retinoblastoma/genética , Proteína do Retinoblastoma/metabolismo , Fatores de Transcrição SOX/metabolismo , Gordura Abdominal/metabolismo , Alelos , Animais , Proteínas Aviárias/genética , Sítios de Ligação , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Íntrons , NF-kappa B/genética , Polimorfismo de Nucleotídeo Único , Ligação Proteica , Fatores de Transcrição SOX/genética
6.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(7): 731-733, 2019 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-31302923

RESUMO

OBJECTIVE: To report on a novel weak D type identified in a Chinese individual. METHODS: Peripheral blood sample was collected for a voluntary blood donor with weakened expression of D antigen. Routine serological testing was carried out to determine the D, C, c, E and e antigens of the Rh blood group. A D-screening kit was used to analyze the RhD epitopes. The 10 exons and flanking intronic regions of the RHD gene were sequenced. The zygosity of RHD was determined with a sequence-specific primer PCR method. RESULTS: A novel RHD allele, RHD (1022T>A), was found in the subject with a weak D phenotype. Serological testing of the RhD epitopes has coined with the weak D phenotype. CONCLUSION: A novel weak D allele has been identified in Chinese population.


Assuntos
Alelos , Sistema do Grupo Sanguíneo Rh-Hr/genética , Grupo com Ancestrais do Continente Asiático , China , Éxons , Genótipo , Humanos , Íntrons
7.
Gene ; 715: 143970, 2019 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-31330235

RESUMO

BACKGROUND: Bicuspid aortic valve (BAV) formation is genetically determined, with reduced penetrance and variable expressivity. NOTCH1 is a proven candidate gene and its mutations have been found in familial and sporadic cases of BAV. METHODS: 66 BAV patients from the GISSI VAR study were genotyped for the NOTCH1 gene. RESULTS: We identified 63 variants, in heterozygous and homozygous states. Fifty-two are common polymorphisms present in almost all patients. Eleven variants are new and never yet reported: two are non-synonymous substitutions, Gly540Asp in exon 10 and Glu851Gln in exon 16; one is in the 3'UTR region and seven in introns, one corresponds to a T allele insertion in intron 27. We selected four statistically noteworthy and seven new variants identified in six BAV patients and correlated them with clinical and demographic variables and with imaging and histological parameters. Preliminary data show that four were BAV patients with isolated stenosis in patients over 60 aged. These variants may correlate with a later need for surgery for the presence of stenosis and not aortic valve regurgitation or ascending aortic aneurysm. CONCLUSIONS: Completing the genotyping of 62 BAV patients we found 11 new variants in the NOTCH1 gene never yet reported. These findings confirm that the identification of new, clinically remarkable biomarkers for BAV requires a deeper genetic understanding of the NOTCH1 gene variants, which could be targeted by future diagnostic and therapeutic strategies.


Assuntos
Estenose da Valva Aórtica/genética , Valva Aórtica/anormalidades , Doenças das Valvas Cardíacas , Mutação de Sentido Incorreto , Penetrância , Receptor Notch1/genética , Adulto , Alelos , Substituição de Aminoácidos , Éxons , Feminino , Heterozigoto , Homozigoto , Humanos , Íntrons , Itália , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Análise de Sequência de DNA
8.
BMC Bioinformatics ; 20(1): 405, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31345161

RESUMO

BACKGROUND: Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, especially with long reads. We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline. RESULTS: Magic-BLAST uses innovative techniques that include the optimization of a spliced alignment score and selective masking during seed selection. We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its ability to discover introns on real RNA-seq data sets from PacBio, Roche and Illumina runs, and on six benchmarks, and compare it to other popular aligners. Additionally, we look at alignments of human idealized RefSeq mRNA sequences perfectly matching the genome. CONCLUSIONS: We show that Magic-BLAST is the best at intron discovery over a wide range of conditions and the best at mapping reads longer than 250 bases, from any platform. It is versatile and robust to high levels of mismatches or extreme base composition, and reasonably fast. It can align reads to a BLAST database or a FASTA file. It can accept a FASTQ file as input or automatically retrieve an accession from the SRA repository at the NCBI.


Assuntos
RNA/genética , Alinhamento de Sequência , Análise de Sequência de RNA/métodos , Software , Algoritmos , Sequência de Bases , Bases de Dados de Ácidos Nucleicos , Humanos , Íntrons/genética , Curva ROC , Fatores de Tempo
9.
Yi Chuan ; 41(6): 469-485, 2019 Jun 20.
Artigo em Chinês | MEDLINE | ID: mdl-31257196

RESUMO

The field of circular non-coding RNAs have been gradually attracted wide attention with the developments of high-throughput sequencing. In this review, we systematically summarize three driving models for circRNAs biogenesis: intron-pairing-driven, RNA binding protein-driven and lariat-driven. In addition, we also briefly introduce the current research methods of circRNAs, which include high-throughput library construction methods, identification through bioinformatics and common experimental verification. Here, we also systematically summarize the functions of circRNAs, including microRNA (miRNA) or protein sponges, regulating the alternative splicing (AS) and expression of host genes, and extensive translation. Finally, we provide a systematic characterization and the latest research progress of circRNAs, which provide a new perspective for further studies of circRNAs in plants.


Assuntos
Processamento Alternativo , RNA/genética , Íntrons , MicroRNAs , Modelos Genéticos , Plantas/genética , Proteínas de Ligação a RNA
10.
BMC Plant Biol ; 19(1): 307, 2019 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-31299897

RESUMO

BACKGROUND: DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway. RESULTS: In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories. CONCLUSIONS: The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.


Assuntos
Metilação de DNA , Epigênese Genética , Impressão Genômica , Plantas/genética , Evolução Molecular , Éxons/genética , Íntrons/genética , Filogenia
11.
Genome Biol ; 20(1): 141, 2019 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-31315652

RESUMO

BACKGROUND: The long introns of mammals are pools of evolutionary potential due to the multiplicity of sequences that permit the acquisition of novel exons. However, the permissibility of genes to this type of acquisition and its influence on the evolution of cell regulation is poorly understood. RESULTS: Here, we observe that human genes are highly permissive to the inclusion of novel exonic regions permitting the emergence of novel regulatory features. Our analysis reveals the potential for novel exon acquisition to occur in over 30% of evaluated human genes. Regulatory processes including the rate of splicing efficiency and RNA polymerase II (RNAPII) elongation control this process by modulating the "window of opportunity" for spliceosomal recognition. DNA damage alters this window promoting the inclusion of repeat-derived novel exons that reduce the ribosomal engagement of cell cycle genes. Finally, we demonstrate that the inclusion of novel exons is suppressed in hematological cancer samples and can be reversed by drugs modulating the rate of RNAPII elongation. CONCLUSION: Our work demonstrates that the inclusion of repeat-associated novel intronic regions is a tightly controlled process capable of expanding the regulatory capacity of cells.


Assuntos
Éxons , Regulação da Expressão Gênica , Genoma Humano , Transcriptoma , Dano ao DNA , Elementos de DNA Transponíveis , Genes cdc , Neoplasias Hematológicas/metabolismo , Humanos , Íntrons , Spliceossomos
12.
Sheng Wu Gong Cheng Xue Bao ; 35(6): 1071-1078, 2019 Jun 25.
Artigo em Chinês | MEDLINE | ID: mdl-31232003

RESUMO

The aim of this study is to investigate the effect of the chimeric intron in different directions on the expression of the nerve growth factor (NGF) in recombinant Chinese hamster ovary (CHO) cells. The chimeric intron that contained the splice sequence of the first intron of the human ß-globin and the human immunoglobulin heavy chain variable region intron was used. NGF gene was cloned into the expression vectors containing the chimeric intron in the forward or reverse direction, followed by transfecting into CHO cells, and screened under G418 to produce the stable transfected CHO cells. Fluorescence quantitative PCR, ELISA, and Western blotting were performed to detect the recombinant NGF gene expression in CHO cells. The results showed that the chimeric introns could significantly enhance the expression of NGF in recombinant CHO cells. Moreover, the enhancing effect on NGF expression level by the intron in the forward direction showed stronger than that of the reverse direction both at mRNA and protein level. In conclusion, the chimeric intron could increase NGF expression in stably transfected CHO cells and the effect is associated with the direction of the intron insertion.


Assuntos
Íntrons , Animais , Animais Geneticamente Modificados , Células CHO , Cricetinae , Cricetulus , Expressão Gênica , Humanos , Transfecção
13.
Mol Biol (Mosk) ; 53(3): 411-420, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31184606

RESUMO

Antithrombin III (AT3) belongs to the superfamily of serine protease inhibitors (serpins) and is a major anticoagulant in physiological conditions. Based on SERPINC1 gene, a minigene coding for human AT3, which is valuable for medicine and biotechnology, was constructed by minimizing the size of lengthy introns and preserving the splicing site-flanking sequences. An analysis of the minigene splicing pattern identified one correct AT3 transcript and two alternatively spliced transcripts, which formed either due to minigene exons 2 and 3 skipping or an aberrant exon insertion via splicing at cryptic splicing sites in intron 1 of the minigene. Site-directed mutagenesis of the cryptic splicing sites successfully optimized the splicing pattern of the AT3 minigene to completely prevent the generation of the alternative transcripts. The presence of the cryptic splicing sites in intron 1 of the minigene was confirmed with Human Splicing Finder v. 3.1 software, thus demonstrating that putative alternative splicing sites are possible to identify in minimized or hybrid introns of minigenes and to eliminate via mutagenesis before experimentally testing the minigene splicing patterns. The approach to the design of minigenes together with the bioinformatical analysis of the nucleotide sequences of minigene introns can be used to construct minigenes in order to generate transgenic animals producing economically valuable proteins in the milk.


Assuntos
Processamento Alternativo/genética , Antitrombina III/genética , Sítios de Splice de RNA/genética , Éxons/genética , Humanos , Íntrons/genética
14.
BMC Bioinformatics ; 20(1): 324, 2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31195961

RESUMO

BACKGROUND: As DNA sequencing technologies are improving and getting cheaper, genomic data can be utilized for diagnosis of many diseases such as cancer. Human raw genome data is huge in size for computational systems. Therefore, there is a need for a compact and accurate representation of the valuable information in DNA. The occurrence of complex genetic disorders often results from multiple gene mutations. The effect of each mutation is not equal for the development of a disease. Inspired from the field of information retrieval, we propose using the term frequency (tf) and BM25 term weighting measures with the inverse document frequency (idf) and relevance frequency (rf) measures to weight genes based on their mutations. The underlying assumption is that the more mutations a gene has in patients with a certain disease and the less mutations it has in other patients, the more discriminative that gene is. RESULTS: We evaluated the proposed representations on the task of cancer type classification. We applied various machine learning techniques using the tf-idf and tf-rf schemes and their BM25 versions. Our results show that the BM25-tf-rf representation leads to improved classification accuracy and f-score values compared to the other representations. The highest accuracy (76.44%) and f-score (76.95%) are achieved with the BM25-tf-rf based data representation. CONCLUSIONS: As a result of our experiments, the BM25-tf-rf scheme and the proposed neural network model is shown to be the best performing classification system for our case study of cancer type classification. This system is further utilized for causal gene analysis. Examples from the most effective genes that are used for decision making are found to be in the literature as target or causal genes.


Assuntos
Genômica/métodos , Modelos Genéticos , Modelos Estatísticos , Mutação/genética , Bases de Dados Genéticas , Éxons/genética , Humanos , Íntrons/genética , Aprendizado de Máquina , Neoplasias/genética , Redes Neurais (Computação)
15.
Nat Commun ; 10(1): 2673, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31209208

RESUMO

Alternative splicing performs a central role in expanding genomic coding capacity and proteomic diversity. However, programming of splicing patterns in engineered biological systems remains underused. Synthetic approaches thus far have predominantly focused on controlling expression of a single protein through alternative splicing. Here, we describe a modular and extensible platform for regulating four programmable exons that undergo a mutually exclusive alternative splicing event to generate multiple functionally-distinct proteins. We present an intron framework that enforces the mutual exclusivity of two internal exons and demonstrate a graded series of consensus sequence elements of varying strengths that set the ratio of two mutually exclusive isoforms. We apply this framework to program the DNA-binding domains of modular transcription factors to differentially control downstream gene activation. This splicing platform advances an approach for generating diverse isoforms and can ultimately be applied to program modular proteins and increase coding capacity of synthetic biological systems.


Assuntos
Processamento Alternativo/genética , Regulação da Expressão Gênica/genética , Engenharia Genética/métodos , RNA/genética , Fatores de Transcrição/genética , Motivos de Aminoácidos/genética , Animais , Linhagem Celular , Biologia Computacional , Sequência Consenso/genética , Éxons/genética , Biblioteca Gênica , Genes Reporter/genética , Humanos , Íntrons/genética , Mutagênese Sítio-Dirigida/métodos , Domínios Proteicos/genética , Isoformas de Proteínas/genética , RNA/metabolismo , Fatores de Transcrição/metabolismo , Transcrição Genética
16.
BMC Bioinformatics ; 20(Suppl 8): 283, 2019 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-31182012

RESUMO

BACKGROUND: Numerous essential algorithms and methods, including entropy-based quantitative methods, have been developed to analyze complex DNA sequences since the last decade. Exons and introns are the most notable components of DNA and their identification and prediction are always the focus of state-of-the-art research. RESULTS: In this study, we designed an integrated entropy-based analysis approach, which involves modified topological entropy calculation, genomic signal processing (GSP) method and singular value decomposition (SVD), to investigate exons and introns in DNA sequences. We optimized and implemented the topological entropy and the generalized topological entropy to calculate the complexity of DNA sequences, highlighting the characteristics of repetition sequences. By comparing digitalizing entropy values of exons and introns, we observed that they are significantly different. After we converted DNA data to numerical topological entropy value, we applied SVD method to effectively investigate exon and intron regions on a single gene sequence. Additionally, several genes across five species are used for exon predictions. CONCLUSIONS: Our approach not only helps to explore the complexity of DNA sequence and its functional elements, but also provides an entropy-based GSP method to analyze exon and intron regions. Our work is feasible across different species and extendable to analyze other components in both coding and noncoding region of DNA sequences.


Assuntos
Entropia , Éxons/genética , Íntrons/genética , Algoritmos , Sequência de Bases , Cromossomos Humanos/genética , DNA/genética , Genoma Humano , Humanos , Regiões Promotoras Genéticas/genética , Curva ROC , Análise de Sequência de DNA/métodos , Processamento de Sinais Assistido por Computador
17.
Gene ; 710: 273-278, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31200082

RESUMO

BACKGROUND: Carotid plaque is a hallmark of advanced carotid atherosclerosis and there is evidence of phosphatase and actin regulator 1 (PHACTR1) involvement in the processes that lead to atherosclerosis. PHACTR1 intronic variants have been associated with coronary artery disease and carotid dissection. Up to date the PHACTR1 haplotypes were not investigated in association with carotid plaque presence (CPP). So, the aims of this study were to investigate possible association of PHACTR1 haplotypes inferred from the intronic variants rs9349379, rs2026458 and rs2876300 with CPP in patients with advanced carotid atherosclerosis and to analyze their possible effect on PHACTR1 relative mRNA expression in carotid plaque tissue specimens. METHODS: The study group consisted of 501 patients with evidence of carotid plaque presence admitted for carotid endarterectomy and 310 healthy controls. PHACTR1 rs9349379, rs2026458, rs2876300 and relative mRNA expression were detected by TaqMan® technology. RESULTS: We have found significant and independent association of haplotype ACA with the CPP, compared to the referent haplotype GTA (adjusted OR = 1.54 95% CI = 1.07-2.21, p = 0.02). The OR was adjusted for gender, age, BMI, hypertension and total cholesterol. The relative expression of PHACTR1 mRNA in carotid plaque tissue proved to be significantly higher in carriers of the ACG haplotype compared to the referent haplotype GTA (p = 0.03). CONCLUSION: Our results suggest that PHACTR1 haplotypes inferred from the variants rs9349379, rs2026458 and rs2876300 affect PHACTR1 mRNA and bear the risk for CPP in patients with advanced carotid atherosclerosis. Further replication and validation studies are inevitable.


Assuntos
Doenças das Artérias Carótidas/genética , Proteínas dos Microfilamentos/genética , Placa Aterosclerótica/genética , Polimorfismo de Nucleotídeo Único , Adulto , Idoso , Doenças das Artérias Carótidas/cirurgia , Estudos de Casos e Controles , Endarterectomia das Carótidas , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Haplótipos , Humanos , Íntrons , Masculino , Pessoa de Meia-Idade , Placa Aterosclerótica/cirurgia , Regulação para Cima
18.
Ann Hematol ; 98(8): 1827-1834, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31190133

RESUMO

In this study, we aimed to investigate the pattern and association of genetic mutations occurring within the alpha hemoglobin-stabilizing protein (AHSP) gene among HbE beta thalassemia patients with varying phenotypic expressions. Fifty-four diagnosed cases of HbE beta thalassemia (transfusion dependent and independent) were included in the study. Among them, 38 patients with similar genotypes (IVS 1-5, alpha gene deletion and triplication, Xmn polymorphism) were selected for further analysis. AHSP gene sequencing was done for these 38 samples to study associated mutations in AHSP gene. HbE beta thalassemia patients with similar genotypes but different phenotypic expressions were found to have mutations in the AHSP gene. There were five mutations found most prevalent among the samples analyzed for AHSP gene sequencing. Among these, two mutations were from intron 1 region of AHSP and three mutations were found in exon 3. The most prevalent mutation was found at the Oct binding site at intron 1 of AHSP. The mutations in exon 3 were more prevalent among the TDT groups. A mutation in exon 3 changing the amino acid (33rd) from serine to phenylalanine was found to be associated with only TDT group. This study documents that among the HbE beta thalassemia patients with varying severity, an exon mutation in AHSP is significantly prevalent only among the TDT group. Further understanding of the mechanism will shed light upon the impact of AHSP in modifying the disease severity in thalassemia.


Assuntos
Proteínas Sanguíneas/genética , Deleção de Genes , Duplicação Gênica , Hemoglobina E/genética , Chaperonas Moleculares/genética , Talassemia beta/genética , Adolescente , Adulto , Sequência de Bases , Proteínas Sanguíneas/metabolismo , Transfusão de Sangue/estatística & dados numéricos , Criança , Pré-Escolar , Análise Mutacional de DNA , Eritrócitos/metabolismo , Eritrócitos/patologia , Éxons , Feminino , Expressão Gênica , Genótipo , Hemoglobina E/metabolismo , Humanos , Íntrons , Masculino , Pessoa de Meia-Idade , Modelos Moleculares , Chaperonas Moleculares/metabolismo , Fenótipo , Estrutura Secundária de Proteína , Índice de Gravidade de Doença , Talassemia beta/metabolismo , Talassemia beta/patologia , Talassemia beta/terapia
19.
Mol Immunol ; 111: 209-219, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31096062

RESUMO

We have previously reported Israa, immune-system-released activating agent, as a novel gene nested in intron 8 of the mouse Zmiz1 gene. We have also shown that Israa encodes for a novel FYN-binding protein and might be involved in the regulation of T-cell activation. In this report, we demonstrate that Israa gene product regulates the expression of a pool of genes involved in T-cell activation and signaling. Real time PCR and GFP knock-in expression analysis showed that Israa is transcribed and expressed in the spleen mainly by CD3+CD8+ cells as well as in the thymus by CD3+ (DP and DN), CD4+SP and CD8+SP cells at different developmental stages. We also showed that Israa is downregulated in T-cells following activation of T-cell receptor. Using yeast two-hybrid analysis, we identified ELF1, a transcription factor involved in T-cell regulation, as an ISRAA-binding partner. Transcriptomic analysis of an EL4 cell line overexpressing ISRAA revealed differential expression of several genes involved in T-cell signaling, activation and development. Among these genes, Prkcb, Mib2, Fos, Ndfip2, Cxxc5, B2m, Gata3 and Cd247 were upregulated whereas Itk, Socs3, Tigit, Ifng, Il2ra and FoxJ1 were downregulated. Our findings support the existence in mouse of a novel FYN-related T-cell regulation pathway involving the product of an intron-nested gene.


Assuntos
Íntrons/imunologia , Ativação Linfocitária/imunologia , Linfócitos/imunologia , Linfocinas/imunologia , Genes Inseridos/imunologia , Transdução de Sinais/imunologia , Linfócitos T/imunologia , Animais , Complexo CD3/imunologia , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD8-Positivos/imunologia , Linhagem Celular , Regulação para Baixo/imunologia , Feminino , Expressão Gênica/imunologia , Camundongos , Camundongos Endogâmicos C57BL , Receptores de Antígenos de Linfócitos T/imunologia , Fatores de Transcrição/imunologia , Regulação para Cima/imunologia
20.
Mol Med Rep ; 19(6): 4989-4997, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31059019

RESUMO

The pathological process of Parkinson's disease (PD) is closely associated with the death of nigral neurons, for which an effective treatment has yet to be found. Lithium, one of the most widely certified anticonvulsant and mood­stabilizing agents, exhibits evident neuroprotective effects in the treatment of epilepsy and bipolar disorder. In the present study, the neuroprotective mechanisms by which lithium acts on a chronic 1­methyl­4­phenyl­1,2,3,6­tetrahydropyridine (MPTP) mouse model of PD were investigated by employing animal behavioral tests, immunohistochemistry, RT­PCR, and western blotting. The results revealed that, in open field tests, lithium treatment counteracted the reduction in movement distance as well as activity time induced by MPTP administration. The compound could also prolong the drop time of MPTP­treated mice in rotarod tests. Moreover, lithium treatment corrected the loss of nigral neurons, the increase of α­synuclein (SNCA) in substantia nigra as well as in the striatum of MPTP­treated mice, and decreased the methylation of SNCA intron 1 in DNA from the same regions. Furthermore, marked changes were observed in the expression of miRNAs including miR­148a, a potential inhibitor of DNMT1, in the MPTP­treated mice. These results suggested that the early application of lithium was important for alleviating the behavioral deficits experienced in the PD model, and that the neuroprotective action of lithium was achieved through a lithium­triggered miRNA regulation mechanism. Essentially, our findings indicated that lithium may be beneficial in the prevention and treatment of PD through the regulation of α­synuclein methylation.


Assuntos
Lítio/uso terapêutico , Intoxicação por MPTP/tratamento farmacológico , Fármacos Neuroprotetores/uso terapêutico , alfa-Sinucleína/metabolismo , Animais , Comportamento Animal/efeitos dos fármacos , DNA (Citosina-5-)-Metiltransferase 1/metabolismo , Modelos Animais de Doenças , Íntrons , Lítio/farmacologia , Intoxicação por MPTP/patologia , Masculino , Metilação/efeitos dos fármacos , Camundongos , Camundongos Endogâmicos C57BL , MicroRNAs/metabolismo , Fármacos Neuroprotetores/farmacologia , Substância Negra/efeitos dos fármacos , Substância Negra/metabolismo , Substância Negra/patologia , alfa-Sinucleína/genética
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