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  1. Article: Regulation of splicing: the importance of being translatable.

    Miriami, Elana / Sperling, Ruth / Sperling, Joseph / Motro, Uzi

    RNA (New York, N.Y.)

    2003  Volume 10, Issue 1, Page(s) 1–4

    Abstract: RNA sequences that conform to the consensus sequence of 5' splice sites but are not used for splicing occur frequently in protein coding genes. Mutational analyses have shown that suppression of splicing at such latent sites may be dictated by the ... ...

    Abstract RNA sequences that conform to the consensus sequence of 5' splice sites but are not used for splicing occur frequently in protein coding genes. Mutational analyses have shown that suppression of splicing at such latent sites may be dictated by the necessity to maintain an open reading frame in the mRNA. Here we show that stop codon frequency in introns having latent 5' splice sites is significantly greater than that of introns lacking such sites and significantly greater than the expected occurrence by chance alone. Both observations suggest the occurrence of a general mechanism that recognizes the mRNA reading frame in the context of pre-mRNA.
    MeSH term(s) Humans ; Introns/genetics ; Open Reading Frames ; Protein Biosynthesis ; RNA Precursors/genetics ; RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances RNA Precursors ; RNA, Messenger
    Language English
    Publishing date 2003-12-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1241540-6
    ISSN 1355-8382
    ISSN 1355-8382
    DOI 10.1261/rna.5112704
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4777: Show issues Location:
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  2. Article ; Online: Conserved sequence elements associated with exon skipping.

    Miriami, Elana / Margalit, Hanah / Sperling, Ruth

    Nucleic acids research

    2003  Volume 31, Issue 7, Page(s) 1974–1983

    Abstract: One of the major forms of alternative splicing, which generates multiple mRNA isoforms differing in the precise combinations of their exon sequences, is exon skipping. While in constitutive splicing all exons are included, in the skipped pattern(s) one ... ...

    Abstract One of the major forms of alternative splicing, which generates multiple mRNA isoforms differing in the precise combinations of their exon sequences, is exon skipping. While in constitutive splicing all exons are included, in the skipped pattern(s) one or more exons are skipped. The regulation of this process is still not well understood; so far, cis- regulatory elements (such as exonic splicing enhancers) were identified in individual cases. We therefore set to investigate the possibility that exon skipping is controlled by sequences in the adjacent introns. We employed a computer analysis on 54 sequences documented as undergoing exon skipping, and identified two motifs both in the upstream and downstream introns of the skipped exons. One motif is highly enriched in pyrimidines (mostly C residues), and the other motif is highly enriched in purines (mostly G residues). The two motifs differ from the known cis-elements present at the 5' and 3' splice site. Interestingly, the two motifs are complementary, and their relative positional order is conserved in the flanking introns. These suggest that base pairing interactions can underlie a mechanism that involves secondary structure to regulate exon skipping. Remarkably, the two motifs are conserved in mouse orthologous genes that undergo exon skipping.
    MeSH term(s) Alternative Splicing/genetics ; Animals ; Base Sequence ; Binding Sites/genetics ; Conserved Sequence/genetics ; Databases, Nucleic Acid ; Exons/genetics ; GC Rich Sequence/genetics ; Humans
    Language English
    Publishing date 2003-03-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkg279
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Conservation of an open-reading frame as an element affecting 5' splice site selection.

    Miriami, Elana / Motro, Uzi / Sperling, Joseph / Sperling, Ruth

    Journal of structural biology

    2002  Volume 140, Issue 1-3, Page(s) 116–122

    Abstract: Splice site selection is a key element of pre-mRNA splicing and involves specific recognition of consensus sequences at the 5(') and 3(') splice sites. Evidently, the compliance of a given sequence with the consensus 5(') splice site sequence is not ... ...

    Abstract Splice site selection is a key element of pre-mRNA splicing and involves specific recognition of consensus sequences at the 5(') and 3(') splice sites. Evidently, the compliance of a given sequence with the consensus 5(') splice site sequence is not sufficient to define it as a functional 5(') splice site, because not all sequences that conform with the consensus are used for splicing. We have previously hypothesized that the necessity to avoid the inclusion of premature termination codons within mature mRNAs may serve as a criterion that differentiates normal 5(') splice sites from unused (latent) ones. We further provided experimental support to this idea, by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5(') splice site were mutated, and showing that splicing using the latent site is indeed activated by such mutations. Here we evaluate this hypothesis by a computerized survey for latent 5(') splice sites in 446 protein-coding human genes. This data set contains 2311 introns, in which we found 10490 latent 5(') splice sites. The utilization of 10045 (95.8%) of these sites for splicing would have led to the inclusion of an in-frame stop codon within the resultant mRNA. The validity of this finding is confirmed here by statistical analyses. This finding, together with our previous experimental results, invokes a nuclear scanning mechanism, as part of the splicing machine, which identifies in-frame stop codons within the pre-mRNA and prevents splicing that could lead to the formation of a prematurely terminated protein.
    MeSH term(s) Algorithms ; Codon ; Databases as Topic ; Exons ; Genetic Techniques ; Humans ; Introns ; Models, Genetic ; Mutation ; Open Reading Frames ; RNA Splicing ; RNA, Messenger/metabolism ; Software
    Chemical Substances Codon ; RNA, Messenger
    Language English
    Publishing date 2002-12-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1032718-6
    ISSN 1095-8657 ; 1047-8477
    ISSN (online) 1095-8657
    ISSN 1047-8477
    DOI 10.1016/s1047-8477(02)00539-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1428: Show issues Location:
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  4. Article: Identification and characterization of a novel splice variant of mouse and rat cytochrome b5/cytochrome b5 reductase.

    Curry, Benjamin J / Roman, Shaun D / Wallace, Ceanne A / Scott, Rebecca / Miriami, Elana / Aitken, R John

    Genomics

    2004  Volume 83, Issue 3, Page(s) 425–438

    Abstract: Cytochrome b5/cytochrome b5 reductase (cb5/cb5r) is a cytosolic fusion protein between the hemoprotein cytochrome b5 and the flavoprotein cytochrome b5 reductase. We describe the identification and characterization of a novel splice variant of cb5/cb5r ... ...

    Abstract Cytochrome b5/cytochrome b5 reductase (cb5/cb5r) is a cytosolic fusion protein between the hemoprotein cytochrome b5 and the flavoprotein cytochrome b5 reductase. We describe the identification and characterization of a novel splice variant of cb5/cb5r in the mouse and rat and show that expression of the variant is conserved in both species but is not expressed in human tissue. Characterization of the exon structure of cb5/cb5r indicated that the variant was due to the deletion of the whole of exon 12, thus the variant was named cb5/cb5rdelta12. Exon 12 codes for the flavin-adenine dinucleotide binding domain of cb5/cb5r. Expression analysis revealed the transcript of cb5/cb5rdelta12 in mouse and rat testis, brain, and skeletal muscle and also in the male germ line. We postulate that cb5/cb5rdelta12 may function in a dominant negative fashion, limiting the amount of damage caused by the production of reactive oxygen species by cb5/cb5r.
    MeSH term(s) Alternative Splicing ; Amino Acid Sequence ; Animals ; Conserved Sequence ; Cytochrome-B(5) Reductase/genetics ; Cytochromes b5/genetics ; Exons ; Gene Expression Profiling ; Germ Cells ; Humans ; Male ; Mice ; Molecular Sequence Data ; Protein Biosynthesis ; Pseudogenes ; Rats ; Rats, Wistar ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Spermatozoa/cytology
    Chemical Substances Recombinant Fusion Proteins ; Cytochromes b5 (9035-39-6) ; Cytochrome-B(5) Reductase (EC 1.6.2.2)
    Language English
    Publishing date 2004-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2003.08.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2367: Show issues Location:
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  5. Article: Stop codons affect 5' splice site selection by surveillance of splicing.

    Li, Binghui / Wachtel, Chaim / Miriami, Elana / Yahalom, Galit / Friedlander, Gilgi / Sharon, Gil / Sperling, Ruth / Sperling, Joseph

    Proceedings of the National Academy of Sciences of the United States of America

    2002  Volume 99, Issue 8, Page(s) 5277–5282

    Abstract: Pre-mRNA splicing involves recognition of a consensus sequence at the 5' splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for ... ...

    Abstract Pre-mRNA splicing involves recognition of a consensus sequence at the 5' splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5' SS for splicing would introduce an in-frame stop codon into the resultant mRNA. This finding suggested a link between SS selection and maintenance of an ORF within the mRNA. Here we tested this idea by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5' SS were mutated. We found that splicing with the latent site is indeed activated by such mutations. Our findings predict the existence of a checking mechanism, as a component of the nuclear pre-mRNA splicing machine, to ensure the maintenance of an ORF. This notion is highly important for accurate gene expression, as perturbations that would lead to splicing at these latent sites are expected to introduce in-frame stop codons into the majority of mRNAs.
    MeSH term(s) Alternative Splicing ; Animals ; Binding Sites ; Cell Line ; Codon ; Codon, Nonsense ; Codon, Terminator ; Cricetinae ; Fibroblasts/metabolism ; Humans ; Iduronidase/chemistry ; Mesocricetus ; Models, Genetic ; Mutation ; Open Reading Frames ; Plasmids/metabolism ; Point Mutation ; Protein Binding ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Transfection
    Chemical Substances Codon ; Codon, Nonsense ; Codon, Terminator ; RNA, Messenger ; Iduronidase (EC 3.2.1.76)
    Language English
    Publishing date 2002-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.082095299
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Show issues Location:
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  6. Article ; Online: Personal omics profiling reveals dynamic molecular and medical phenotypes.

    Chen, Rui / Mias, George I / Li-Pook-Than, Jennifer / Jiang, Lihua / Lam, Hugo Y K / Chen, Rong / Miriami, Elana / Karczewski, Konrad J / Hariharan, Manoj / Dewey, Frederick E / Cheng, Yong / Clark, Michael J / Im, Hogune / Habegger, Lukas / Balasubramanian, Suganthi / O'Huallachain, Maeve / Dudley, Joel T / Hillenmeyer, Sara / Haraksingh, Rajini /
    Sharon, Donald / Euskirchen, Ghia / Lacroute, Phil / Bettinger, Keith / Boyle, Alan P / Kasowski, Maya / Grubert, Fabian / Seki, Scott / Garcia, Marco / Whirl-Carrillo, Michelle / Gallardo, Mercedes / Blasco, Maria A / Greenberg, Peter L / Snyder, Phyllis / Klein, Teri E / Altman, Russ B / Butte, Atul J / Ashley, Euan A / Gerstein, Mark / Nadeau, Kari C / Tang, Hua / Snyder, Michael

    Cell

    2012  Volume 148, Issue 6, Page(s) 1293–1307

    Abstract: Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines ... ...

    Abstract Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.
    MeSH term(s) Diabetes Mellitus, Type 2/genetics ; Female ; Gene Expression Profiling ; Genome, Human ; Genomics ; Humans ; Male ; Metabolomics ; Middle Aged ; Mutation ; Precision Medicine ; Proteomics ; Respiratory Syncytial Viruses/isolation & purification ; Rhinovirus/isolation & purification
    Language English
    Publishing date 2012-12-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2012.02.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

    Chen, Rui / Mias, George I. / Li-Pook-Than, Jennifer / Jiang, Lihua / Lam, Hugo Y.K. / Chen, Rong / Miriami, Elana / Karczewski, Konrad J. / Hariharan, Manoj / Dewey, Frederick E. / Cheng, Yong / Clark, Michael J. / Im, Hogune / Habegger, Lukas / Balasubramanian, Suganthi / O'Huallachain, Maeve / Dudley, Joel T. / Hillenmeyer, Sara / Haraksingh, Rajini /
    Sharon, Donald / Euskirchen, Ghia / Lacroute, Phil / Bettinger, Keith / Boyle, Alan P. / Kasowski, Maya / Grubert, Fabian / Seki, Scott / Garcia, Marco / Whirl-Carrillo, Michelle / Gallardo, Mercedes / Blasco, Maria A. / Greenberg, Peter L. / Snyder, Phyllis / Klein, Teri E. / Altman, Russ B. / Butte, Atul J. / Ashley, Euan A. / Gerstein, Mark / Nadeau, Kari C. / Tang, Hua / Snyder, Michael

    Cell

    Volume v. 148,, Issue no. 6

    Abstract: Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines ... ...

    Abstract Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.
    Keywords risk ; monitoring ; autoantibodies ; noninsulin-dependent diabetes mellitus ; transcriptomics ; RNA editing ; genomics ; phenotype ; proteomics ; medicine ; metabolomics
    Language English
    Document type Article
    ISSN 0092-8674
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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