Bio

Honors & Awards


  • Stanford Graduate Fellow, Stanford University (2011 - 2014)
  • Chancellor Scholarship and National Scholarship, China Agricultural University (2010)
  • “Triple Excellent” Student of University, China Agricultural University (2009 - 2011)
  • “Xizhi” Education Foundation Scholarship, “Xizhi” Education Foundation (2008)

Education & Certifications


  • Bachelor of Science, China Agricultural University, Biochemistry and Molecular Bio (2011)

Stanford Advisors


  • Rhiju Das, Doctoral Dissertation Advisor (AC)

Publications

All Publications


  • Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic acids research Tian, S., Yesselman, J. D., Cordero, P., Das, R. 2015; 43 (W1): W522-6

    Abstract

    Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both. Online servers are currently not available or maintained for the task. We report here a server named Primerize that makes available an efficient algorithm for primer design developed and experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides. Free access: http://primerize.stanford.edu.

    View details for DOI 10.1093/nar/gkv538

    View details for PubMedID 25999345

  • RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures RNA Miao, Z., Adamiak, R. W., Blanchet, M., Boniecki, M., Bujnicki, J. M., Chen, S., Cheng, C., Chojnowski, G., Chou, F., Cordero, P., Cruz, J. A., Ferre-D'Amare, A. R., Das, R., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T. H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K. J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xia, Y., Xu, X., Zhang, J., Zha, P., Zok, T., Westhof, E. 2015; 21 (6): 1066-1084

    Abstract

    This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.

    View details for DOI 10.1261/rna.049502.114

    View details for Web of Science ID 000356316200002

    View details for PubMedID 25883046

  • RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature Xue, S., Tian, S., Fujii, K., Kladwang, W., Das, R., Barna, M. 2015; 517 (7532): 33-38

    Abstract

    Emerging evidence suggests that the ribosome has a regulatory function in directing how the genome is translated in time and space. However, how this regulation is encoded in the messenger RNA sequence remains largely unknown. Here we uncover unique RNA regulons embedded in homeobox (Hox) 5' untranslated regions (UTRs) that confer ribosome-mediated control of gene expression. These structured RNA elements, resembling viral internal ribosome entry sites (IRESs), are found in subsets of Hox mRNAs. They facilitate ribosome recruitment and require the ribosomal protein RPL38 for their activity. Despite numerous layers of Hox gene regulation, these IRES elements are essential for converting Hox transcripts into proteins to pattern the mammalian body plan. This specialized mode of IRES-dependent translation is enabled by an additional regulatory element that we term the translation inhibitory element (TIE), which blocks cap-dependent translation of transcripts. Together, these data uncover a new paradigm for ribosome-mediated control of gene expression and organismal development.

    View details for DOI 10.1038/nature14010

    View details for PubMedID 25409156

  • Consistent global structures of complex RNA states through multidimensional chemical mapping. eLife Cheng, C. Y., Chou, F., Kladwang, W., Tian, S., Cordero, P., Das, R. 2015; 4

    Abstract

    Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

    View details for DOI 10.7554/eLife.07600

    View details for PubMedID 26035425

  • High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states RNA-A PUBLICATION OF THE RNA SOCIETY Tian, S., Cordero, P., Kladwang, W., Das, R. 2014; 20 (11): 1815-1826
  • Standardization of RNA Chemical Mapping Experiments BIOCHEMISTRY Kladwang, W., Mann, T. H., Becka, A., Tian, S., Kim, H., Yoon, S., Das, R. 2014; 53 (19): 3063-3065

    Abstract

    Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing. We show that simple dilutions, referencing standards (GAGUA hairpins), and HiTRACE/MAPseeker analysis allow rigorous overmodification correction, background subtraction, and normalization for electrophoretic data and a ligation bias correction needed for accurate deep sequencing data. Comparisons across six noncoding RNAs stringently test the proposed standardization of dimethyl sulfate (DMS), 2'-OH acylation (SHAPE), and carbodiimide measurements. Identification of new signatures for extrahelical bulges and DMS "hot spot" pockets (including tRNA A58, methylated in vivo) illustrates the utility and necessity of standardization for quantitative RNA mapping.

    View details for DOI 10.1021/bi5003426

    View details for Web of Science ID 000336413700001

    View details for PubMedID 24766159

  • The glutamate carboxypeptidase AMP1 mediates abscisic acid and abiotic stress responses in Arabidopsis. New phytologist Shi, Y., Wang, Z., Meng, P., Tian, S., Zhang, X., Yang, S. 2013; 199 (1): 135-150

    Abstract

    ALTERED MERISTEM PROGRAM1 (AMP1) encodes a glutamate carboxypeptidase that plays an important role in shoot apical meristem development and phytohormone homeostasis. We isolated a new mutant allele of AMP1, amp1-20, from a screen for abscisic acid (ABA) hypersensitive mutants and characterized the function of AMP1 in plant stress responses. amp1 mutants displayed ABA hypersensitivity, while overexpression of AMP1 caused ABA insensitivity. Moreover, endogenous ABA concentration was increased in amp1-20- and decreased in AMP1-overexpressing plants under stress conditions. Application of ABA reduced the AMP1 protein level in plants. Interestingly, amp1 mutants accumulated excess superoxide and displayed hypersensitivity to oxidative stress. The hypersensitivity of amp1 to ABA and oxidative stress was partially rescued by reactive oxygen species (ROS) scavenging agent. Furthermore, amp1 was tolerant to freezing and drought stress. The ABA hypersensitivity and freezing tolerance of amp1 was dependent on ABA signaling. Moreover, amp1 had elevated soluble sugar content and showed hypersensitivity to high concentrations of sugar. By contrast, the contents of amino acids were changed in amp1 mutant compared to the wild-type. This study suggests that AMP1 modulates ABA, oxidative and abotic stress responses, and is involved in carbon and amino acid metabolism in Arabidopsis.

    View details for DOI 10.1111/nph.12275

    View details for PubMedID 23621575

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