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Pesquisa : G02.111.570.080.708.800.325 [Categoria DeCS]
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[PMID]:29297914
[Au] Autor:Swadling JB; Ishii K; Tahara T; Kitao A
[Ad] Endereço:School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, M6-13, Meguro, Tokyo 152-8550, Japan. akitao@bio.titech.ac.jp.
[Ti] Título:Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation.
[So] Source:Phys Chem Chem Phys;20(5):2990-3001, 2018 Jan 31.
[Is] ISSN:1463-9084
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.
[Mh] Termos MeSH primário: DNA/química
Simulação de Dinâmica Molecular
RNA/química
[Mh] Termos MeSH secundário: Transferência Ressonante de Energia de Fluorescência
Ligações de Hidrogênio
Sequências Repetidas Invertidas/genética
Conformação de Ácido Nucleico
Termodinâmica
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1039/c7cp06355e


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[PMID]:29352114
[Au] Autor:Rehage N; Davydova E; Conrad C; Behrens G; Maiser A; Stehklein JE; Brenner S; Klein J; Jeridi A; Hoffmann A; Lee E; Dianzani U; Willemsen R; Feederle R; Reiche K; Hackermüller J; Leonhardt H; Sharma S; Niessing D; Heissmeyer V
[Ad] Endereço:Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
[Ti] Título:Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA.
[So] Source:Nat Commun;9(1):299, 2018 01 19.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The ubiquitously expressed RNA-binding proteins Roquin-1 and Roquin-2 are essential for appropriate immune cell function and postnatal survival of mice. Roquin proteins repress target mRNAs by recognizing secondary structures in their 3'-UTRs and by inducing mRNA decay. However, it is unknown if other cellular proteins contribute to target control. To identify cofactors of Roquin, we used RNA interference to screen ~1500 genes involved in RNA-binding or mRNA degradation, and identified NUFIP2 as a cofactor of Roquin-induced mRNA decay. NUFIP2 binds directly and with high affinity to Roquin, which stabilizes NUFIP2 in cells. Post-transcriptional repression of human ICOS by endogenous Roquin proteins requires two neighboring non-canonical stem-loops in the ICOS 3'-UTR. This unconventional cis-element as well as another tandem loop known to confer Roquin-mediated regulation of the Ox40 3'-UTR, are bound cooperatively by Roquin and NUFIP2. NUFIP2 therefore emerges as a cofactor that contributes to mRNA target recognition by Roquin.
[Mh] Termos MeSH primário: Linfócitos T CD4-Positivos/imunologia
Proteína Coestimuladora de Linfócitos T Induzíveis/genética
Proteínas Nucleares/genética
Proteínas de Ligação a RNA/genética
Receptores OX40/genética
Proteínas Repressoras/genética
Ubiquitina-Proteína Ligases/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Sítios de Ligação
Linfócitos T CD4-Positivos/citologia
Regulação da Expressão Gênica
Células HEK293
Células HeLa
Seres Humanos
Proteína Coestimuladora de Linfócitos T Induzíveis/antagonistas & inibidores
Proteína Coestimuladora de Linfócitos T Induzíveis/imunologia
Sequências Repetidas Invertidas
Camundongos
Camundongos Endogâmicos C57BL
Proteínas Nucleares/antagonistas & inibidores
Proteínas Nucleares/imunologia
Conformação de Ácido Nucleico
Cultura Primária de Células
Ligação Proteica
Estabilidade de RNA
RNA Interferente Pequeno/genética
RNA Interferente Pequeno/metabolismo
Proteínas de Ligação a RNA/antagonistas & inibidores
Proteínas de Ligação a RNA/imunologia
Receptores OX40/antagonistas & inibidores
Receptores OX40/imunologia
Proteínas Recombinantes/genética
Proteínas Recombinantes/imunologia
Proteínas Repressoras/imunologia
Alinhamento de Sequência
Homologia de Sequência de Aminoácidos
Ubiquitina-Proteína Ligases/imunologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (ICOS protein, human); 0 (Inducible T-Cell Co-Stimulator Protein); 0 (NUFIP2 protein, human); 0 (Nuclear Proteins); 0 (RC3H1 protein, human); 0 (RNA, Small Interfering); 0 (RNA-Binding Proteins); 0 (Receptors, OX40); 0 (Recombinant Proteins); 0 (Repressor Proteins); 0 (TNFRSF4 protein, human); 0 (roquin-2 protein, human); EC 2.3.2.27 (Ubiquitin-Protein Ligases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02582-1


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[PMID]:27770365
[Au] Autor:Varkonyi-Gasic E
[Ad] Endereço:The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland, 1142, New Zealand. erika.varkonyi-gasic@plantandfood.co.nz.
[Ti] Título:Stem-Loop qRT-PCR for the Detection of Plant microRNAs.
[So] Source:Methods Mol Biol;1456:163-175, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Plant microRNAs (miRNAs) play important roles in the posttranscriptional regulation of protein-coding genes, and they are essential for a normal development and survival. Mature miRNAs are cleaved from larger precursor RNAs and are typically 21-22 nt long.The small size, the lack of a common feature like a poly(A) tail, 3' end-modifications, and presence of a precursor-all these factors affect the detection and hinder the quantification of miRNAs. The stem-loop qRT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate, and reliable manner. Firstly, a miRNA-specific stem-loop RT primer is hybridized to miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and a universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA, and it is suitable for a relatively high-throughput analysis of miRNA expression.
[Mh] Termos MeSH primário: Sequências Repetidas Invertidas
MicroRNAs/genética
RNA de Plantas
Reação em Cadeia da Polimerase em Tempo Real
Reação em Cadeia da Polimerase Via Transcriptase Reversa
[Mh] Termos MeSH secundário: Primers do DNA
Perfilação da Expressão Gênica/métodos
Hidrólise
MicroRNAs/química
Conformação de Ácido Nucleico
Plantas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Primers); 0 (MicroRNAs); 0 (RNA, Plant)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


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[PMID]:29035162
[Au] Autor:Whittum ME; Blose JM
[Ad] Endereço:a Department of Chemistry and Biochemistry, The College at Brockport , State University of New York , Brockport , New York , USA.
[Ti] Título:Effects of osmolytes on stable UUCG tetraloops and their preference for a CG closing base pair.
[So] Source:Nucleosides Nucleotides Nucleic Acids;36(9):583-597, 2017 Sep 02.
[Is] ISSN:1532-2335
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Osmolytes have the potential to affect the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in the cell. To contribute to the understanding of the in vivo function of RNA we observed the effects of different classes of osmolytes on the UNCG tetraloop motif. UNCG tetraloops are the most common and stable of the RNA tetraloops and are nucleation sites for RNA folding. They also have a significant thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing UUCG loops was monitored using UV-Vis spectroscopy in the presence of osmolytes with different chemical properties. Interestingly, all of the osmolytes tested destabilized the hairpins, but all had little effect on the thermodynamic preference for a CG base pair, except for polyethylene glycol (PEG) 200. PEG 200 destabilized the loop with the CG closing base pair relative to the loop with a GC closing base pair. The destabilization was linear with increasing concentrations of PEG 200, and the slope of this relationship was not perturbed by changes in the hairpin stem outside of the closing pair. This result suggests that in the presence of PEG 200, the UUCG loop with a GC closing base pair may retain some preferential interactions with the cosolute that are lost in the presence of the CG closing base pair. These results reveal that relatively small structural changes may influence how osmolytes tune the stability, and thus the function of a secondary structure motif in vivo.
[Mh] Termos MeSH primário: Pareamento de Bases/efeitos dos fármacos
Sequências Repetidas Invertidas/efeitos dos fármacos
Motivos de Nucleotídeos
Osmose
Polietilenoglicóis/farmacologia
RNA/química
RNA/genética
[Mh] Termos MeSH secundário: Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
30IQX730WE (Polyethylene Glycols); 63231-63-0 (RNA)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171017
[St] Status:MEDLINE
[do] DOI:10.1080/15257770.2017.1375518


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[PMID]:28977594
[Au] Autor:Coons LA; Hewitt SC; Burkholder AB; McDonnell DP; Korach KS
[Ad] Endereço:Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, North Carolina 27709.
[Ti] Título:DNA Sequence Constraints Define Functionally Active Steroid Nuclear Receptor Binding Sites in Chromatin.
[So] Source:Endocrinology;158(10):3212-3234, 2017 Oct 01.
[Is] ISSN:1945-7170
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Gene regulatory programs are encoded in the sequence of the DNA. Since the completion of the Human Genome Project, millions of gene regulatory elements have been identified in the human genome. Understanding how each of those sites functionally contributes to gene regulation, however, remains a challenge for nearly every field of biology. Transcription factors influence cell function by interpreting information contained within cis-regulatory elements in chromatin. Whereas chromatin immunoprecipitation-sequencing has been used to identify and map transcription factor-DNA interactions, it has been difficult to assign functionality to the binding sites identified. Thus, in this study, we probed the transcriptional activity, DNA-binding competence, and functional activity of select nuclear receptor mutants in cellular and animal model systems and used this information to define the sequence constraints of functional steroid nuclear receptor cis-regulatory elements. Analysis of the architecture within sNR chromatin interacting sites revealed that only a small fraction of all sNR chromatin-interacting events is associated with transcriptional output and that this functionality is restricted to elements that vary from the consensus palindromic elements by one or two nucleotides. These findings define the transcriptional grammar necessary to predict functionality from regulatory sequences, with a multitude of future implications.
[Mh] Termos MeSH primário: Cromatina/química
DNA/química
Receptores Citoplasmáticos e Nucleares/fisiologia
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Sítios de Ligação/fisiologia
DNA/metabolismo
Receptor alfa de Estrogênio/genética
Feminino
Seres Humanos
Sequências Repetidas Invertidas/genética
Sequências Repetidas Invertidas/fisiologia
Camundongos
Mutação
Receptor Cross-Talk/fisiologia
Receptores Citoplasmáticos e Nucleares/genética
Receptores de Esteroides/genética
Receptores de Esteroides/fisiologia
Elementos Reguladores de Transcrição/genética
Sequências Reguladoras de Ácido Nucleico
Fatores de Transcrição/metabolismo
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Estrogen Receptor alpha); 0 (Receptors, Cytoplasmic and Nuclear); 0 (Receptors, Steroid); 0 (Transcription Factors); 9007-49-2 (DNA)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171115
[Lr] Data última revisão:
171115
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:171005
[St] Status:MEDLINE
[do] DOI:10.1210/en.2017-00468


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[PMID]:28934495
[Au] Autor:Feng L; Wang G; Hamilton EP; Xiong J; Yan G; Chen K; Chen X; Dui W; Plemens A; Khadr L; Dhanekula A; Juma M; Dang HQ; Kapler GM; Orias E; Miao W; Liu Y
[Ad] Endereço:Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
[Ti] Título:A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement.
[So] Source:Nucleic Acids Res;45(16):9481-9502, 2017 Sep 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation. Large NMC contain genes implicated in development-specific roles. One such gene encodes the domesticated piggyBac transposase TPB6, required for heterochromatin-dependent precise excision of IES residing within exons of functionally important genes. These conserved exonic IES determine alternative transcription products in the developing macronucleus; some even contain free-standing genes. Examples of precise loss of some exonic IES in the micronucleus and retention of others in the macronucleus of related species suggest an evolutionary analogy to introns. Our results reveal that germline-limited sequences can encode genes with specific expression patterns and development-related functions, which may be a recurring theme in eukaryotic organisms experiencing programmed genome rearrangement during germline to soma differentiation.
[Mh] Termos MeSH primário: Proteínas de Protozoários/metabolismo
Tetrahymena thermophila/genética
Transposases/metabolismo
[Mh] Termos MeSH secundário: Cromossomos/genética
Éxons
Rearranjo Gênico
Heterocromatina/genética
Sequências Repetidas Invertidas
Macronúcleo/genética
Micronúcleo Germinativo
Proteínas de Protozoários/genética
Interferência de RNA
Transposases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Heterochromatin); 0 (Protozoan Proteins); EC 2.7.7.- (Transposases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx652


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[PMID]:28918899
[Au] Autor:Jagodnik J; Chiaruttini C; Guillier M
[Ad] Endereço:CNRS UMR8261, Associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France.
[Ti] Título:Stem-Loop Structures within mRNA Coding Sequences Activate Translation Initiation and Mediate Control by Small Regulatory RNAs.
[So] Source:Mol Cell;68(1):158-170.e3, 2017 Oct 05.
[Is] ISSN:1097-4164
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Initiation is the rate-limiting step of translation, and in bacteria, mRNA secondary structure has been extensively reported as limiting the efficiency of translation by occluding the ribosome-binding site. In striking contrast with this inhibitory effect, we report here that stem-loop structures located within coding sequences instead activate translation initiation of the Escherichia coli fepA and bamA mRNAs involved in iron acquisition and outer membrane proteins assembly, respectively. Both structures promote ribosome binding in vitro, independently of their nucleotide sequence. Moreover, two small regulatory RNAs, OmrA and OmrB, base pair to and most likely disrupt the fepA stem-loop structure, thereby repressing FepA synthesis. By expanding our understanding of how mRNA cis-acting elements regulate translation, these data challenge the widespread view of mRNA secondary structures as translation inhibitors and show that translation-activating elements embedded in coding sequences can be targeted by small RNAs to inhibit gene expression.
[Mh] Termos MeSH primário: Proteínas da Membrana Bacteriana Externa/genética
Proteínas de Transporte/genética
Proteínas de Escherichia coli/genética
Escherichia coli/genética
Regulação Bacteriana da Expressão Gênica
RNA Bacteriano/genética
RNA Mensageiro/genética
Pequeno RNA não Traduzido/genética
Receptores de Superfície Celular/genética
[Mh] Termos MeSH secundário: Proteínas da Membrana Bacteriana Externa/metabolismo
Pareamento de Bases
Sequência de Bases
Proteínas de Transporte/metabolismo
Escherichia coli/metabolismo
Proteínas de Escherichia coli/metabolismo
Sequências Repetidas Invertidas
Ferro/metabolismo
Conformação de Ácido Nucleico
Fases de Leitura Aberta
Iniciação Traducional da Cadeia Peptídica
RNA Bacteriano/metabolismo
RNA Mensageiro/metabolismo
Pequeno RNA não Traduzido/metabolismo
Receptores de Superfície Celular/metabolismo
Ribossomos/genética
Ribossomos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Outer Membrane Proteins); 0 (BamA protein, E coli); 0 (Carrier Proteins); 0 (Escherichia coli Proteins); 0 (RNA, Bacterial); 0 (RNA, Messenger); 0 (RNA, Small Untranslated); 0 (Receptors, Cell Surface); 0 (enterobactin receptor); E1UOL152H7 (Iron)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171017
[Lr] Data última revisão:
171017
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170919
[St] Status:MEDLINE


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[PMID]:28910967
[Au] Autor:Bertels F; Gallie J; Rainey PB
[Ad] Endereço:New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.
[Ti] Título:Identification and Characterization of Domesticated Bacterial Transposases.
[So] Source:Genome Biol Evol;9(8):2110-2121, 2017 Aug 01.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication. RAYTs encompass exceptional diversity and are divisible into at least five distinct groups. They possess features more similar to housekeeping genes than insertion sequences, are predominantly vertically transmitted and have persisted through evolutionary time to the point where they are now found in 24% of all species for which at least one fully sequenced genome is available. Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell.
[Mh] Termos MeSH primário: Proteínas de Bactérias/genética
Evolução Molecular
Genoma Bacteriano
Sequências Repetitivas de Ácido Nucleico
Análise de Sequência de DNA/métodos
Transposases/classificação
Transposases/genética
[Mh] Termos MeSH secundário: Biologia Computacional/métodos
Regulação Enzimológica da Expressão Gênica
Sequências Repetidas Invertidas
Filogenia
Tirosina/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 42HK56048U (Tyrosine); EC 2.7.7.- (Transposases)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170916
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evx146


  9 / 1474 MEDLINE  
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[PMID]:28846694
[Au] Autor:Skov L; Schierup MH; Danish Pan Genome Consortium
[Ad] Endereço:Bioinformatics Research Centre, Aarhus University, Aarhus C., Denmark.
[Ti] Título:Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion.
[So] Source:PLoS Genet;13(8):e1006834, 2017 Aug.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller's ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome.
[Mh] Termos MeSH primário: Cromossomos Humanos Y/genética
Evolução Molecular
Heterocromatina/genética
Mutação INDEL/genética
[Mh] Termos MeSH secundário: Dinamarca
Pai
Conversão Gênica/genética
Seres Humanos
Infertilidade Masculina/genética
Infertilidade Masculina/patologia
Sequências Repetidas Invertidas/genética
Masculino
Núcleo Familiar
Filogenia
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Heterochromatin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171011
[Lr] Data última revisão:
171011
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170829
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006834


  10 / 1474 MEDLINE  
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[PMID]:28841794
[Au] Autor:Lee H; Park Y; Kim S
[Ad] Endereço:Department of Chemistry, Seoul National University , Seoul 08826, Republic of Korea.
[Ti] Título:Enzymatic Cross-Linking of Side Chains Generates a Modified Peptide with Four Hairpin-like Bicyclic Repeats.
[So] Source:Biochemistry;56(37):4927-4930, 2017 Sep 19.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Macrocyclization of peptides is often employed to generate novel structures and biological activities in the biosynthesis of natural products and drug discovery. The enzymatic cross-linking of two side chains in a peptide via an ester or amide has a high potential for making topologically diverse cyclic peptides but is found with only a single consensus sequence in the microviridin class of natural products. Here, we report that a peptide with a new sequence pattern can be enzymatically cross-linked to make a novel microviridin-like peptide, plesiocin, which contains four repeats of a distinct hairpin-like bicyclic structure and shows strong inhibition of proteases. A single ATP-grasp enzyme binds to a leader peptide, of which only 13 residues are required for binding, and performs eight esterification reactions on the core peptide. We also demonstrate that the combination of tandem mass spectrometry and an ester-specific reaction greatly facilitates the determination of connectivity. We suggest that the enzymatic cross-linking of peptide side chains can generate more diverse structures in nature or by engineering.
[Mh] Termos MeSH primário: Organismos Aquáticos/metabolismo
Desenho de Drogas
Myxococcales/metabolismo
Peptídeos Cíclicos/metabolismo
Peptídeos/metabolismo
Inibidores de Proteases/metabolismo
Processamento de Proteína Pós-Traducional
[Mh] Termos MeSH secundário: Organismos Aquáticos/enzimologia
Proteínas de Bactérias/química
Proteínas de Bactérias/metabolismo
Proteínas de Bactérias/farmacologia
Cromatografia Líquida de Alta Pressão
Quimotripsina/antagonistas & inibidores
Quimotripsina/metabolismo
Esterificação
Interações Hidrofóbicas e Hidrofílicas
Sequências Repetidas Invertidas
Cinética
Estrutura Molecular
Família Multigênica
Myxococcales/enzimologia
Elastase Pancreática/antagonistas & inibidores
Elastase Pancreática/metabolismo
Peptídeos/química
Peptídeos/farmacologia
Peptídeos Cíclicos/química
Peptídeos Cíclicos/farmacologia
Inibidores de Proteases/química
Inibidores de Proteases/farmacologia
Conformação Proteica
Proteólise/efeitos dos fármacos
Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
Espectrometria de Massas em Tandem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Peptides); 0 (Peptides, Cyclic); 0 (Protease Inhibitors); 0 (plesiocin); EC 3.4.21.1 (Chymotrypsin); EC 3.4.21.36 (Pancreatic Elastase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171003
[Lr] Data última revisão:
171003
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170827
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00808



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