Marcel Dinger

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Marcel completed his PhD in 2003 at the University of Waikato (New Zealand) and joined the Mattick group in June 2005 with a NZ Foundation of Research, Science & Technology Postdoctoral Fellowship to study the role of long noncoding RNAs in mammalian disease and development. In 2010, he was awarded an NHMRC Career Development Award (CDA). In October 2011, Marcel has established his own lab at the University of Queensland Diamantina Institute to extend his work on long noncoding RNAs and apply this knowledge to understand and treat disease. In October 2012, Marcel was recruited to the Garvan Institute of Medical Research as Head of Clinical Genomics and Genome Informatics.

Marcel manages this wiki and the group websites listed below. He also regularly updates and helps to maintain the long noncoding RNA entry in the Wikipedia. You can find his Epernicus profile at http://www.epernicus.com/med.

Email: m.dinger@garvan.org.au

Contents

Websites

ABA ncRNA Expression Database Public database containing expression data from the Allen Brain Atlas (Instructions also available).

ncRNA Expression Database Database containing expression data from the v1 noncoding array and the Allen Brain Atlas.

lncRNAdb Database of long noncoding RNAs.

Marcel Dinger

Genomic and Transcriptomic Analysis Tools

I have developed a number of tools to facilitate the analysis of deep sequencing data. Most of these revolve around UCSC Genome Browser file formats (BED and WIG) and ZOOM outputs.

bedToWiggle | bedOffset | wigConvert | wiggyWin | wiggySum | wiggyMerge | wiggyCorrelate | wiggyCompare | wiggyBin | ziggySum | ziggyWin

For detailed usage information or copies of these scripts, please contact me.

Microarray Analysis Tutorials

The Mattick Lab designed the NCode microarrays for analysing the expression of long noncoding RNAs in mouse and human. These arrays are based on the Agilent platform. Below are descriptions of the procedures we developed for analysing data from one and two colour high-density Agilent microarrays using the Limma library (part of Bioconductor) in R.

Single channel analysis of Agilent microarray data with Limma

Two channel analysis of Agilent microarray data with Limma

Publications

  1. Aftab MN, Dinger ME, Perera RJ (2014). The role of microRNAs and long non-coding RNAs in the pathology, diagnosis, and management of melanoma. Archives of Biochemistry and Biophysics Published online 24 July 2014.
  2. Bauer D, Gaff C, Dinger ME, Caramins M, Buske FA, Fenech M, Hansen D, Cobiac L (2014). Genomics and personalised whole-of-life healthcare. Trends in Molecular Medicine Published online May 4 2014.
  3. Mazar J, Zhao W, Lee B, Shelley J, Govindarajan S, Yamamoto F, Ratnam M, Brill LM, Collins S, Finck BN, Han X, Mattick JS, Dinger ME, Perera RJ (2014). The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells. Oncotarget Accepted 18 March 2014.
  4. Liu PY, Erriquez D, Marshall GM, Tee AE, Polly P, Wong M, Liu B, Bell JL, Zhang XD, Milazzo G, Cheung, BB, Fox A, Swarbrick A, Hüttelmaier S, Kavallaris M, Perini G, Mattick JS, Dinger ME, Liu T (2014). Effects of a novel long noncoding RNA, lncUSMycN, on N-Myc expression and neuroblastoma progression. J Natl Cancer Inst 106: dju113.
  5. Mattick JS, Dziadek M, Terrill B, Kaplan W, Spigelman AD, Bowling F, Dinger ME (2014). The impact of genomics on the future of medicine and health. Medical Journal of Australia. Accepted 2 February 2014.
  6. Tee A, Ling D, Nelson C, Atmadibrata B, Dinger ME, Xu N, Mizukami T, Liu PY, Liu B, Cheung B, Pasquier E, Haber M, Norris MD, Suzuki T, Marshall GM, Liu T (2014). The histone demethylase JMJD1A induces cell migration and invasion by up-regulating the expression of the long noncoding RNA MALAT1. Oncotarget 5: 1793-804
  7. Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nature Protocols 9: 989-1009.
  8. Vogelzang A, McGuire H, Liu SM, Gloss B, Mercado K, Earls P, Dinger ME, Batten M, Sprent, King C (2014). Interleukin-21 contributes to fatal inflammatory disease in the absence of FoxP3+ T regulatory cells. Journal of Immunology. Published online 20 January 2014.
  9. Li JL, Mazer J, Zhong C, Faulkner GJ, Govindarajan SS, Zhang Z, Dinger ME, Meredith G, Adams C, Zhang S, Mattick JS, Ray A, Perera RJ (2013). Genome-wide assessment of methylated CpG island signatures in melanoma cell lines. Scientific Reports 3: 2962
  10. Mattick JS, Dinger ME (2013). The extent of functionality in the human genome. HUGO Journal 7: 2.
  11. Dave RK, Dinger ME, Andrew M, Askarian-Amiri M, Hume DA, Kellie S (2013). Regulated expression of PTPRJ/CD148 and an antisense long noncoding RNA in macrophages by proinflammatory stimuli. PLoS One 8: e68306.
  12. Cheetham S, Gruhl F, Mattick JS, Dinger ME. Long noncoding RNAs and the genetics of cancer (2013). Long noncoding RNAs and the genetics of cancer. Brit J Cancer 108: 2419-25.
  13. Amaral PP, Dinger ME, Mattick JS (2013). Regulatory RNAs in homeostasis, disease and stress responses: an evolutionary perspective. Brief Funct Genomic 12: 254-78.
  14. Marcellin E, Mercer TR, Licona-Cassani C, Palfreyman RW, Dinger ME, Steen JA, Mattick JS, Nielsen LK (2013). Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics 14: 15.
  15. Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME*, Mattick JS* (2012). Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics 28: 3042-50.
  16. Shore AN, Kabotyanski EB, Roarty K, Smith MA, Zhang Y, Creighton CJ, Dinger ME, Rosen JM (2012). Pregnancy-Induced Noncoding RNA (PINC) associates with Polycomb Repressive Complex 2 and regulates mammary epithelial differentiation. PLoS Genet 8: e1002840.
  17. Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME*, Mattick JS* (2012). Genome-wide analysis of long noncoding RNA stability. Genome Res 22: 885-898.
  18. Chen H, Palmer JS, Thiagarajan RD, Dinger ME, Lesieur E, Chiu H, Schulz A, Spiller C, Grimmond SM, Little MH, Koopman P, Wilhelm D (2012). Identification of novel markers of mouse fetal ovary development. PLoS One 7: e41683.
  19. Smart CE, Askarian-Amiri ME, Wronski A, Dinger ME, Crawford J, Ovchinnikov DA, Cristina-Vargas A, Reid L, Simpson PT, Song S, Wiesner C, French JD, Dave RK, de Silva L, Purdon A, Andrew M, Lakhani SR, Mattick JS, Brown MA, Kellie S (2012). Expression and function of the protein tyrosine phosphatase receptor J (PTPRJ) in normal mammary epithelial cells and breast tumors. PLoS One 7: e40742.
  20. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn, JL (2012). Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotech 30: 99-104
  21. Dinger ME (2011). lncRNAs: finding the forest among the trees? Mol Therapy 19: 2109-11.
  22. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C (2011). RNAcentral: A vision for an international database of RNA sequences. RNA 17: 1941-6.
  23. Dinger ME, Gascoigne DK, Mattick JS (2011). The evolution of multifunctional RNAs. Biochimie. 93: 2013-8.
  24. Mercer TR, Neph S, Dinger ME, Crawford J, Smith MS, Shearwood A-MJ, Rackham O, Haugen E, Stamatoyannopoulos JA, Filopovska A, and Mattick JS (2011). The human mitochondrial transcriptome. Cell 146: 645-658.
  25. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KJ, Morillon A, Rozowsky JS, Gerstein M, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS (2011). The reality of pervasive transcription. PLoS Biology 9: e1000625.
  26. Khaitan D*, Dinger ME*, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ (2011). The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res 71: 3852-3862.
  27. Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME*, Mattick JS* (2011). SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17: 878-891.
  28. Bracken CP, Szubert JM, Mercer TR, Dinger ME, Thomson DW, Mattick JS, Michael MZ, Goodall GJ (2011). Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage. Nucleic Acids Res 39: 5658-5668.
  29. Mercer TR, Wilhelm D, Dinger ME, Solda G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, Saint R, Koopman P, Mattick JS (2010). Expression of distinct RNAs from 3’ untranslated regions. Nucleic Acids Res 39: 2393-2403.
  30. Amaral PP, Clark MB, Gascoigne DK, Dinger ME*, Mattick JS* (2010). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-151.
  31. Mercer TR, Dinger ME, Bracken CP, Kolle G, Szubert JM, Korbie DJ, Askarian-Amiri, ME, Gardiner BB, Goodall GJ, Grimmond SM, Mattick JS (2010). Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res 20: 1639-1650.
  32. Mazar J, Sinha S, Dinger ME, Mattick JS, Perera RJ (2010). Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent. Mol Genet Genom 284: 1-9.
  33. Lai J, Lehman ML, Dinger ME, Hendy SC, Mercer TR, Seim I, Lawrence MG, Mattick JS, Clements JA, Nelson CC (2010). A variant of the KLK4 gene is expressed as a cis sense–antisense chimeric transcript in prostate cancer cells. RNA 16: 1156-66.
  34. Risueño A, Fontanillo C, Dinger ME, De Las Rivas J (2010). GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics 11: 221.
  35. Mercer TR, Qureshi IA, Goken S, Dinger ME, Li G, Mattick JS, Mehler MF (2010). Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neuroscience 11: 14.
  36. Taft RJ, Pang KC, Mercer TR, Dinger ME, Mattick JS (2010). Non-coding RNAs: regulators of disease. J Pathol 220: 126-39.
  37. Dinger ME, Amaral PP, Mercer TR, Mattick JS (2009). Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic. 8: 407-23 Free access preprint (15 June 2009).
  38. Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chan W, Mattick JS (2009). Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol. 182: 7738-7748.
  39. Mercer TR, Dinger ME, Mattick JS (2009). Long noncoding RNAs: insights into function. Nature Rev Genet. 10: 155-159.
  40. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009). MEN ϵ/β nuclear retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.
  41. Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009). RNA control of epigenetic processes. Australian Biochemist 39: 4-8
  42. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS (2009). NRED: a database of long noncoding RNA expression. Nucleic Acid Res 37: D122-6.
  43. Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009). RNA regulation of epigenetic processes. Bioessays. 31: 51-59.
  44. Mercer TR, Dinger ME, Mariani J, Kosik KS, Mehler MF, Mattick JS (2008). Noncoding RNAs in long-term memory formation. Neuroscientist. 14: 434-445.
  45. Dinger ME, Pang KC, Mercer TR, Mattick JS (2008). Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comp Biol 4: e1000176.
  46. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.
  47. Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008). The eukaryotic genome as an RNA machine. Science 319: 1787-1789.
  48. Dinger ME, Mercer TR, Mattick JS (2008). RNAs as extracellular signaling molecules. J Mol Endocrinol 40: 151-159.
  49. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008). Specific expression of long noncoding RNAs in the adult mouse brain. Proc Natl Acad Sci USA 105: 716-721.
  50. Pang, KC, Stephen, S, Dinger, ME, Engstrom, PG, Lenhard, B, Mattick, JS (2007). RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 35: D178-182.
  51. Musgrave DR, Zhang X, Dinger ME (2002). Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life. Astrobiology 2: 241-253.
  52. Dinger ME, Baillie GJ, Musgrave DR (2000). Growth phase-dependent expression and degradation of histones in the thermophilic archaeon Thermococcus zilligii. Mol Microbiol 36: 876-885.
  53. Dinger ME, Musgrave DR (2000). Identification of archaeal genes encoding a novel stationary phase-response protein. Biochim Biophys Acta 1490: 115-120.
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