RNA Detection

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  1. Liepelt A, Naarmann-de Vries IS, Simons N,
    Eichelbaum K, Fohr S, Archer SK, Castello A,
    Usadel B, Krijgsveld J, Preiss T, Marx G,
    Hentze MW, Ostareck DH, Ostareck-Lederer
    A (2016) Identification of RNA-binding pro-
    teins in macrophages by interactome capture.
    Mol Cell Proteomics 15(8):2699–2714.
    doi:10.1074/mcp.M115.056564

  2. Wessels HH, Imami K, Baltz AG, Kolinski M,
    Beldovskaya A, Selbach M, Small S, Ohler U,
    Landthaler M (2016) The mRNA-bound pro-
    teome of the early fly embryo. Genome Res 26
    (7):1000–1009. doi:10.1101/gr.200386.115

  3. Sysoev VO, Fischer B, Frese CK, Gupta I,
    Krijgsveld J, Hentze MW, Castello A, Ephrussi
    A (2016) Global changes of the RNA-bound
    proteome during the maternal-to-zygotic tran-
    sition in Drosophila. Nat Commun 7:12128.
    doi:10.1038/ncomms12128

  4. Matia-Gonzalez AM, Laing EE, Gerber AP
    (2015) Conserved mRNA-binding proteomes
    in eukaryotic organisms. Nat Struct Mol Biol
    22(12):1027–1033. doi:10.1038/nsmb.3128

  5. Bunnik EM, Batugedara G, Saraf A, Prud-
    homme J, Florens L, Le Roch KG (2016) The
    mRNA-bound proteome of the human malaria
    parasite Plasmodium falciparum. Genome Biol
    17(1):147. doi:10.1186/s13059-016-1014-0

  6. Marondedze C, Thomas L, Serrano NL, Lilley
    KS, Gehring C (2016) The RNA-binding pro-
    tein repertoire of Arabidopsis thaliana. Sci Rep
    6:29766. doi:10.1038/srep29766

  7. Reichel M, Liao Y, Rettel M, Ragan C, Evers
    M, Alleaume AM, Horos R, Hentze MW, Pre-
    iss T, Millar AA (2016) In planta determination
    of the mRNA-binding proteome of Arabidop-
    sis etiolated seedlings. Plant Cell. doi:10.
    1105/tpc.16.00562

  8. Mitchell SF, Jain S, She M, Parker R (2013)
    Global analysis of yeast mRNPs. Nat Struct
    Mol Biol 20(1):127–133. doi:10.1038/nsmb.
    2468

  9. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A,
    Darnell RB (2003) CLIP identifies Nova-
    regulated RNA networks in the brain. Science
    302(5648):1212–1215. doi:10.1126/science.

  10. 302/5648/1212 [pii]

  11. Konig J, Zarnack K, Rot G, Curk T, Kayikci M,
    Zupan B, Turner DJ, Luscombe NM, Ule J
    (2010) iCLIP reveals the function of hnRNP
    particles in splicing at individual nucleotide
    resolution. Nat Struct Mol Biol 17
    (7):909–915. doi:10.1038/nsmb.1838

  12. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci
    M, Chi SW, Clark TA, Schweitzer AC, Blume
    JE, Wang X, Darnell JC, Darnell RB (2008)
    HITS-CLIP yields genome-wide insights into
    brain alternative RNA processing. Nature 456
    (7221):464–469. doi:10.1038/nature07488

  13. Hafner M, Landthaler M, Burger L, Khorshid
    M, Hausser J, Berninger P, Rothballer A,
    Ascano M Jr, Jungkamp AC, Munschauer M,
    Ulrich A, Wardle GS, Dewell S, Zavolan M,
    Tuschl T (2010) Transcriptome-wide identifi-
    cation of RNA-binding protein and microRNA
    target sites by PAR-CLIP. Cell 141
    (1):129–141. doi:10.1016/j.cell.2010.03.009

  14. Kramer K, Sachsenberg T, Beckmann BM,
    Qamar S, Boon KL, Hentze MW, Kohlbacher
    O, Urlaub H (2014) Photo-cross-linking and
    high-resolution mass spectrometry for assign-
    ment of RNA-binding sites in RNA-binding
    proteins. Nat Methods 11(10):1064–1070.
    doi:10.1038/nmeth.3092

  15. Gerstberger S, Hafner M, Tuschl T (2014) A
    census of human RNA-binding proteins. Nat
    Rev Genet 15(12):829–845. doi:10.1038/
    nrg3813

  16. Keene JD (2007) RNA regulons: coordination
    of post-transcriptional events. Nat Rev Genet 8
    (7):533–543. doi:10.1038/nrg2111

  17. Keene JD (2007) Biological clocks and the
    coordination theory of RNA operons and reg-
    ulons. Cold Spring Harb Symp Quant Biol
    72:157–165. doi:10.1101/sqb.2007.72.013

  18. Dutertre M, Lambert S, Carreira A, Amor-
    Gueret M, Vagner S (2014) DNA damage:
    RNA-binding proteins protect from near and
    far. Trends Biochem Sci 39(3):141–149.
    doi:10.1016/j.tibs.2014.01.003

  19. Ong SE, Blagoev B, Kratchmarova I, Kristen-
    sen DB, Steen H, Pandey A, Mann M (2002)
    Stable isotope labeling by amino acids in cell
    culture, SILAC, as a simple and accurate
    approach to expression proteomics. Mol Cell
    Proteomics 1(5):376–386

  20. Radle B, Rutkowski AJ, Ruzsics Z, Friedel CC,
    Koszinowski UH, Dolken L (2013) Metabolic
    labeling of newly transcribed RNA for high
    resolution gene expression profiling of RNA
    synthesis, processing and decay in cell culture.
    J Vis Exp 78. doi:10.3791/50195

  21. Garzia A, Meyer C, Morozov P, Sajek M,
    Tuschl T (2016) Optimization of PAR-CLIP
    for transcriptome-wide identification of bind-
    ing sites of RNA-binding proteins. Methods.
    doi:10.1016/j.ymeth.2016.10.007

  22. Hardcastle TJ, Kelly KA (2010) baySeq: empir-
    ical Bayesian methods for identifying differen-
    tial expression in sequence count data. BMC
    Bioinformatics 11:422. doi:10.1186/1471-
    2105-11-422

  23. LoveMI,HuberW,AndersS (2014)Moderated
    estimation of fold change and dispersion for
    RNA-seq data with DESeq2. Genome Biol 15
    (12):550. doi:10.1186/s13059-014-0550-8


Isolation and Differential Analysis of RBPs 417
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