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  1. Article: Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

    Geisberg, Joseph V / Zarmik Moqtaderi / Xiaochun Fan / Fatih Ozsolak / Kevin Struhl

    Cell. 2014 Feb. 13, v. 156

    2014  

    Abstract: We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, ... ...

    Abstract We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A)-binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilizing and stabilizing elements are linked to the propensity of the poly(A) tail to engage in double-stranded structures. Isoforms engineered to fold into 3′ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at 3′ ends are a major determinant of mRNA stability.
    Keywords DNA-directed RNA polymerase ; genes ; half life ; messenger RNA ; sequence analysis ; yeasts
    Language English
    Dates of publication 2014-0213
    Size p. 812-824.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2013.12.026
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: “Jump Start and Gain” Model for Dosage Compensation in Drosophila Based on Direct Sequencing of Nascent Transcripts

    Francesco Ferrari / Annette Plachetka / Artyom A. Alekseyenko / Youngsook L. Jung / Fatih Ozsolak / Peter V. Kharchenko / Peter J. Park / Mitzi I. Kuroda

    Cell Reports, Vol 5, Iss 3, Pp 629-

    2013  Volume 636

    Abstract: Dosage compensation in Drosophila is mediated by the MSL complex, which increases male X-linked gene expression approximately 2-fold. The MSL complex preferentially binds the bodies of active genes on the male X, depositing H4K16ac with a 3′ bias. Two ... ...

    Abstract Dosage compensation in Drosophila is mediated by the MSL complex, which increases male X-linked gene expression approximately 2-fold. The MSL complex preferentially binds the bodies of active genes on the male X, depositing H4K16ac with a 3′ bias. Two models have been proposed for the influence of the MSL complex on transcription: one based on promoter recruitment of RNA polymerase II (Pol II), and a second featuring enhanced transcriptional elongation. Here, we utilize nascent RNA sequencing to document dosage compensation during transcriptional elongation. We also compare X and autosomes from published data on paused and elongating polymerase in order to assess the role of Pol II recruitment. Our results support a model for differentially regulated elongation, starting with release from 5′ pausing and increasing through X-linked gene bodies. Our results highlight facilitated transcriptional elongation as a key mechanism for the coordinated regulation of a diverse set of genes.
    Keywords Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2013-11-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: “Jump Start and Gain” Model for Dosage Compensation in Drosophila Based on Direct Sequencing of Nascent Transcripts

    Francesco Ferrari / Annette Plachetka / Artyom A. Alekseyenko / Youngsook L. Jung / Fatih Ozsolak / Peter V. Kharchenko / Peter J. Park / Mitzi I. Kuroda

    Cell Reports, Vol 5, Iss 4, p

    2013  Volume 1157

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2013-11-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article: Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains

    Slawson, Elizabeth E / Andrea Zeug / Andrew S Nett / Carolyn A Craig / Christopher D Shaffer / Colin D Malone / Elaine R Mardis / Elmer Kellmann / Emiko TA Morimoto / Fatih Ozsolak / James Bogenpohl II / James Dee / Jenny Myoung / Jeremy Buhler / Mary-Lou Pardue / Mindy E Tittiger / Rachel B Shevchek / Sarah CR Elgin / Seth M Bloom /
    Wilson Leung

    Genome biology. 2006 Feb., v. 7, no. 2

    2006  

    Abstract: BACKGROUND: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 ...

    Abstract BACKGROUND: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago. RESULTS: Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %). CONCLUSION: Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.
    Keywords antibodies ; DNA ; Drosophila melanogaster ; genes ; heterochromatin ; histones ; introns ; packaging ; RNA interference ; sequence analysis ; staining ; transposons
    Language English
    Dates of publication 2006-02
    Size p. 1283.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2006-7-2-r15
    Database NAL-Catalogue (AGRICOLA)

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