Publications – University of Copenhagen

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RNAtrain > Publications

Publications

Here the publications produced by this project will be added continuously. Underlined are researchers from the RNA Train Consortium

Publications within RNA-Train Consortium

(49) Huarte M (2016). p53 partners with RNA in the DNA damage response. Nature Genetics Volume: 48, Pages:1298–1299 Doi:10.1038/ng.3702. Published 27 October 2016.

(48) Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M (2016). Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 8:106 DOI:10.1186/s13148-016-0274-6. Published online 12 October 2016.    

(48) Huarte M (2016). p53 partners with RNA in the DNA damage response. Nature Genetics Volume: 48, Pages:1298–1299 Doi:10.1038/ng.3702. Published 27 October 2016.

(47) Marchese FP, Huarte M (2016). A long noncoding RNA in DNA replication and chromosome dynamics. Cell Cycle Volume 13:1-2 DOI: 10.1080/15384101.2016.1241604. Published online 13 October 2016.

(46) Frankel LB, Lubas M, Lund AH (2016). Review: Emerging connections between RNA and autophagy. Autophagy Vol 12, No 11 Pages 1-21. DOI 10.1080/15548627.2016.1222992. Published online 7 October 2016. 

(45) Marchese FP, Grossi E, Marín-Béjar O, Bharti SK, Raimondi I, González J, Martínez-Herrera DJ, Athie A, Amadoz A, Brosh RM Jr, Huarte M (2016). A Long Noncoding RNA Regulates Sister Chromatid Cohesion. Molecular Cell Volume 63(3):397-407. doi: 10.1016/j.molcel.2016.06.031. Published 4 August 2016. 

(44) Häfner SJ, Talvard TG, Lund AH (2016). Long noncoding RNAs in normal and pathological pluripotency. Seminars in Cell & Developmental Biology  pii: S1084-9521(16)30206-3. doi: 10.1016/j.semcdb.2016.07.011. Published 18 July 2016.  

(43) Hasler D, Lehmann G, Murakawa Y, Klironomos F, Jakob L, Grässer FA, Rajewsky N, Landthaler M, Meister G (2016). The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway. Molecular Cell 63(1):110-24 doi: 10.1016/j.molcel.2016.05.026. Published 7 July 2016.

(42) Lopes R, Korkmaz G, Agami R (2016). Applying CRISPR-Cas9 tools to identify and characterize transcriptional enhancers. Nature Reviews Molecular Cell Biology Volume 17:597-604. Doi:10.1038/nrm.2016.79. Published 6 July 2016.

(41) Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M (2016). A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome Res 26(8):1145-59 doi: 10.1101/gr.202432.115. Published 5 July 2016.

(40) Arribas-Hernández L, Marchais A, Poulsen C, Haase B, Hauptmann J, Benes V, Meister G, Brodersen P (2016). The Slicer Activity of ARGONAUTE1 Is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis. Plant Cell Volume 28(7):1563-80 doi: 10.1105/tpc.16.00121. Published online 27 June 2016. 

(39) Ballarino M, Morlando M, Fatica A, Bozzoni I (2016). Non-coding RNAs in muscle differentiation and musculoskeletal disease. The Journal of Clinical Investigation 126(6):2021-30 doi: 10.1172/JCI84419. Published online 1 June 2016.

(38) Krogh N, Jansson MD, Häfner S, Tehler D, Birkedal U, Christensen-Dalsgaard M, Lund AH, Nielsen H (2016). Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Research doi: 10.1093/nar/gkw482. First published online: 1 June 2016. 

(37) Antoine T, Ott D, Ebell K, Hansen K, Henry L, Backer F, Hannus S (2016). Homogeneous time-resolved G protein-coupled receptor–ligand binding assay based on fluorescence cross-correlation spectroscopy. Analytical Biochemistry Volume 502:24-35 doi: 10.1016/j.ab.2016.02.017. Published 1 June 2016. 

(36) Martin G, Zavolan M (2016). Redesigning CLIP for efficiency, accuracy and speed. Nature Methods Volume 13(6):482-3 doi: 10.1038/nmeth.3870. Published online 31 May 2016.

(35) Loayza-Puch F, Agami R (2016). Monitoring amino acid deficiencies in cancer. Cell Cycle Volume 15, Issue 17:2229-30. doi: 10.1080/15384101.2016.1191256. Published online 31 May 2016. 

(34) Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR (2016). An updated human snoRNAome. Nucleic Acids Research 44(11):5068-82 doi: 10.1093/nar/gkw386. Published 12 May 2016.

(33) Kretz M, Medenbach J, Meister G (2016). Special issue: RNA biology in physiology and disease. Pflugers Arch 468(6):933-4 doi: 10.1007/s00424-016-1833-6. Published online 14 May 2016.

(32) Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M (2016). The mRNA-bound proteome of the early fly embryo. Genome Research 26(7):1000-9 doi: 10.1101/gr.200386.115. Published online 18 April 2016.

(31) Ganesh S, Svoboda P (2016). Retrotransposon-associated long non-coding RNAs in mice and men. Pflugers Arch 468(6):1049-60 doi: 10.1007/s00424-016-1818-5. Published online 5 April 2016.

(30) Svobodova E, Kubikova J, Svoboda P (2016). Production of small RNAs by mammalian Dicer. Pflugers Arch 468(6):1089-102  doi: 10.1007/s00424-016-1817-6. Published online 6 April 2016.

(29) Montes M, Lund AH (2016). Emerging roles of lncRNAs in senescence. The FEBS Journal Volume 283, Issue 13:2414-2426 DOI: 10.1111/febs.13679. Published 2 March 2016.

(28) Huarte M (2016). RNA. A lncRNA links genomic variation with celiac disease. Science 352(6281):43-4  doi: 10.1126/science.aaf6015. Published online 31 March 2016. 

(27) Hoffman Y, Bublik DR, Ugalde AP, Elkon R, Biniashivili T, Agami R, Oren M (2016). 3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells. PLOS Genetics http://dx.doi.org/10.1371/journal.pgen.1005879. Published 23 February 2016.

(26) Loayza-Puch F, Rooijers K, Buil LCM, Zijlstra J, Vrielink JFO, Lopes R, Ugalde AP, van Breugel P, Hofland I, Wesseling J, van Tellingen O, Bex A, Agami R (2016). Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. Nature 530:490-494 doi:10.1038/nature16982. Published 25 February 2016. 

(25) Jakob L, Treiber T, Treiber N, Gust A, Kramm K, Hansen K, Stotz M, Wankerl L, Herzog F, Hannus S, Grohmann D, Meister G (2016). Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA 22(3):383-96 doi: 10.1261/rna.055426.115. Published online 14 January 2016.

(24) Melo CA, Léveillé N, Rooijers K, Wijchers PJ, Geeven G, Tal A, Melo SA, de Laat W, Agami R (2016). A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response. Oncognene 35(33):4399-406 doi: 10.1038/onc.2015.502. Published online January 18 2016.

(23) Martone J, Briganti F, Legnini I, Morlando M, Picillo E, Sthandier O, Politano L, Bozzoni I (2016). The lack of the Celf2a splicing factor converts a Duchenne genotype into a Becker phenotype. Nature Communications Volume 7, 10488 doi:10.1038/ncomms10488. Published 22 January 2016.  

(22) Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R (2016). Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nature Biotechnol. 34(2):192-8 doi: 10.1038/nbt.3450. Published online 11 January 2016.

(21) Rzepiela AJ, Vina-Vilaseca A, Breda J, Ghosh S, Syed AP, Gruber AJ, Grandy WA, Eschbach K, Beisel C, van Nimwegen E, Zavolan M (2016). Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets. BioRxiv doi: http://dx.doi.org/10.1101/035097. Published 23 December 2015.

(20) Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann J, Krahn MP, Meister G (2016). The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Reports Volume 13, Issue 6: 1206-1220 http://dx.doi.org/10.1016/j.celrep.2015.09.068. Published 10 November 2015.

(19) Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AFM, Wolf E, Lorenzin F, Eilers M, Agami R (2016). Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO reports e201540717 DOI 10.15252/embr.201540717. Published online 4 November 2015.  

(18) Huarte M (2015). The emerging role of lncRNAs in cancer. Nature medicine 21(11):1253-61 doi: 10.1038/nm.3981. Published 5 November 2015.

(17) Hauptmann J, Schraivogel D, Bruckmann A, Manickavel S, Jakob L, Eichner N, Pfaff J, Urban M, Sprunck S, Hafner M, Tuschl T, Deutzmann R, Meister G (2015). Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc Natl Acad Sci USA 112(38):11841-5 doi: 10.1073/pnas.1506116112. Published online 8 September 2015.

(16) Svoboda P, Franke V, Schultz RM (2015). Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse. Curr Top Dev Biol 113:305-49  doi: 10.1016/bs.ctdb.2015.06.004. Published online 29 July 2015.

(15) Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO (2015). Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Research doi: 10.1101/gr.183160.114. Published 31 July 2015.

(14) Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, Mitra S, Mohammed A, James AR, Hoberg E, Moustakas A, Gyllensten U, Jones SJM, Gustafsson CM, Sims AH, Westerlund F, Gorab E, Kanduri C (2015). MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures. Nature Communications 6, 7743 doi:10.1038/ncomms8743. Published 24 July 2015. 

(13) Zavolan M (2015). Inferring gene expression regulatory networks from high-throughput measurements. Methods 85:1-2  doi: 10.1016/j.ymeth.2015.07.006. Published 15 July 2015. 

(12) Grossi E, Sánchez Y & Huarte M. (2015). Expanding the p53 regulatory network: LncRNAs take up the challenge. Biochim Biophys Acta. 18. pii: S1874-9399(15)00163-7. doi: 10.1016/j.bbagrm.2015.07.011. Published 18 July 2015.

(11) Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G & Zavolan M. (2015). Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol. 23;16:150. doi: 10.1186/s13059-015-0702-5. Published 23 July 2015.

(10) Schraivogel D, Schindler S, Danner J, Kremmer E, Pfaff J, Hannus S, Depping R, Meister G (2015). Importin-β facilitates nuclear import of human GW proteins and balances cytoplasmic gene silencing protein levels. Nucl Acids Res. doi: 10.1093/nar/gkv705. Published 13 July 2015. 

(9) Murakawa Y, Hinz M, Mothes J, Schuetz A, Uhl M, Wyler E, Yasuda T, Mastrobuoni G, Friedel CC, Dölken L, Kempa S, Schmidt-Supprian M, Blüthgen N, Backofen R, Heinemann U, Wolf J, Scheidereit C, & Landthaler M (2015). RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. Nature Communications 6, Article number: 7367, doi:10.1038/ncomms8367. Published 14 July 2015.

(8) Wen J, Leucci E, Vendramin R, Kauppinen S, Lund AH, Krogh A, Parker BJ. (2015)Transcriptome dynamics of the microRNA inhibition response. Nucleic Acids Res. 27;43(13):6207-21. doi: 10.1093/nar/gkv603. Epub 2015 Jun 18.

(7) Pandey GK, Kanduri C. (2015) Long noncoding RNAs and neuroblastoma.
Oncotarget. 30;6 (21):18265-75. Published 30 July 2015.

(6) Kanduri C. (2015). Long noncoding RNAs: Lessons from genomic imprinting.
Biochim Biophys Acta. 2015 May 22. pii: S1874-9399(15)00104-2. doi: 10.1016/j.bbagrm.2015.05.006. Published 22 May 2015.

(5) Lenzi J, De Santis R, de Turris V, Morlando M, Laneve P, Calvo A, Caliendo V, Chiò A, Rosa A, Bozzoni I. (2015). ALS mutant FUS proteins are recruited into stress granules in induced pluripotent stem cell-derived motoneurons.
Dis Model Mech. 1;8 (7):755-66. doi: 10.1242/dmm.020099. Epub 2015 Apr 23.

(4) Svoboda, P. (2015) A toolbox for miRNA analysis. FEBS Lett. 22;589 (14):1694-701. doi: 10.1016/j.febslet.2015.04.054. Epub 2015 May 7.

(3) Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M (2015). Quantifying the strength of miRNA-target interactions. Methods 85:90-9. doi:10.1016/j.ymeth. Epub 2015 Apr 6.

(2) Montes, M, Nielsen, M M, Maglieri, G, Jacobsen, A., Højfeldt, Agrawal-Singh, S., Hansen, K., Helin, K., van de Werken, H., Pedersen, J., & Lund, AH. (2015). The lncRNA MIR31HG regulates p16INK4A expression to modulate senescence. Nature Communications Volume 6. (available online) doi:10.1038/ncomms7967.

(1) Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G. (2015). The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Reports, Volume 13, Issue 6, Pages 1206–122