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1.
Gene ; 747: 144684, 2020 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-32311412

RESUMO

PRMT8 is a neuron-specific protein arginine methyltransferase in vertebrates. From data mining, we found a novel prmt8e6+43 splicing variant with a 43-nucleotide (nt) extension at the 5' of exon 6 in chicken. RT-PCR analyses confirmed the existence of two splicing variants but also detected a third upper signal. The triplet pattern detected in chicken suggests that one strand from the prmt8e6+43 transcript and one strand from the regular splicing products form a heteroduplex with a bulb conformation and the two transcripts are of similar abundance. One short plus one faint upper heteroduplex signal detected in mouse and human indicate that the level of the variant is much less than the normal one in mammals. The relative expression of the normal and prmt8e6+43 variants in different species can be inferred from the reads of intron 5 that contains the 43-nt extension or not in the RNA-seq data of NCBI Gene database. The results of the analyses showed that the prmt8e6+43 variant is relatively abundant in birds but much less or even not detected in mammalian species. As conserved intron 5 sequences and evidences of alternative splicing (AS) are detected in elephant shark, a cartilaginous fish with the slowest-evolving genome, we propose that the prmt8e6+43 variant is present in the common ancestor of jawed vertebrates. The prmt8e6+43 variant includes a premature termination codon and thus should encode a truncated PRMT8 with deletion from the dimerization arm. Western blot analyses showed very weak low-molecular-weight signals in chicken, which might be the C-terminal truncated PRMT8. Why avian species maintain high RNA but not protein levels of the prmt8e6+43 variant and whether the evolutionary conserved sequence and AS might regulate PRMT8 expression require further investigation.


Assuntos
Processamento Alternativo/genética , Aves/genética , Variação Genética , Íntrons/genética , Proteína-Arginina N-Metiltransferases/genética , Sítios de Splice de RNA/genética , Vertebrados/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Galinhas/genética , Humanos , Camundongos , Nucleotídeos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
2.
Nat Commun ; 11(1): 1221, 2020 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-32144266

RESUMO

Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent.


Assuntos
Metilação de DNA/genética , Elementos de DNA Transponíveis/genética , Nucleotídeos/genética , Sistemas CRISPR-Cas/genética , Cromatina/metabolismo , Evolução Molecular , Inativação Gênica , Lycopersicon esculentum/genética , Lycopersicon esculentum/crescimento & desenvolvimento , Mutação/genética , Fenótipo , Proteínas de Plantas/metabolismo , RNA Polimerase II/metabolismo , Sequências Repetidas Terminais/genética
3.
Nucleic Acids Res ; 48(6): 3156-3164, 2020 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-32009150

RESUMO

The hexametric T7 helicase (gp4) adopts a spiral lock-washer form and encircles a coil-like DNA (tracking) strand with two nucleotides bound to each subunit. However, the chemo-mechanical coupling mechanism in unwinding has yet to be elucidated. Here, we utilized nanotensioner-enhanced Förster resonance energy transfer with one nucleotide precision to investigate gp4-induced unwinding of DNA that contains an abasic lesion. We observed that the DNA unwinding activity of gp4 is hindered but not completely blocked by abasic lesions. Gp4 moves back and forth repeatedly when it encounters an abasic lesion, whereas it steps back only occasionally when it unwinds normal DNA. We further observed that gp4 translocates on the tracking strand in step sizes of one to four nucleotides. We propose that a hypothetical intermediate conformation of the gp4-DNA complex during DNA unwinding can help explain how gp4 molecules pass lesions, providing insights into the unwinding dynamics of gp4.


Assuntos
Bacteriófago T7/genética , DNA Helicases/genética , DNA Primase/genética , DNA/genética , Bacteriófago T7/química , DNA/química , DNA Primase/química , Transferência Ressonante de Energia de Fluorescência , Cinética , Conformação Molecular , Nucleotídeos/química , Nucleotídeos/genética
4.
Nucleic Acids Res ; 48(5): 2544-2563, 2020 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-32016395

RESUMO

The evolution of gene expression regulation has contributed to species differentiation. The 3' untranslated regions (3'UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3'UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3'UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3'UTR of orthologous genes and demonstrated that 3'UTR sequence variations affect protein production. This suggested that species-specific functional 3'UTRs might be specifically selected during evolution. 3'UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3'UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3'UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3'UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.


Assuntos
Regiões 3' não Traduzidas/genética , Evolução Molecular , Regulação Bacteriana da Expressão Gênica , Staphylococcus/genética , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Elementos de DNA Transponíveis/genética , Rearranjo Gênico/genética , Genes Bacterianos , Hemólise , Nucleotídeos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ovinos , Especificidade da Espécie
5.
Nucleic Acids Res ; 48(6): 3165-3180, 2020 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-32034423

RESUMO

Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain-especially the O helix-to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO-POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.


Assuntos
DNA Polimerase I/genética , DNA Polimerase Dirigida por DNA/genética , Endonucleases Flap/genética , Fosfodiesterase I/genética , Sítios de Ligação , Cristalografia por Raios X , DNA Polimerase I/química , Replicação do DNA/genética , DNA Polimerase Dirigida por DNA/química , Endonucleases Flap/química , Magnésio/química , Mycobacterium/enzimologia , Mycobacterium/genética , Conformação de Ácido Nucleico , Nucleotídeos/genética , Fosfodiesterase I/química
6.
Nat Genet ; 52(2): 208-218, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32015527

RESUMO

Cancer genomes contain large numbers of somatic mutations but few of these mutations drive tumor development. Current approaches either identify driver genes on the basis of mutational recurrence or approximate the functional consequences of nonsynonymous mutations by using bioinformatic scores. Passenger mutations are enriched in characteristic nucleotide contexts, whereas driver mutations occur in functional positions, which are not necessarily surrounded by a particular nucleotide context. We observed that mutations in contexts that deviate from the characteristic contexts around passenger mutations provide a signal in favor of driver genes. We therefore developed a method that combines this feature with the signals traditionally used for driver-gene identification. We applied our method to whole-exome sequencing data from 11,873 tumor-normal pairs and identified 460 driver genes that clustered into 21 cancer-related pathways. Our study provides a resource of driver genes across 28 tumor types with additional driver genes identified according to mutations in unusual nucleotide contexts.


Assuntos
Biologia Computacional/métodos , Mutação , Neoplasias/genética , Nucleotídeos/genética , Proteínas/genética , Análise por Conglomerados , Humanos , Proteínas/química , Sequenciamento Completo do Exoma/métodos
7.
Nucleic Acids Res ; 48(4): 1607-1626, 2020 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-31984425

RESUMO

7-Methylguanosine 5' cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5'-terminal nucleotides and additional methylations (2'-O-methylation and m6A). Currently available 5'-capping methods do not address this diversity. We report trinucleotide 5' cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (±2'-O-methylation). HPLC-purified mRNAs carrying these 5' caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa and JAWS II). The highest expression was observed for mRNAs carrying 5'-terminal A/Am and m6Am, whereas the lowest was observed for G and Gm. The mRNAs carrying 2'-O-methyl at the first transcribed nucleotide (cap 1) had significantly higher expression than unmethylated counterparts (cap 0) only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.


Assuntos
Biossíntese de Proteínas/genética , Capuzes de RNA/genética , RNA Mensageiro/isolamento & purificação , Transcrição Genética , Animais , Eucariotos/genética , Fator de Iniciação 4E em Eucariotos/genética , Regulação da Expressão Gênica/genética , Células HeLa , Humanos , Metilação , Nucleotídeos/genética , Processamento de Proteína Pós-Traducional/genética , RNA Mensageiro/genética
8.
Top Curr Chem (Cham) ; 378(1): 10, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31894426

RESUMO

Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.


Assuntos
DNA/química , DNA/genética , Variação Genética , Nucleotídeos/genética , Humanos , Nanotecnologia , Hibridização de Ácido Nucleico , Sondas de Ácido Nucleico/genética , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase
9.
Nucleic Acids Res ; 48(3): 1583-1598, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31956908

RESUMO

Cyclic dimeric 3'-5' guanosine monophosphate, c-di-GMP, is a ubiquitous second messenger controlling diverse cellular processes in bacteria. In streptomycetes, c-di-GMP plays a crucial role in a complex morphological differentiation by modulating an activity of the pleiotropic regulator BldD. Here we report that c-di-GMP plays a key role in regulating secondary metabolite production in streptomycetes by altering the expression levels of bldD. Deletion of cdgB encoding a diguanylate cyclase in Streptomycesghanaensis reduced c-di-GMP levels and the production of the peptidoglycan glycosyltransferase inhibitor moenomycin A. In contrast to the cdgB mutant, inactivation of rmdB, encoding a phosphodiesterase for the c-di-GMP hydrolysis, positively correlated with the c-di-GMP and moenomycin A accumulation. Deletion of bldD adversely affected the synthesis of secondary metabolites in S. ghanaensis, including the production of moenomycin A. The bldD-deficient phenotype is partly mediated by an increase in expression of the pleiotropic regulatory gene wblA. Genetic and biochemical analyses demonstrate that a complex of c-di-GMP and BldD effectively represses transcription of wblA, thus preventing sporogenesis and sustaining antibiotic synthesis. These results show that manipulation of the expression of genes controlling c-di-GMP pool has the potential to improve antibiotic production as well as activate the expression of silent gene clusters.


Assuntos
Proteínas de Bactérias/genética , Bambermicinas/biossíntese , Produtos Biológicos/metabolismo , GMP Cíclico/análogos & derivados , Proteínas de Ligação a DNA/genética , Fatores de Transcrição/genética , Proteínas de Bactérias/antagonistas & inibidores , GMP Cíclico/genética , GMP Cíclico/metabolismo , Proteínas de Ligação a DNA/antagonistas & inibidores , Proteínas de Escherichia coli/genética , Deleção de Genes , Regulação Bacteriana da Expressão Gênica/genética , Nucleotídeos/genética , Peptidoglicano Glicosiltransferase/antagonistas & inibidores , Fósforo-Oxigênio Liases/genética , Sistemas do Segundo Mensageiro/genética , Streptomycetaceae/genética , Streptomycetaceae/metabolismo , Fatores de Transcrição/antagonistas & inibidores
10.
Gene ; 726: 144226, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31669644

RESUMO

Hereditary spherocytosis is a congenital red blood cell disorder. Typical clinical manifestations include anemia, jaundice and splenomegaly, which overlap with the thalassemia phenotype. Therefore, in high prevalence thalassemia regions, hereditary spherocytosis cases are often misdiagnosed. Here, a case once diagnosed as thalassemia, based on preliminary clinical examinations, underwent genetic testing in our laboratory, where analysis of globin gene mutations proved negative. We conducted both clinical and genetic analyses on the patient and his family. We collected clinical data, performed erythrocyte membrane protein analysis by SDS-PAGE and sequenced the ANK1 gene. We also investigated pathogenic mechanisms through cDNA sequencing and literature studies. From patient clinical data, we diagnosed the patient with moderate to severe hereditary spherocytosis, rather than thalassemia. SDS-PAGE data showed that Ankyrin protein expression was reduced. Sequencing of genomic DNA identified a frameshift mutation (ANK1:c.2394_2397del CAGT). cDNA sequencing showed that the expression of a mutant allele was significantly decreased. Our study corrected a clinical misdiagnosis and confirmed the diagnosis of hereditary spherocytosis in this patient. Identification of such causative mutations is important for accurate downstream patient therapy and is critically important for the prevention/detection of another affected birth. Additionally, the disruption of mRNA transcribed from the mutant allele resulted in a significant reduction in Ankyrin expression and was speculatively considered the pathogenic mechanism behind this mutation.


Assuntos
Anquirinas/genética , Nucleotídeos/genética , Deleção de Sequência/genética , Esferocitose Hereditária/diagnóstico , Esferocitose Hereditária/genética , Alelos , Criança , Erros de Diagnóstico , Mutação da Fase de Leitura/genética , Humanos , Masculino , Mutação/genética , Fenótipo , RNA Mensageiro/genética , Talassemia/genética
11.
Nat Biotechnol ; 38(1): 66-75, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31740838

RESUMO

Molecular barcoding technologies that uniquely identify single cells are hampered by limitations in barcode measurement. Readout by sequencing does not preserve the spatial organization of cells in tissues, whereas imaging methods preserve spatial structure but are less sensitive to barcode sequence. Here we introduce a system for image-based readout of short (20-base-pair) DNA barcodes. In this system, called Zombie, phage RNA polymerases transcribe engineered barcodes in fixed cells. The resulting RNA is subsequently detected by fluorescent in situ hybridization. Using competing match and mismatch probes, Zombie can accurately discriminate single-nucleotide differences in the barcodes. This method allows in situ readout of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors without requiring barcode expression in live cells. Zombie functions across diverse contexts, including cell culture, chick embryos and adult mouse brain tissue. The ability to sensitively read out compact and diverse DNA barcodes by imaging will facilitate a broad range of barcoding and genomic recording strategies.


Assuntos
Pareamento de Bases/genética , Código de Barras de DNA Taxonômico/métodos , Edição de Genes , Transcrição Genética , Animais , Sequência de Bases , Encéfalo/metabolismo , Embrião de Galinha , RNA Polimerases Dirigidas por DNA/metabolismo , Biblioteca Gênica , Células HEK293 , Humanos , Lentivirus/genética , Camundongos , Nucleotídeos/genética , Polimorfismo de Nucleotídeo Único/genética , Regiões Promotoras Genéticas/genética
12.
Gene ; 730: 144257, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-31759983

RESUMO

Genetic sequence analysis, classification of genome sequence and evolutionary relationship between species using their biological sequences, are the emerging research domain in Bioinformatics. Several methods have already been applied to DNA sequence comparison under tri-nucleotide representation. In this paper, a new form of tri-nucleotide representation is proposed for sequence comparison. The comparison does not depend on the alignment of the sequences. In this representation, the bio-chemical properties of the nucleotides are considered. The novelty of this method is that the sequences of unequal lengths are represented by vectors of the same length and each of the tri-nucleotide formed out of the given sequence has its unique representation. To validate the proposed method, it is verified on several data sets related to mammalians, viruses and bacteria. The results of this method are further compared with those obtained by methods such as probabilistic method, natural vector method, Fourier power spectrum method, multiple encoding vector method, and feature frequency profiles method. Moreover, this method produces accurate phylogeny in all the cases. It is also proved that the time complexity of the present method is less.


Assuntos
Nucleotídeos/química , Análise de Sequência de DNA/métodos , Repetições de Trinucleotídeos/genética , Algoritmos , Animais , Bactérias/genética , Sequência de Bases , Mapeamento Cromossômico/métodos , Análise por Conglomerados , Biologia Computacional/métodos , Genômica/métodos , Humanos , Mamíferos/genética , Nucleotídeos/genética , Filogenia , Alinhamento de Sequência , Vírus/genética
13.
DNA Cell Biol ; 39(2): 177-186, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31804855

RESUMO

The chemical or prebiotic evolution referred also to as pre-Darwinian evolution describes chemical reactions up to the origin of a self-replicating system that was capable of Darwinian evolution. These chemical processes took place on Earth between about 3.7 and 4.5 billion years ago when cellular life came into being. The pre-Darwinian chemical evolution usually assumes hereditary elements, but does not regard them as self-organizing processes. Physical and chemical self-organization led to uninterrupted pre-Darwinian and Darwinian evolution. Thus, it is not justified to distinguish between different types of evolution. From the many possible solutions, evolution selected among those reactions that generated catalytic networks incorporating chemical sequence information and under gradually changing circumstances produced a reproducible and stable living system that adapted to these conditions. Major issues in this review involve prebiotic reactions leading to genetic evolution involving (1) abiotic sources of components of ribonucleotides and xenobiotic nucleotides, (2) formation of prebiotic RNA, (3) development of genetic RNA from random-sequence noncoding RNA, (4) transition from RNA World to DNA Empire, (5) the role of oxygenic photosynthesis in genetic transitions, and (6) hierarchical arrangement of processes involved in the optimized genetic system.


Assuntos
Nucleotídeos/genética , Origem da Vida , RNA/genética , Ribose/metabolismo , Animais , Evolução Química , Evolução Molecular , Humanos
14.
Nucleic Acids Res ; 48(3): 1423-1434, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31832688

RESUMO

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.


Assuntos
Evolução Molecular , Proteínas Mitocondriais/genética , Diester Fosfórico Hidrolases/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Sítios de Ligação/genética , Domínio Catalítico/genética , Humanos , Kluyveromyces/química , Proteínas Mitocondriais/química , Modelos Moleculares , Conformação de Ácido Nucleico , Nucleotídeos/química , Nucleotídeos/genética , Fosfatos/metabolismo , Diester Fosfórico Hidrolases/química , Processamento de RNA/genética , RNA Nuclear Pequeno/química , RNA Nuclear Pequeno/genética , Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/química , Spliceossomos/química , Spliceossomos/genética
15.
Mol Carcinog ; 59(1): 15-23, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31583785

RESUMO

Tumor suppressor genes encode different proteins that inhibit the uncontrolled proliferation of cell growth and tumor development. To acquire clues for predicting gene expression level, it is essential to understand the codon usage bias (CUB) of genes to characterize genome which possesses its own compositional characteristics and unique coding sequences. We used bioinformatic tools to analyze the codon usage patterns of 637 human tumor suppressor genes as no work was reported earlier. The mean effective number of codons of these genes was 48, indicating low CUB. Our results exhibited a significant positive correlation among different nucleotide compositions and the codons ending with C base was most frequently used along with the most over-represented codon CTG and GTG codifying leucine and valine amino acid, respectively, in human tumor suppressor genes. The neutrality plot showed a significant positive correlation (Pearson, r = 0. 646; P < .01) suggesting that mutation on GC bias might affect the CUB. However, the linear regression coefficient of GC12 on GC3 in human tumor suppressor genes suggested that natural selection played a major role while mutation pressure played a minor role in the codon usage patterns of tumor suppressor genes in human. Our study would throw light into the factors that affect CUB and the codon usage patterns in the human tumor suppressor genes.


Assuntos
Uso do Códon , Genes Supressores de Tumor , Bases de Dados Genéticas , Genômica , Humanos , Neoplasias/genética , Nucleotídeos/genética
16.
Sci Adv ; 5(12): eaav9963, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31840052

RESUMO

The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.


Assuntos
Fenômenos Ecológicos e Ambientais , Genoma , Animais , Braquiúros/fisiologia , Inversão Cromossômica , Ecossistema , Variação Genética/genética , Geografia , Nucleotídeos/genética , Caramujos/genética , Movimentos da Água
17.
BMC Bioinformatics ; 20(1): 654, 2019 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-31829137

RESUMO

BACKGROUND: In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging. RESULTS: Here, we introduce a new algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences. CONCLUSIONS: We introduced an algorithm to perform dynamic alignment of reads on a distant reference. We showed that such approach can improve the reconstruction of an amplicon compared to classically used bioinformatic pipelines. Although not portable to genomic scale in the current form, we suggested several improvements to be investigated to make this method more flexible and allow dynamic alignment to be used for large genome assemblies.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Aprendizado de Máquina , Algoritmos , Animais , Sequência de Bases , Genoma Mitocondrial , Macropodidae/genética , Nucleotídeos/genética
18.
PLoS One ; 14(12): e0225633, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31800603

RESUMO

The 3'-end of the coding sequence in several species is known to show specific codon usage bias. Several factors have been suggested to underlie this phenomenon, including selection against translation efficiency, selection for translation accuracy, and selection against RNA folding. All are supported by some evidence, but there is no general agreement as to which factors are the main determinants. Nor is it known how universal this phenomenon is, and whether the same factors explain it in different species. To answer these questions, we developed a measure that quantifies the codon usage bias at the gene end, and used it to compute this bias for 91 species that span the three domains of life. In addition, we characterized the codons in each species by features that allow discrimination between the different factors. Combining all these data, we were able to show that there is a universal trend to favor AT-rich codons toward the gene end. Moreover, we suggest that this trend is explained by avoidance from forming RNA secondary structures around the stop codon, which may interfere with normal translation termination.


Assuntos
Composição de Bases/genética , Uso do Códon/genética , Nucleotídeos/genética , Viés , Códon/genética , Regulação da Expressão Gênica , Humanos , Dobramento de RNA , RNA Mensageiro/química , RNA Mensageiro/genética
19.
BMC Bioinformatics ; 20(1): 663, 2019 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-31830908

RESUMO

BACKGROUND: Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data. RESULTS: Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision. CONCLUSION: Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at https://github.com/iprada/Circle-Map.


Assuntos
DNA Circular/genética , Nucleotídeos/genética , Alinhamento de Sequência/métodos , Bases de Dados Genéticas , Humanos , Software
20.
Nat Commun ; 10(1): 5799, 2019 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-31862872

RESUMO

Single-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.


Assuntos
Quebras de DNA de Cadeia Simples , DNA de Cadeia Simples/genética , Genoma Humano/genética , Genômica/métodos , Nucleotídeos/genética , Animais , Senescência Celular/genética , Éxons/genética , Células HeLa , Humanos , Íntrons/genética , Células K562 , Camundongos , Nucleotídeos/isolamento & purificação , Software
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