Deputy Executive Director,
Laboratory of RNA Genomics and Structure
Associate Director,
Epigenetic and Epitranscriptomic Systems





Research Summary

My research aims to identify functional RNA elements in transcriptomes through genome-wide detection of RNA structures. RNA play an important role in regulating cellular gene expression. Its ability to fold into complex secondary and tertiary structures is fundamental to its function in the cell. In almost every step of its life cycle, RNA structure has been found to influence diverse processes including transcription, translation mRNA transcript and decay. Alterations in RNA structure have been implicated in several diseases. Despite the importance of RNA structure, structural information for most cellular RNAs, such as mRNAs, is lacking due to the low throughput nature of RNA structure probing and difficulties in probing long RNAs. To fully assess the impact of RNA structure in biology, I aim to utilize and extend high throughput ways to probe RNA structures in solution by coupling structure probing to high throughput sequencing. This enables us to probe RNA structures for thousands of RNAs simultaneously. This expansion of RNA structural data will likely enhance our understanding of how RNA function in different cellular systems, as well as open doors to potentially targeting these structural elements in diseases.

Selected Publications

  • Wan Y.*ᶧ, Qu K.*, Zhang QF, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E and Chang HYᵼ. (2013) Landscape and variation of RNA secondary structure across the human transcriptome. Nature, in press. *These authors contributed equally. ᶧ Co-corresponding authors. Abstract
  • Wan Y, Qu K, Ouyang Z, Chang HY "Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing." Nat Protoc 2013 Apr 4 ; 8(5) : 849-69 Epub 2013 Apr 4 Abstract
  • Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A "Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila." Mol Cell 2013 Jul 25 ; 51(2) : 156-73 Abstract
  • Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY "Genome-wide measurement of RNA folding energies." Mol Cell 2012 Oct 26 ; 48(2) : 169-81 Epub 2012 Sep 13 Abstract
  • Chisholm KM, Wan Y, Li R, Montgomery KD, Chang HY, West RB "Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma." PLoS One 2012 ; 7(10) : e47998 Epub 2012 Oct 25 Abstract
  • Zhang M, Li L, Wang Z, Liu H, Hou J, Zhang M, Hao A, Liu Y, He G, Shi Y, He L, Wang X, Wan Y, Li B "A role for c-Abl in cell senescence and spontaneous immortalization." Age (Dordr) 2012 Jul 13 Epub 2012 Jul 13 Abstract
  • Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY "Understanding the transcriptome through RNA structure." Nat Rev Genet 2011 Sep ; 12(9) : 641-55 Abstract
  • Kertesz M*, Wan Y*, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E "Genome-wide measurement of RNA secondary structure in yeast." Nature 2010 Sep 2 ; 467(7311) : 103-7 *These authors contributed equally. Abstract
  • Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY "Long noncoding RNA as modular scaffold of histone modification complexes." Science 2010 Aug 6 ; 329(5992) : 689-93 Epub 2010 Jul 8 Abstract
  • Wan Y, Chang HY "HOTAIR: Flight of noncoding RNAs in cancer metastasis." Cell Cycle 2010 Sep 1 ; 9(17) : 3391-2 Epub 2010 Sep 21 Abstract