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[PMID]:28463571
[Au] Autor:Penaud-Budloo M; Lecomte E; Guy-Duché A; Saleun S; Roulet A; Lopez-Roques C; Tournaire B; Cogné B; Léger A; Blouin V; Lindenbaum P; Moullier P; Ayuso E
[Ad] Endereço:1 INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France.
[Ti] Título:Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.
[So] Source:Hum Gene Ther Methods;28(3):148-162, 2017 06.
[Is] ISSN:1946-6544
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Recombinant adeno-associated viral (rAAV) vectors have proven excellent tools for the treatment of many genetic diseases and other complex diseases. However, the illegitimate encapsidation of DNA contaminants within viral particles constitutes a major safety concern for rAAV-based therapies. Moreover, the development of rAAV vectors for early-phase clinical trials has revealed the limited accuracy of the analytical tools used to characterize these new and complex drugs. Although most published data concerning residual DNA in rAAV preparations have been generated by quantitative PCR, we have developed a novel single-strand virus sequencing (SSV-Seq) method for quantification of DNA contaminants in AAV vectors produced in mammalian cells by next-generation sequencing (NGS). Here, we describe the adaptation of SSV-Seq for the accurate identification and quantification of DNA species in rAAV stocks produced in insect cells. We found that baculoviral DNA was the most abundant contaminant, representing less than 2.1% of NGS reads regardless of serotype (2, 8, or rh10). Sf9 producer cell DNA was detected at low frequency (≤0.03%) in rAAV lots. Advanced computational analyses revealed that (1) baculoviral sequences close to the inverted terminal repeats preferentially underwent illegitimate encapsidation, and (2) single-nucleotide variants were absent from the rAAV genome. The high-throughput sequencing protocol described here enables effective DNA quality control of rAAV vectors produced in insect cells, and is adapted to conform with regulatory agency safety requirements.
[Mh] Termos MeSH primário: Dependovirus/genética
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Animais
Baculoviridae/genética
Contaminação por DNA
Células HEK293
Sequenciamento de Nucleotídeos em Larga Escala/normas
Seres Humanos
Análise de Sequência de DNA/normas
Células Sf9
Spodoptera
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.1089/hgtb.2016.185


  2 / 17668 MEDLINE  
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[PMID]:29462204
[Au] Autor:Li H; Li M; Yang X; Gui X; Chen G; Chu J; He X; Wang W; Han F; Li P
[Ad] Endereço:Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
[Ti] Título:Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation.
[So] Source:PLoS One;13(2):e0190318, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Xiaguan Tuo Tea is largely consumed by the Chinese, but there is little research into the microbial diversity and component changes during the fermentation of this tea. In this study, we first used fluorescence in situ hybridization (FISH), next-generation sequencing (NGS) and chemical analysis methods to determine the microbial abundance and diversity and the chemical composition during fermentation. The FISH results showed that the total number of microorganisms ranges from 2.3×102 to 4.0×108 cells per gram of sample during fermentation and is mainly dominated by fungi. In the early fermentation stages, molds are dominant (0.6×102~2.8×106 cells/g, 0~35 d). However, in the late stages of fermentation, yeasts are dominant (3.6×104~9.6×106 cells/g, 35~56 d). The bacteria have little effect during the fermentation of tea (102~103 cells/g, <1% of fungus values). Of these fungi, A. niger (Aspergillus niger) and B. adeninivorans (Blastobotrys adeninivorans) are identified as the two most common strains, based on Next-generation Sequencing (NGS) analysis. Peak diversity in tea was observed at day 35 of fermentation (Shannon-Weaver index: 1.195857), and lower diversity was observed on days 6 and 56 of fermentation (Shannon-Weaver index 0.860589 and 1.119106, respectively). During the microbial fermentation, compared to the unfermented tea, the tea polyphenol content decreased by 54%, and the caffeine content increased by 59%. Theanine and free amino acid contents were reduced during fermentation by 81.1 and 92.85%, respectively.
[Mh] Termos MeSH primário: Fermentação
Chá/microbiologia
[Mh] Termos MeSH secundário: Bactérias/isolamento & purificação
China
Contagem de Colônia Microbiana
Fungos/isolamento & purificação
Sequenciamento de Nucleotídeos em Larga Escala
Hibridização in Situ Fluorescente
Chá/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Tea)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180221
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190318


  3 / 17668 MEDLINE  
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[PMID]:29389989
[Au] Autor:Almutairy M; Torng E
[Ad] Endereço:Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America.
[Ti] Título:Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.
[So] Source:PLoS One;13(2):e0189960, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.
[Mh] Termos MeSH primário: Biologia Computacional
[Mh] Termos MeSH secundário: Animais
Genoma Humano
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Camundongos
Modelos Teóricos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180202
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189960


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[PMID]:29287889
[Au] Autor:Cesca F; Bettella E; Polli R; Cama E; Scimemi P; Santarelli R; Murgia A
[Ad] Endereço:Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Italy.
[Ti] Título:A novel mutation of the EYA4 gene associated with post-lingual hearing loss in a proband is co-segregating with a novel PAX3 mutation in two congenitally deaf family members.
[So] Source:Int J Pediatr Otorhinolaryngol;104:88-93, 2018 Jan.
[Is] ISSN:1872-8464
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:OBJECTIVES: This work was aimed at establishing the molecular etiology of hearing loss in a 9-year old girl with post-lingual non-syndromic mild sensorineural hearing loss with a complex family history of clinically heterogeneous deafness. METHODS: The proband's DNA was subjected to NGS analysis of a 59-targeted gene panel, with the use of the Ion Torrent PGM platform. Conventional Sanger sequencing was used for segregation analysis in all the affected relatives. The proband and all the other hearing impaired members of the family underwent a thorough clinical and audiological evaluation. RESULTS: A new likely pathogenic mutation in the EYA4 gene (c.1154C > T; p.Ser385Leu) was identified in the proband and in her 42-year-old father with post-lingual non-syndromic profound sensorineural hearing loss. The EYA4 mutation was also found in the proband's grandfather and uncle, both showing clinical features of Waardenburg syndrome type 1. A novel pathogenic splice-site mutation (c.321+1G > A) of the PAX3 gene was found to co-segregate with the EYA4 mutation in these two subjects. CONCLUSION: The identified novel EYA4 mutation can be considered responsible of the hearing loss observed in the proband and her father, while a dual molecular diagnosis was reached in the relatives co-segregating the EYA4 and the PAX3 mutations. In these two subjects the DFNA10 phenotype was masked by Waardenburg syndrome. The use of NGS targeted gene-panel, in combination with an extensive clinical and audiological examination led us to identify the genetic cause of the hearing loss in members of a family in which different forms of autosomal dominant deafness segregate. These results provide precise and especially important prognostic and follow-up information for the future audiologic management in the youngest affected member.
[Mh] Termos MeSH primário: Surdez/genética
Perda Auditiva Neurossensorial/genética
Fator de Transcrição PAX3/genética
Transativadores/genética
Síndrome de Waardenburg/genética
[Mh] Termos MeSH secundário: Adulto
Audiometria
Criança
Família
Feminino
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Masculino
Mutação
Linhagem
Fenótipo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (EYA4 protein, human); 0 (PAX3 Transcription Factor); 0 (PAX3 protein, human); 0 (Trans-Activators)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171231
[St] Status:MEDLINE


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[PMID]:29212533
[Au] Autor:Gutiérrez G; Millán-Zambrano G; Medina DA; Jordán-Pla A; Pérez-Ortín JE; Peñate X; Chávez S
[Ad] Endereço:Departamento de Genética, Universidad de Sevilla, Seville, Spain.
[Ti] Título:Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.
[So] Source:Epigenetics Chromatin;10(1):58, 2017 12 07.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. RESULTS: To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. CONCLUSIONS: The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.
[Mh] Termos MeSH primário: Nuclease do Micrococo/metabolismo
Nucleossomos/metabolismo
Fatores de Elongação da Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sequenciamento de Nucleotídeos em Larga Escala
Reação em Cadeia da Polimerase em Tempo Real
Saccharomyces cerevisiae/metabolismo
Técnica de Subtração
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Nucleosomes); 0 (Transcriptional Elongation Factors); 0 (transcription factor S-II); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0165-x


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[PMID]:28465312
[Au] Autor:Noorani A; Bornschein J; Lynch AG; Secrier M; Achilleos A; Eldridge M; Bower L; Weaver JMJ; Crawte J; Ong CA; Shannon N; MacRae S; Grehan N; Nutzinger B; O'Donovan M; Hardwick R; Tavaré S; Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
[Ad] Endereço:Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0XZ, United Kingdom.
[Ti] Título:A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.
[So] Source:Genome Res;27(6):902-912, 2017 06.
[Is] ISSN:1549-5469
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post-chemotherapy increased the proportion of late-stage tumors. When comparing matched pre- and post-chemotherapy samples from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogeneity in this disease. Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a point prior to chemotherapy. For cases in which pre- and post-chemotherapy samples do show substantial differences, the timing of the divergence is near-synchronous with endoreduplication. Comparison across a large prospective cohort (62 treatment-naive, 58 chemotherapy-treated samples) reveals no significant differences in the overall mutation rate, mutation signatures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status. In conclusion, whole-genome sequencing of samples obtained following neoadjuvant chemotherapy is representative of the genomic landscape of esophageal adenocarcinoma. Excluding these samples reduces the material available for cataloging and introduces a bias toward the earlier stages of cancer.
[Mh] Termos MeSH primário: Adenocarcinoma/genética
Antineoplásicos/uso terapêutico
Neoplasias Esofágicas/genética
Regulação Neoplásica da Expressão Gênica
Genoma Humano
Taxa de Mutação
Proteínas de Neoplasias/genética
[Mh] Termos MeSH secundário: Adenocarcinoma/tratamento farmacológico
Adenocarcinoma/metabolismo
Adenocarcinoma/patologia
Idoso
Transformação Celular Neoplásica/genética
Transformação Celular Neoplásica/metabolismo
Transformação Celular Neoplásica/patologia
Biologia Computacional
Variações do Número de Cópias de DNA
Neoplasias Esofágicas/tratamento farmacológico
Neoplasias Esofágicas/metabolismo
Neoplasias Esofágicas/patologia
Esôfago/metabolismo
Esôfago/patologia
Feminino
Perfilação da Expressão Gênica
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Masculino
Meia-Idade
Terapia Neoadjuvante/métodos
Proteínas de Neoplasias/metabolismo
Mutação Puntual
Polimorfismo de Nucleotídeo Único
Estudos Prospectivos
Fatores de Tempo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antineoplastic Agents); 0 (Neoplasm Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1101/gr.214296.116


  7 / 17668 MEDLINE  
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[PMID]:28457750
[Au] Autor:Li L; Dong J; Yan L; Yong J; Liu X; Hu Y; Fan X; Wu X; Guo H; Wang X; Zhu X; Li R; Yan J; Wei Y; Zhao Y; Wang W; Ren Y; Yuan P; Yan Z; Hu B; Guo F; Wen L; Tang F; Qiao J
[Ad] Endereço:Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing 100871, China; Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Educ
[Ti] Título:Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.
[So] Source:Cell Stem Cell;20(6):858-873.e4, 2017 Jun 01.
[Is] ISSN:1875-9777
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human fetal germ cells (FGCs) are precursors to sperm and eggs and are crucial for maintenance of the species. However, the developmental trajectories and heterogeneity of human FGCs remain largely unknown. Here we performed single-cell RNA-seq analysis of over 2,000 FGCs and their gonadal niche cells in female and male human embryos spanning several developmental stages. We found that female FGCs undergo four distinct sequential phases characterized by mitosis, retinoic acid signaling, meiotic prophase, and oogenesis. Male FGCs develop through stages of migration, mitosis, and cell-cycle arrest. Individual embryos of both sexes simultaneously contain several subpopulations, highlighting the asynchronous and heterogeneous nature of FGC development. Moreover, we observed reciprocal signaling interactions between FGCs and their gonadal niche cells, including activation of the bone morphogenic protein (BMP) and Notch signaling pathways. Our work provides key insights into the crucial features of human FGCs during their highly ordered mitotic, meiotic, and gametogenetic processes in vivo.
[Mh] Termos MeSH primário: Divisão Celular/fisiologia
Células Germinativas Embrionárias/metabolismo
Feto/metabolismo
Gônadas/enzimologia
Transdução de Sinais/fisiologia
Nicho de Células-Tronco/fisiologia
[Mh] Termos MeSH secundário: Proteínas Morfogenéticas Ósseas/metabolismo
Células Germinativas Embrionárias/citologia
Feminino
Feto/citologia
Gônadas/citologia
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Masculino
Receptores Notch/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bone Morphogenetic Proteins); 0 (Receptors, Notch)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE


  8 / 17668 MEDLINE  
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[PMID]:28456785
[Au] Autor:Huang H; Wang Y; Chen H; Chen Y; Wu J; Chiang PW; Fan N; Su Y; Deng J; Chen D; Li Y; Zhang X; Zhang M; Liang S; Banerjee S; Qi M; Liu X
[Ad] Endereço:BGI-Shenzhen, Shenzhen, China.
[Ti] Título:Targeted next generation sequencing identified novel mutations in RPGRIP1 associated with both retinitis pigmentosa and Leber's congenital amaurosis in unrelated Chinese patients.
[So] Source:Oncotarget;8(21):35176-35183, 2017 May 23.
[Is] ISSN:1949-2553
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:As the most common inherited retinal degenerations, retinitis pigmentosa (RP) is clinically and genetically heterogeneous. Some of the RP genes are also associated with other retinal diseases, such as LCA (Leber's congenital amaurosis) and CORD (cone-rod dystrophy). Here, in our molecular diagnosis of 99 Chinese RP patients using targeted gene capture sequencing, three probands were found to carry mutations of RPGRIP1, which was known to be associated with pathogenesis of LCA and CORD. By further clinical analysis, two probands were confirmed to be RP patients and one was confirmed to be LCA patient. These novel mutations were co-segregated with the disease phenotype in their families. Our result not only expands the mutational spectrum of the RPGRIP1 gene but also gives supports to clinical diagnosis and molecular treatment of RP patients.
[Mh] Termos MeSH primário: Grupo com Ancestrais do Continente Asiático/genética
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Amaurose Congênita de Leber/genética
Mutação
Proteínas/genética
Retinite Pigmentosa/genética
[Mh] Termos MeSH secundário: Adulto
China
Feminino
Estudos de Associação Genética
Predisposição Genética para Doença
Seres Humanos
Masculino
Linhagem
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins); 0 (RPGRIP1 protein, human)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170501
[St] Status:MEDLINE
[do] DOI:10.18632/oncotarget.17052


  9 / 17668 MEDLINE  
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[PMID]:29286779
[Au] Autor:Chuang HM; Reifenberger JG; Cao H; Dorfman KD
[Ad] Endereço:Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA.
[Ti] Título:Sequence-Dependent Persistence Length of Long DNA.
[So] Source:Phys Rev Lett;119(22):227802, 2017 Dec 01.
[Is] ISSN:1079-7114
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Using a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.
[Mh] Termos MeSH primário: DNA/química
DNA/genética
Modelos Químicos
Modelos Genéticos
[Mh] Termos MeSH secundário: Sequência de Bases
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Seres Humanos
Relação Estrutura-Atividade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171230
[St] Status:MEDLINE
[do] DOI:10.1103/PhysRevLett.119.227802


  10 / 17668 MEDLINE  
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[PMID]:29434199
[Au] Autor:Hayashi T; Ozaki H; Sasagawa Y; Umeda M; Danno H; Nikaido I
[Ad] Endereço:Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan.
[Ti] Título:Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
[So] Source:Nat Commun;9(1):619, 2018 02 12.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/métodos
Células-Tronco Embrionárias Murinas/metabolismo
Processamento de RNA
RNA Longo não Codificante/genética
RNA Mensageiro/genética
Análise de Célula Única/métodos
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Diferenciação Celular
Elementos Facilitadores Genéticos
Éxons
Histonas/genética
Histonas/metabolismo
Íntrons
Camundongos
Células-Tronco Embrionárias Murinas/citologia
RNA Longo não Codificante/metabolismo
RNA Mensageiro/metabolismo
Análise de Sequência de RNA
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Histones); 0 (NEAT1 long non-coding RNA, mouse); 0 (RNA, Long Noncoding); 0 (RNA, Messenger)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180214
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-02866-0



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