Global Mapping of Human RNA-RNA Interactions.

The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, "LIGation of interacting RNA followed by high-throughput sequencing" (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.

[1]  S. Stamm,et al.  SNORD116 and SNORD115 change expression of multiple genes and modify each other's activity. , 2015, Gene.

[2]  S. Stamm,et al.  The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.

[3]  Peter F. Stadler,et al.  PLEXY: efficient target prediction for box C/D snoRNAs , 2011, Bioinform..

[4]  D. Haussler,et al.  FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.

[5]  C. Will,et al.  The Spliceosome: Design Principles of a Dynamic RNP Machine , 2009, Cell.

[6]  Marcel Schilling,et al.  Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. , 2014, Molecular cell.

[7]  Jernej Ule,et al.  hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1 , 2015, Nature.

[8]  C. Will,et al.  Splicing of a rare class of introns by the U12-dependent spliceosome , 2005, Biological chemistry.

[9]  Manolis Kellis,et al.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.

[10]  J. Steitz,et al.  A base-pairing interaction between U2 and U6 small nuclear RNAs occurs in > 150S complexes in HeLa cell extracts: implications for the spliceosome assembly pathway. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Markus Brameier,et al.  Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs , 2010, Nucleic Acids Res..

[12]  R. Terns,et al.  Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs , 2007, Nature Reviews Molecular Cell Biology.

[13]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[14]  R. Lührmann,et al.  Localization of a base-paired interaction between small nuclear RNAs U4 and U6 in intact U4/U6 ribonucleoprotein particles by psoralen cross-linking. , 1985, Journal of molecular biology.

[15]  L. Wilkinson,et al.  Loss of the imprinted snoRNA mbii-52 leads to increased 5htr2c pre-RNA editing and altered 5HT2CR-mediated behaviour. , 2009, Human molecular genetics.

[16]  S. Stamm,et al.  Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing , 2016, Proceedings of the National Academy of Sciences.

[17]  Qiangfeng Cliff Zhang,et al.  Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.

[18]  Woan-Yuh Tarn,et al.  Highly Diverged U4 and U6 Small Nuclear RNAs Required for Splicing Rare AT-AC Introns , 1996, Science.

[19]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[20]  H. Noller.  Biochemical characterization of the ribosomal decoding site. , 2006, Biochimie.

[21]  Georgios A. Pavlopoulos,et al.  Prediction of miRNA targets. , 2015, Methods in molecular biology.

[22]  T. Kiss.  Small Nucleolar RNAs An Abundant Group of Noncoding RNAs with Diverse Cellular Functions , 2002, Cell.

[23]  J. Dekker,et al.  Chromosome Conformation Capture (3C) in Budding Yeast. , 2015, Cold Spring Harbor Protocols.

[24]  David Tollervey,et al.  Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast , 2011, Proceedings of the National Academy of Sciences.

[25]  J. Manley,et al.  A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing. , 1995, Genes & development.

[26]  Hiten D. Madhani,et al.  A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome , 1992, Cell.

[27]  Y. Zhang,et al.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.

[28]  Spitale Robert,et al.  Structural imprints in vivo decode RNA regulatory mechanisms , 2016 .

[29]  R. Padgett,et al.  Requirement of U12 snRNA for in Vivo Splicing of a Minor Class of Eukaryotic Nuclear Pre-mRNA Introns , 1996, Science.

[30]  T. Lowe,et al.  Small nucleolar RNAs and RNA-guided post-transcriptional modification. , 2013, Essays in biochemistry.

[31]  Daniel N. Wilson,et al.  Structures of the human and Drosophila 80S ribosome , 2013, Nature.

[32]  D. Tollervey,et al.  Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.

[33]  J. Shendure,et al.  High-throughput determination of RNA structure by proximity ligation , 2015, Nature Biotechnology.

[34]  J. Calvet,et al.  Heterogeneous nuclear RNA double-stranded regions probed in living HeLa cells by crosslinking with the psoralen derivative aminomethyltrioxsalen. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Lührmann,et al.  Immunoaffinity purification of a [U4/U6.U5] tri-snRNP from human cells. , 1991, Genes & development.

[36]  Peter F. Stadler,et al.  RNAsnoop: efficient target prediction for H/ACA snoRNAs , 2010, Bioinform..

[37]  M. Deutscher,et al.  Substrate Recognition and Catalysis by the Exoribonuclease RNase R* , 2006, Journal of Biological Chemistry.