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Identificação de perfis de expressão de RNAs codificadores e não codificadores de proteína como preditores de recorrência de câncer de próstata; Identification of protein-coding and non-coding RNA expression profiles as prognostic marker of prostate cancer biochemical recurrence

Moreira, Yuri José de Camargo Barros
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 27/08/2010 Português
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75.91%
O câncer de próstata é o quinto tipo mais comum de câncer no mundo e o mais comum em homens. Fatores clínicos e anatomopatológicos atualmente usados na clínica não são capazes de distinguir entre a doença indolente e a agressiva. Existe uma grande necessidade de novos marcadores de prognóstico, a fim de melhorar o gerenciamento clínico de pacientes de câncer de próstata. Além das anormalidades em genes codificadores de proteínas, alterações em RNAs não codificadores (ncRNAs) contribuem para a patogênese do câncer e, portanto, representam outra fonte potencial de biomarcadores de câncer de próstata. Entretanto, até o momento, poucos estudos de perfis de expressão de ncRNAs foram publicados. Este projeto teve como principal objetivo identificar perfis de expressão de genes codificadores e não codificadores de proteína correlacionados com recorrência de tumor de próstata, a fim de gerar um perfil prognóstico com potencial uso como biomarcadores e elucidar o possível papel de ncRNAs no desenvolvimento do câncer. Para isso, foram analisados os perfis de expressão de genes codificadores e não codificadores de proteína de um conjunto de 42 amostras de tecido tumoral de câncer de próstata de pacientes de amostras de pacientes submetidos à prostatectomia radical...

Bioinformática aplicada em RNomics: estratégias computacionais para caracterização de RNAs não-codificadores; Bioinformatics in RNomics: Computational characterization of non-coding RNAs

Paschoal, Alexandre Rossi
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 13/04/2012 Português
Relevância na Pesquisa
86.06%
A visao sobre o dogma central da biologia molecular passou por aperfeicoamentos na virada deste seculo. Muito se deve ao interesse por pesquisas feitas para compreensao do que ate entao eram regioes do genoma conhecidas como DNA Lixo. Neste contexto, projetos de transcriptoma, avancos em tecnologias de sequenciamento, bem como analises em bioinformatica, contribuiram para elucidar o que estava sendo transcrito. Tais regioes foram denominadas como RNAs nao-codificadores ou non-coding RNA (ncRNA) que eram transcritas, mas nao traduzidas em proteinas. Apesar da quantidade de metodos para o estudo in silico dos ncRNAs, existem lacunas a serem preenchidas nas pesquisas desta molecula, tais como: metodos de anotacao em geral, caracterizacao de novas classes e mecanismos alternativos de busca por similaridade de sequencia primaria. Alem disso, nao se havia uma ferramenta que reunisse num unico local as informacoes dos bancos de dados publicos de ncRNA disponiveis. Neste trabalho, buscou-se preencher tais lacunas, contribuindo para o desenvolvimento de metodos computacionais nas pesquisas em ncRNAs. Foram utilizados os genomas de Hymenoptera e Diptera como sistema biologico para aplicar e testar os metodos desenvolvidos.; The classical vision of the central dogma of molecular biology was not changes dramatic until the end of the 20th century. At this time the scientific communities were interesting to understand what have in the regions of the genome known as "Junk DNA". Transcriptome projects together with sequencing Technologies anda bioinformatics analysis help to elucidate that this transcripts were regions that do not coding proteins and maybe has function. These transcripts are called non-coding RNA (ncRNA). Although there are a lot of computational approaches to the in silico research of ncRNA...

The Non-coding RNA gadd7 Is a Regulator of Lipid-induced Oxidative and Endoplasmic Reticulum Stress*S⃞

Brookheart, Rita T.; Michel, Carlos I.; Listenberger, Laura L.; Ory, Daniel S.; Schaffer, Jean E.
Fonte: American Society for Biochemistry and Molecular Biology Publicador: American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
Publicado em 20/03/2009 Português
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75.99%
In obesity and diabetes, an imbalance in fatty acid uptake and fatty acid utilization leads to excess accumulation of lipid in non-adipose tissues. This lipid overload is associated with cellular dysfunction and cell death, which contribute to organ failure, a phenomenon termed lipotoxicity. To elucidate the molecular mechanism of lipid-mediated cell death, we generated and characterized a mutant Chinese hamster ovary cell line that is resistant to palmitate-induced cell death. In this mutant, random insertion of a retroviral promoter trap has disrupted the gene for the non-coding RNA, growth arrested DNA-damage inducible gene 7 (gadd7). Here we report that gadd7 is induced by lipotoxic stress in a reactive oxygen species (ROS)-dependent fashion and is necessary for both lipid- and general oxidative stress-mediated cell death. Depletion of gadd7 by mutagenesis or short hairpin RNA knockdown significantly reduces lipid and non-lipid induced ROS. Furthermore, depletion of gadd7 delays and diminishes ROS-induced endoplasmic reticulum stress. Together these data are the first to implicate a non-coding RNA in a feed-forward loop with oxidative stress and its induction of the endoplasmic reticulum stress response.

Tfold: efficient in silico prediction of non-coding RNA secondary structures

Engelen, Stéfan; Tahi, Fariza
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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75.89%
Predicting RNA secondary structures is a very important task, and continues to be a challenging problem, even though several methods and algorithms are proposed in the literature. In this article, we propose an algorithm called Tfold, for predicting non-coding RNA secondary structures. Tfold takes as input a RNA sequence for which the secondary structure is searched and a set of aligned homologous sequences. It combines criteria of stability, conservation and covariation in order to search for stems and pseudoknots (whatever their type). Stems are searched recursively, from the most to the least stable. Tfold uses an algorithm called SSCA for selecting the most appropriate sequences from a large set of homologous sequences (taken from a database for example) to use for the prediction. Tfold can take into account one or several stems considered by the user as belonging to the secondary structure. Tfold can return several structures (if requested by the user) when ‘rival’ stems are found. Tfold has a complexity of O(n2), with n the sequence length. The developed software, which offers several different uses, is available on the web site: http://tfold.ibisc.univ-evry.fr/TFold.

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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76.03%
While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features.

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

Nolte-’t Hoen, Esther N. M.; Buermans, Henk P. J.; Waasdorp, Maaike; Stoorvogel, Willem; Wauben, Marca H. M.; ’t Hoen, Peter A. C.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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76.08%
Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

Livyatan, Ilana; Harikumar, Arigela; Nissim-Rafinia, Malka; Duttagupta, Radharani; Gingeras, Thomas R.; Meshorer, Eran
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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75.96%
The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention, albeit mostly confined to the polyadenylated fraction of RNA, whereas the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in ESCs using a combination of whole-genome tiling arrays and deep sequencing technologies. In addition to identifying previously characterized and new non-coding RNA members, we describe a group of novel conserved RNAs (snacRNAs: small NPA conserved), some of which are differentially expressed between ESC and neuronal progenitor cells, providing the first evidence of a novel group of potentially functional NPA RNA involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal small nuclear RNAs, which are NPA, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that NPA RNA, both known and novel, play important roles in ESCs.

Identification of proteins binding coding and non-coding human RNAs using protein microarrays

Siprashvili, Zurab; Webster, Dan E; Kretz, Markus; Johnston, Danielle; Rinn, John L; Chang, Howard Y; Khavari, Paul A
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Português
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76.07%
Background: The regulation and function of mammalian RNAs has been increasingly appreciated to operate via RNA-protein interactions. With the recent discovery of thousands of novel human RNA molecules by high-throughput RNA sequencing, efficient methods to uncover RNA-protein interactions are urgently required. Existing methods to study proteins associated with a given RNA are laborious and require substantial amounts of cell-derived starting material. To overcome these limitations, we have developed a rapid and large-scale approach to characterize binding of in vitro transcribed labeled RNA to ~9,400 human recombinant proteins spotted on protein microarrays. Results: We have optimized methodology to probe human protein microarrays with full-length RNA molecules and have identified 137 RNA-protein interactions specific for 10 coding and non-coding RNAs. Those proteins showed strong enrichment for common human RNA binding domains such as RRM, RBD, as well as K homology and CCCH type zinc finger motifs. Previously unknown RNA-protein interactions were discovered using this technique, and these interactions were biochemically verified between TP53 mRNA and Staufen1 protein as well as between HRAS mRNA and CNBP protein. Functional characterization of the interaction between Staufen 1 protein and TP53 mRNA revealed a novel role for Staufen 1 in preserving TP53 RNA stability. Conclusions: Our approach demonstrates a scalable methodology...

Identification and function of long non-coding RNA

Ernst, Carl; Morton, Cynthia C.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Português
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86.01%
Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment.

Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA

Miranda, Kevin C.; Bond, Daniel T.; Levin, Joshua Z.; Adiconis, Xian; Sivachenko, Andrey; Russ, Carsten; Brown, Dennis; Nusbaum, Chad; Russo, Leileata M.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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76.11%
Intact RNA from exosomes/microvesicles (collectively referred to as microvesicles) has sparked much interest as potential biomarkers for the non-invasive analysis of disease. Here we use the Illumina Genome Analyzer to determine the comprehensive array of nucleic acid reads present in urinary microvesicles. Extraneous nucleic acids were digested using RNase and DNase treatment and the microvesicle inner nucleic acid cargo was analyzed with and without DNase digestion to examine both DNA and RNA sequences contained in microvesicles. Results revealed that a substantial proportion (∼87%) of reads aligned to ribosomal RNA. Of the non-ribosomal RNA sequences, ∼60% aligned to non-coding RNA and repeat sequences including LINE, SINE, satellite repeats, and RNA repeats (tRNA, snRNA, scRNA and srpRNA). The remaining ∼40% of non-ribosomal RNA reads aligned to protein coding genes and splice sites encompassing approximately 13,500 of the known 21,892 protein coding genes of the human genome. Analysis of protein coding genes specific to the renal and genitourinary tract revealed that complete segments of the renal nephron and collecting duct as well as genes indicative of the bladder and prostate could be identified. This study reveals that the entire genitourinary system may be mapped using microvesicle transcript analysis and that the majority of non-ribosomal RNA sequences contained in microvesicles is potentially functional non-coding RNA...

Non-Coding RNAs Including miRNAs and lncRNAs in Cardiovascular Biology and Disease

Kataoka, Masaharu; Wang, Da-Zhi
Fonte: MDPI Publicador: MDPI
Tipo: Artigo de Revista Científica
Português
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75.91%
It has been recognized for decades that proteins, which are encoded by our genome and produced via transcription and translation steps, are building blocks that play vital roles in almost all biological processes. Mutations identified in many protein-coding genes are linked to various human diseases. However, this “protein-centered” dogma has been challenged in recent years with the discovery that the majority of our genome is “non-coding” yet transcribed. Non-coding RNA has become the focus of “next generation” biology. Here, we review the emerging field of non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), and their role in cardiovascular function and disease.

Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA

Broadbent, Kate M; Broadbent, Jill C; Ribacke, Ulf; Wirth, Dyann; Rinn, John L; Sabeti, Pardis C
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Português
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86.06%
Background: The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs (lncRNAs) could represent a missing regulatory layer across a broad range of organisms. Results: To investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs...

Secondary structure prediction of non-coding RNA

Lu, Zhi John ; Mathews, David H. (1971 - )
Fonte: Universidade de Rochester Publicador: Universidade de Rochester
Tipo: Tese de Doutorado Formato: Number of Pages:xix, 298 leaves
Português
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Thesis (Ph. D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biochemistry and Biophysics, 2008.; RNA is an active character in cellular function rather than simply a transient information carrier for protein coding as was once believed. Many of the functional RNAs, called non-coding RNA, evolved to be functional by having stable tertiary and secondary structure. Traditionally, RNA secondary structure is predicted with free energy minimization and nearest neighbor parameters at 37 °C. A set of enthalpy parameters is derived to calculate the free energy change at temperatures other than 37 °C. Compared with a previous set of enthalpy parameters, the sensitivity of base pair prediction is improved from 65.2% to 68.9% at organism optimal growth temperature ranging from 10-60 °C. RNA secondary structure prediction has applications in genomics. Secondary structure prediction in the OligoWalk algorithm predicts the hybridization affinity between siRNA/ODNs and target mRNA. Combined with a Support Vector Machine (SVM) method, OligoWalk can select efficient siRNA sequences for a given target. The positive predictive value is as high as 87.6%. A web server is constructed to design siRNA sequences for the scientific community. Moreover...

Predicting RNA Structure and Discovering Functional RNA Sequences in Genomes Using Folding Thermodynamics

Tyagi, Rahul ; Mathews, David H. (1971 - )
Fonte: Universidade de Rochester Publicador: Universidade de Rochester
Tipo: Tese de Doutorado
Português
Relevância na Pesquisa
76.01%
Thesis (Ph.D.)--University of Rochester. School of Medicine and Dentistry. Dept. of Biochemistry and Biophysics, 2008.; RNA is more than just an information carrier that constitutes the intermediate stage between DNA and protein as suggested in the original Central Dogma of Biology. With the discovery of novel non-protein-coding functions of RNA molecules whose secondary and tertiary structure are crucial for their function, it is becoming increasingly important to understand the details of RNA folding. In this work, RNA folding thermodynamics have been used to predict stacking in RNA multibranch loops and to find novel non-coding RNA candidates in genome-wide scans. Here, nearest-neighbor folding free energy parameters are used to predict coaxial stacking configurations in RNA multibranch loops. The method uses a partition function calculation to predict coaxial stacking and achieves significant accuracy (66.7% sensitivity and 51.9% positive predictive value) when compared to RNA molecules with available high-resolution crystal structures. Dynalign, an algorithm for determining the most stable RNA secondary structure common to two sequences, has been used to search yeast genomes (S. cerevisiae and C. albicans) for unannotated regions with predicted high stability of secondary structure. A support vector machine is used to find regions that are predicted to be more stable than random background. Initial results suggest that some of the candidate regions are part of these organisms’ transcriptomes and are likely to be novel ncRNAs.

Exploring TERRA (TElomeric Repeat-containing RNA) Expression and Regulation During Cell Growth in Saccharomyces cerevisiae

Perez Romero, Carmina Angelica
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
Português
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75.97%
The physical ends of eukaryotic chromosomes consist of repetitive DNA sequences, which are associated with specialized proteins forming a nucleoprotein structure essential for the integrity of the linear chromosomes, and are known as telomeres. Telomerase is an enzyme responsible for the maintenance of the telomeric repeats at the end of the chromosomes. Telomerase is a ribonucleoprotein, which contains a catalytic subunit that possesses reverse transcriptase activity, and a RNA subunit that acts as a template, since it possess the telomeric repeat sequences necessary to amplify telomere ends. Telomeres are transcribed in most eukaryotes into a non-coding RNA know as TERRA (Telomeric repeats-containing RNA). It has been proposed that TERRA may act as a regulator of telomere homeostasis, and as an inhibitor of telomerase, however, its specific function is still unknown. In Saccharomyces cerevisiae, TERRA is rapidly degraded by the 5’-3’ Rat1 exonuclease, which has hampered its study by classic biochemical experiments in yeast. In this thesis, we report the use of cytological approaches to study TERRA in budding yeast. Two different approaches were used for this purpose: the fluorescent in-situ hybridization (FISH) and the labeling of TERRA by the MS2-GFP system...

Control of muscle differentiation in normal and pathological condition: the role of dystrophin and non coding RNAs

TWAYANA, SHYAM SUNDAR
Fonte: La Sapienza Universidade de Roma Publicador: La Sapienza Universidade de Roma
Tipo: Tese de Doutorado
Português
Relevância na Pesquisa
85.92%
Muscle differentiation is an excellent system to study the mechanisms of transcriptional and post-transcriptional gene regulation in vertebrates. A regulatory circuitry in which competing endogenous RNAs (ceRNAs) act as a sponges to micro-RNAs was first demonstrated in in-vitro mouse myoblast differentiation for the muscle specific pro-myogenic long non coding RNA, linc-MD1. Here we characterized linc-hMD1, the human homologue of murine linc-MD1. We demonstrated that linc-hMD1 is down regulated in Dunchenne Muscular Dystrophy (DMD) myoblast and it is rescued towards wild type levels in exon skipping treated cells. We showed that it can act as a sponge for miR-133. One of the interesting features of linc-hMD1 is that it is also the host transcript for miR-133b and the biogenesis of these two non-coding RNAs is mutually exclusive. Towards this we showed that the alternative biogenesis of linc-hMD1 and miR-133b is regulated post transcriptionally through binding of HuR protein to pri-linc-hMD1 transcript. We studied the physiological relevance of this regulatory circuitry in human myoblast differentiation and showed that sponging activity of linc-hMD1 occurs during early stages of differentiation while at later stages,linc-hMD1 acts as a precursor for miR-133b.; Sapienza-University of Rome

Imprinted and X-linked non-coding RNAs as potential regulators of human placental function

Buckberry, S.; Bianco-Miotto, T.; Roberts, C.
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
Publicado em //2014 Português
Relevância na Pesquisa
75.85%
Pregnancy outcome is inextricably linked to placental development, which is strictly controlled temporally and spatially through mechanisms that are only partially understood. However, increasing evidence suggests non-coding RNAs (ncRNAs) direct and regulate a considerable number of biological processes and therefore may constitute a previously hidden layer of regulatory information in the placenta. Many ncRNAs, including both microRNAs and long non-coding transcripts, show almost exclusive or predominant expression in the placenta compared with other somatic tissues and display altered expression patterns in placentas from complicated pregnancies. In this review, we explore the results of recent genome-scale and single gene expression studies using human placental tissue, but include studies in the mouse where human data are lacking. Our review focuses on the ncRNAs epigenetically regulated through genomic imprinting or X-chromosome inactivation and includes recent evidence surrounding the H19 lincRNA, the imprinted C19MC cluster microRNAs, and X-linked miRNAs associated with pregnancy complications.; Sam Buckberry, Tina Bianco-Miotto, and Claire T Roberts

Uncovering RNA Editing Sites in Long Non-Coding RNAs

Picardi, Ernesto; D´Erchia, Anna Maria; Gallo, Angela; Montalvo Correa, Antonio; Pesole, Graziano
Fonte: Frontiers Publicador: Frontiers
Tipo: info:eu-repo/semantics/article; publishedVersion
Português
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76.14%
RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins. Although A-to-I editing can occur in both coding and non-coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs, introns, long non-coding RNAs (lncRNAs), and low molecular weight RNAs (tRNA, miRNAs, and others). An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work...

Functional roles of non-coding Y RNAs

Kowalski, Madzia P.; Krude, Torsten
Fonte: Elsevier Publicador: Elsevier
Tipo: Article; published version
Português
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76.1%
This is the final version. It was first published by Elsevier at http://www.sciencedirect.com/science/article/pii/S1357272515001806.; Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains...

Use of Comparative Genomics for Non-coding Rna Prediction and Investigation of Dna Introgression in Yeast

Kavanaugh, Laura Anne
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação Formato: 5182874 bytes; application/pdf
Publicado em 23/04/2008 Português
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95.97%
The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics...