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  1. Article: Long Noncoding RNAs as a Key Player in Hepatocellular Carcinoma.

    Mehra, Mrigaya / Chauhan, Ranjit

    Biomarkers in cancer

    2017  Volume 9, Page(s) 1179299X17737301

    Abstract: Hepatocellular carcinoma (HCC) is a major malignancy in the liver and has emerged as one of the main cancers in the world with a high mortality rate. However, the molecular mechanisms of HCC are still poorly understood. Long noncoding RNAs (lncRNAs) have ...

    Abstract Hepatocellular carcinoma (HCC) is a major malignancy in the liver and has emerged as one of the main cancers in the world with a high mortality rate. However, the molecular mechanisms of HCC are still poorly understood. Long noncoding RNAs (lncRNAs) have recently come to the forefront as functional non-protein-coding RNAs that are involved in a variety of cellular processes ranging from maintaining the structural integrity of chromosomes to gene expression regulation in a spatiotemporal manner. Many recent studies have reported the involvement of lncRNAs in HCC which has led to a better understanding of the underlying molecular mechanisms operating in HCC. Long noncoding RNAs have been shown to regulate development and progression of HCC, and thus, lncRNAs have both diagnostic and therapeutic potentials. In this review, we present an overview of the lncRNAs involved in different stages of HCC and their potential in clinical applications which have been studied so far.
    Language English
    Publishing date 2017-11-02
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2592049-2
    ISSN 1179-299X
    ISSN 1179-299X
    DOI 10.1177/1179299X17737301
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  2. Article ; Online: A Deluge of Complex Repeats

    Mrigaya Mehra / Indu Gangwar / Ravi Shankar

    PLoS ONE, Vol 10, Iss 8, p e

    The Solanum Genome.

    2015  Volume 0133962

    Abstract: Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae ...

    Abstract Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50-60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
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  3. Article ; Online: A Deluge of Complex Repeats: The Solanum Genome.

    Mehra, Mrigaya / Gangwar, Indu / Shankar, Ravi

    PloS one

    2015  Volume 10, Issue 8, Page(s) e0133962

    Abstract: Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae ...

    Abstract Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50-60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.
    MeSH term(s) Base Sequence ; Binding Sites ; Chromosomes, Plant/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Exons/genetics ; Gene Expression Regulation, Plant/genetics ; Genome, Plant ; Humans ; INDEL Mutation ; Solanum lycopersicum/genetics ; MicroRNAs/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/metabolism ; RNA, Messenger/biosynthesis ; RNA, Messenger/genetics ; RNA, Plant/biosynthesis ; RNA, Plant/genetics ; Repetitive Sequences, Nucleic Acid ; Retroelements/genetics ; Sequence Alignment ; Solanum tuberosum/genetics ; Species Specificity ; Terminal Repeat Sequences ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances DNA, Plant ; MicroRNAs ; Plant Proteins ; RNA, Messenger ; RNA, Plant ; Retroelements ; Transcription Factors
    Language English
    Publishing date 2015-08-04
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0133962
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  4. Article ; Online: The regulatory epicenter of miRNAs.

    Jha, Ashwani / Mehra, Mrigaya / Shankar, Ravi

    Journal of biosciences

    2011  Volume 36, Issue 4, Page(s) 621–638

    Abstract: miRNAs are small non-coding RNAs with average length of ~21 bp. miRNA formation seems to be dependent upon multiple factors besides Drosha and Dicer, in a tissue/stage-specific manner, with interplay of several specific binding factors. In the present ... ...

    Abstract miRNAs are small non-coding RNAs with average length of ~21 bp. miRNA formation seems to be dependent upon multiple factors besides Drosha and Dicer, in a tissue/stage-specific manner, with interplay of several specific binding factors. In the present study, we have investigated transcription factor binding sites in and around the genomic sequences of precursor miRNAs and RNA-binding protein (RBP) sites in miRNA precursor sequences, analysed and tested in comprehensive manner. Here, we report that miRNA precursor regions are positionally enriched for binding of transcription factors as well as RBPs around the 3' end of mature miRNA region in 5' arm. The pattern and distribution of such regulatory sites appears to be a characteristic of precursor miRNA sequences when compared with non-miRNA sequences as negative dataset and tested statistically.When compared with 1 kb upstreamregions, a sudden sharp peak for binding sites arises in the enriched zone near the mature miRNA region. An expression-data-based correlation analysis was performed between such miRNAs and their corresponding transcription factors and RBPs for this region. Some specific groups of binding factors and associated miRNAs were identified. We also identified some of the overrepresented transcription factors and associated miRNAs with high expression correlation values which could be useful in cancer-related studies. The highly correlated groups were found to host experimentally validated composite regulatory modules, in which Lmo2-GATA1 appeared as the predominant one. For many of RBP-miRNAs associations, coexpression similarity was also evident among the associated miRNA common to given RBPs, supporting the Regulon model, suggesting a common role and common control of these miRNAs by the associated RBPs. Based on our findings, we propose that the observed characteristic distribution of regulatory sites in precursor miRNA sequence regions could be critical inmiRNA transcription, processing, stability and formation and are important for therapeutic studies. Our findings also support the recently proposed theory of self-sufficient mode of transcription by miRNAs, which states that miRNA transcription can be carried out in host-independent mode too.
    MeSH term(s) Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Binding Sites/genetics ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Databases, Genetic ; GATA1 Transcription Factor/genetics ; GATA1 Transcription Factor/metabolism ; Genome, Human ; Genomics/methods ; Humans ; LIM Domain Proteins/genetics ; LIM Domain Proteins/metabolism ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Nucleic Acid Conformation ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; RNA Precursors/chemistry ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Stability ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; Sequence Analysis, RNA ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances Adaptor Proteins, Signal Transducing ; GATA1 Transcription Factor ; GATA1 protein, human ; LIM Domain Proteins ; LMO2 protein, human ; MicroRNAs ; Proto-Oncogene Proteins ; RNA Precursors ; RNA-Binding Proteins ; Transcription Factors ; DICER1 protein, human (EC 3.1.26.3) ; DROSHA protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2011-08-21
    Publishing country India
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-011-9109-y
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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  5. Article ; Online: miR-BAG

    Ashwani Jha / Rohit Chauhan / Mrigaya Mehra / Heikham Russiachand Singh / Ravi Shankar

    PLoS ONE, Vol 7, Iss 9, p e

    bagging based identification of microRNA precursors.

    2012  Volume 45782

    Abstract: Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ∼21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. ... ...

    Abstract Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ∼21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. Discovering miRNA candidate regions across the genome has been a challenging problem. Most of the existing tools work reliably only for limited datasets. Here, we have presented a novel reliable approach, miR-BAG, developed to identify miRNA candidate regions in genomes by scanning sequences as well as by using next generation sequencing (NGS) data. miR-BAG utilizes a bootstrap aggregation based machine learning approach, successfully creating an ensemble of complementary learners to attain high accuracy while balancing sensitivity and specificity. miR-BAG was developed for wide range of species and tested extensively for performance over a wide range of experimentally validated data. Consideration of position-specific variation of triplet structural profiles and mature miRNA anchored structural profiles had a positive impact on performance. miR-BAG's performance was found consistent and the accuracy level was observed to be >90% for most of the species considered in the present study. In a detailed comparative analysis, miR-BAG performed better than six existing tools. Using miR-BAG NGS module, we identified a total of 22 novel miRNA candidate regions in cow genome in addition to a total of 42 cow specific miRNA regions. In practice, discovery of miRNA regions in a genome demands high-throughput data analysis, requiring large amount of processing. Considering this, miR-BAG has been developed in multi-threaded parallel architecture as a web server as well as a user friendly GUI standalone version.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
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  6. Article ; Online: miR-BAG: bagging based identification of microRNA precursors.

    Jha, Ashwani / Chauhan, Rohit / Mehra, Mrigaya / Singh, Heikham Russiachand / Shankar, Ravi

    PloS one

    2012  Volume 7, Issue 9, Page(s) e45782

    Abstract: Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ∼21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. ... ...

    Abstract Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ∼21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. Discovering miRNA candidate regions across the genome has been a challenging problem. Most of the existing tools work reliably only for limited datasets. Here, we have presented a novel reliable approach, miR-BAG, developed to identify miRNA candidate regions in genomes by scanning sequences as well as by using next generation sequencing (NGS) data. miR-BAG utilizes a bootstrap aggregation based machine learning approach, successfully creating an ensemble of complementary learners to attain high accuracy while balancing sensitivity and specificity. miR-BAG was developed for wide range of species and tested extensively for performance over a wide range of experimentally validated data. Consideration of position-specific variation of triplet structural profiles and mature miRNA anchored structural profiles had a positive impact on performance. miR-BAG's performance was found consistent and the accuracy level was observed to be >90% for most of the species considered in the present study. In a detailed comparative analysis, miR-BAG performed better than six existing tools. Using miR-BAG NGS module, we identified a total of 22 novel miRNA candidate regions in cow genome in addition to a total of 42 cow specific miRNA regions. In practice, discovery of miRNA regions in a genome demands high-throughput data analysis, requiring large amount of processing. Considering this, miR-BAG has been developed in multi-threaded parallel architecture as a web server as well as a user friendly GUI standalone version.
    MeSH term(s) Animals ; Artificial Intelligence ; Cattle ; Computational Biology/methods ; Dogs ; Drosophila ; Humans ; Mice ; MicroRNAs/metabolism ; Models, Statistical ; Nematoda ; Predictive Value of Tests ; Probability ; Programming Languages ; Rats ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Species Specificity
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2012-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0045782
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