Shanhai Xie

Publications (4)104.61 Total impact

• Article: Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels.

  Masato Kato, Tina W Han, Shanhai Xie, Kevin Shi, Xinlin Du, Leeju C Wu, Hamid Mirzaei, Elizabeth J Goldsmith, Jamie Longgood, Jimin Pei, Nick V Grishin, Douglas E Frantz, Jay W Schneider, She Chen, Lin Li, Michael R Sawaya, David Eisenberg, Robert Tycko, Steven L McKnight
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  ABSTRACT: Eukaryotic cells contain assemblies of RNAs and proteins termed RNA granules. Many proteins within these bodies contain KH or RRM RNA-binding domains as well as low complexity (LC) sequences of unknown function. We discovered that exposure of cell or tissue lysates to a biotinylated isoxazole (b-isox) chemical precipitated hundreds of RNA-binding proteins with significant overlap to the constituents of RNA granules. The LC sequences within these proteins are both necessary and sufficient for b-isox-mediated aggregation, and these domains can undergo a concentration-dependent phase transition to a hydrogel-like state in the absence of the chemical. X-ray diffraction and EM studies revealed the hydrogels to be composed of uniformly polymerized amyloid-like fibers. Unlike pathogenic fibers, the LC sequence-based polymers described here are dynamic and accommodate heterotypic polymerization. These observations offer a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane bound.
  Cell 05/2012; 149(4):753-67. · 32.40 Impact Factor
• Article: Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies.

  Tina W Han, Masato Kato, Shanhai Xie, Leeju C Wu, Hamid Mirzaei, Jimin Pei, Min Chen, Yang Xie, Jeffrey Allen, Guanghua Xiao, Steven L McKnight
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  ABSTRACT: Cellular granules lacking boundary membranes harbor RNAs and their associated proteins and play diverse roles controlling the timing and location of protein synthesis. Formation of such granules was emulated by treatment of mouse brain extracts and human cell lysates with a biotinylated isoxazole (b-isox) chemical. Deep sequencing of the associated RNAs revealed an enrichment for mRNAs known to be recruited to neuronal granules used for dendritic transport and localized translation at synapses. Precipitated mRNAs contain extended 3' UTR sequences and an enrichment in binding sites for known granule-associated proteins. Hydrogels composed of the low complexity (LC) sequence domain of FUS recruited and retained the same mRNAs as were selectively precipitated by the b-isox chemical. Phosphorylation of the LC domain of FUS prevented hydrogel retention, offering a conceptual means of dynamic, signal-dependent control of RNA granule assembly.
  Cell 05/2012; 149(4):768-79. · 32.40 Impact Factor
• Source

  Available from: Noelle S Williams

  Article: Discovery of a proneurogenic, neuroprotective chemical.

  Andrew A Pieper, Shanhai Xie, Emanuela Capota, Sandi Jo Estill, Jeannie Zhong, Jeffrey M Long, Ginger L Becker, Paula Huntington, Shauna E Goldman, Ching-Han Shen, [......], Kerstin Ure, Daniel J Brat, Noelle S Williams, Karen S MacMillan, Jacinth Naidoo, Lisa Melito, Jenny Hsieh, Jef De Brabander, Joseph M Ready, Steven L McKnight
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  ABSTRACT: An in vivo screen was performed in search of chemicals capable of enhancing neuron formation in the hippocampus of adult mice. Eight of 1000 small molecules tested enhanced neuron formation in the subgranular zone of the dentate gyrus. Among these was an aminopropyl carbazole, designated P7C3, endowed with favorable pharmacological properties. In vivo studies gave evidence that P7C3 exerts its proneurogenic activity by protecting newborn neurons from apoptosis. Mice missing the gene encoding neuronal PAS domain protein 3 (NPAS3) are devoid of hippocampal neurogenesis and display malformation and electrophysiological dysfunction of the dentate gyrus. Prolonged administration of P7C3 to npas3(-/-) mice corrected these deficits by normalizing levels of apoptosis of newborn hippocampal neurons. Prolonged administration of P7C3 to aged rats also enhanced neurogenesis in the dentate gyrus, impeded neuron death, and preserved cognitive capacity as a function of terminal aging. PAPERCLIP:
  Cell 07/2010; 142(1):39-51. · 32.40 Impact Factor
• Article: Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS.

  Jaeick Lee, Yingda Xu, Yue Chen, Robert Sprung, Sung Chan Kim, Shanhai Xie, Yingming Zhao
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  ABSTRACT: IMAC in combination with mass spectrometry is a promising approach for global analysis of protein phosphorylation. Nevertheless this approach suffers from two shortcomings: inadequate efficiency of IMAC and poor fragmentation of phosphopeptides in the mass spectrometer. Here we report optimization of the IMAC procedure using (32)P-labeled tryptic peptides and development of MS/MS/MS (MS3) for identifying phosphopeptide sequences and phosphorylation sites. The improved IMAC method allowed recovery of phosphorylated tryptic peptides up to approximately 77% with only minor retention of unphosphorylated peptides. MS3 led to efficient fragmentation of the peptide backbone in phosphopeptides for sequence assignment. Proteomics of mitochondrial phosphoproteins using the resulting IMAC protocol and MS3 revealed 84 phosphorylation sites in 62 proteins, most of which have not been reported before. These results revealed diverse phosphorylation pathways involved in the regulation of mitochondrial functions. Integration of the optimized batchwise IMAC protocol with MS3 offers a relatively simple and more efficient approach for proteomics of protein phosphorylation.
  Molecular &amp Cellular Proteomics 05/2007; 6(4):669-76. · 7.40 Impact Factor