Xin Liu is a postdoctoral Research Scientist in the Department of Genetics at Stanford University. Xin holds a PhD in Chemistry from the University of Michigan, Ann Arbor. Her basic research interests include RNA and protein biochemistry, enzymology, cancer immunology, and autoimmune disease. She has published papers in several prestigious journals in the field of biochemistry, including Nature Communications, Journal of American Chemical Society, and Nucleic Acids Research. The highlight of her multidisciplinary research includes the development of high-throughput enzymatic methods to discover anti-microbial agents and to reveal mechanisms behind human mitochondrial diseases, as well as innovative applications of genome engineering and machine-learning to decode principles of RNA editing in human cells. Her current research focuses on the mechanistic study of innate immune pathways.
Education & Certifications
PhD, University of Michigan, Ann Arbor, Chemistry (2013)
MS, Wuhan University, Analytical Chemistry (2007)
BS, Wuhan University, Chemistry (2005)
Postdoctral Research Scientist, Stanford University School of Medicine, Genetics (9/1/2020 - Present)
Postdoctoral Research Fellow, Stanford University School of Medicine, Genetics (10/1/2016 - 8/31/2020)
Postdoctoral Research Fellow, Stanford University, Chemistry (9/1/2015 - 9/30/2016)
Postdoctoral Research Fellow, University of Michigan, Ann Arbor, Chemistry (8/17/2013 - 8/25/2015)
Ann Arbor, MI
Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis.
2021; 12 (1): 2165
Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs. Despite a compelling need towards predictive understanding of natural and engineered editing events, how the RNA sequence and structure determine the editing efficiency and specificity (i.e., cis-regulation) is poorly understood. We apply a CRISPR/Cas9-mediated saturation mutagenesis approach to generate libraries of mutations near three natural editing substrates at their endogenous genomic loci. We use machine learning to integrate diverse RNA sequence and structure features to model editing levels measured by deep sequencing. We confirm known features and identify new features important for RNA editing. Training and testing XGBoost algorithm within the same substrate yield models that explain 68 to 86 percent of substrate-specific variation in editing levels. However, the models do not generalize across substrates, suggesting complex and context-dependent regulation patterns. Our integrative approach can be applied to larger scale experiments towards deciphering the RNA editing code.
View details for DOI 10.1038/s41467-021-22489-2
View details for PubMedID 33846332
- Updates to the RNA mapping database (RMDB), version 2 NUCLEIC ACIDS RESEARCH 2018; 46 (D1): D375–D379
Fluorescence-Based Real-Time Activity Assays to Identify RNase P Inhibitors.
Methods in molecular biology (Clifton, N.J.)
2017; 1520: 201-225
Transfer RNA is transcribed as precursor molecules that are processed before participating in translation catalyzed by the ribosome. Ribonuclease P is the endonuclease that catalyzes the 5' end maturation of precursor tRNA and it is essential for cell survival. Bacterial RNase P has a distinct subunit composition compared to the eukaryal counterparts; therefore, it is an attractive antibacterial target. Here, we describe a real-time fluorescence-based RNase P activity assay using fluorescence polarization/anisotropy with a 5' end fluorescein-labeled pre-tRNA(Asp) substrate. This FP/FA assay is sensitive, robust, and easy to transition to a high-throughput mode and it also detects ligands that interact with pre-tRNA. We apply this FP/FA assay to measure Bacillus subtilis RNase P activity under single and multiple turnover conditions in a continuous format and a high-throughput screen of inhibitors, as well as determining the dissociation constant of pre-tRNA for small molecules.
View details for DOI 10.1007/978-1-4939-6634-9_12
View details for PubMedID 27873254
Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.
Journal of the American Chemical Society
2017; 139 (48): 17457–63
Identification of the function of metal ions and the RNA moieties, particularly nucleobases, that bind metal ions is important in RNA catalysis. Here we combine single-atom and abasic substitutions to probe functions of conserved nucleobases in ribonuclease P (RNase P). Structural and biophysical studies of bacterial RNase P propose direct coordination of metal ions by the nucleobases of conserved uridine and guanosine in helix P4 of the RNA subunit (P RNA). To biochemically probe the function of metal ion interactions, we substituted the universally conserved bulged uridine (U51) in the P4 helix of circularly permuted Bacillus subtilis P RNA with 4-thiouridine, 4-deoxyuridine, and abasic modifications and G378/379 with 2-aminopurine, N7-deazaguanosine, and 6-thioguanosine. The functional group modifications of U51 decrease RNase P-catalyzed phosphodiester bond cleavage 16- to 23-fold, as measured by the single-turnover cleavage rate constant. The activity of the 4-thiouridine RNase P is partially rescued by addition of Cd(II) or Mn(II) ions. This is the first time a metal-rescue experiment provides evidence for inner-sphere divalent metal ion coordination with a nucleobase. Modifications of G379 modestly decrease the cleavage activity of RNase P, suggesting outer-sphere coordination of O6 on G379 to a metal ion. These data provide biochemical evidence for catalytically important interactions of the P4 helix of P RNA with metal ions, demonstrating that the bulged uridine coordinates at least one catalytic metal ion through an inner-sphere interaction. The combination of single-atom and abasic nucleotide substitutions provides a powerful strategy to probe functions of conserved nucleobases in large RNAs.
View details for PubMedID 29116782
The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions.
2016; 6 (2)
Ribonuclease P (RNase P) is an essential endonuclease responsible for catalyzing 5' end maturation in precursor transfer RNAs. Since its discovery in the 1970s, RNase P enzymes have been identified and studied throughout the three domains of life. Interestingly, RNase P is either RNA-based, with a catalytic RNA subunit, or a protein-only (PRORP) enzyme with differential evolutionary distribution. The available structural data, including the active site data, provides insight into catalysis and substrate recognition. The hydrolytic and kinetic mechanisms of the two forms of RNase P enzymes are similar, yet features unique to the RNA-based and PRORP enzymes are consistent with different evolutionary origins. The various RNase P enzymes, in addition to their primary role in tRNA 5' maturation, catalyze cleavage of a variety of alternative substrates, indicating a diversification of RNase P function in vivo. The review concludes with a discussion of recent advances and interesting research directions in the field.
View details for DOI 10.3390/biom6020027
View details for PubMedID 27187488
Noncanonical Secondary Structure Stabilizes Mitochondrial tRNA(Ser(UCN)) by Reducing the Entropic Cost of Tertiary Folding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2015; 137 (10): 3592-3599
Mammalian mitochondrial tRNA(Ser(UCN)) (mt-tRNA(Ser)) and pyrrolysine tRNA (tRNA(Pyl)) fold to near-canonical three-dimensional structures despite having noncanonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these noncanonical tRNAs compensate for their loss of tertiary interactions remains unclear. Furthermore, in human mt-tRNA(Ser), lengthening the variable loop by the 7472insC mutation reduces mt-tRNA(Ser) concentration in vivo through poorly understood mechanisms and is strongly associated with diseases such as deafness and epilepsy. Using simulations of the TOPRNA coarse-grained model, we show that increased topological constraints encoded by the unique secondary structure of wild-type mt-tRNA(Ser) decrease the entropic cost of folding by ∼2.5 kcal/mol compared to canonical tRNA, offsetting its loss of tertiary interactions. Further simulations show that the pathogenic 7472insC mutation disrupts topological constraints and hence destabilizes the mutant mt-tRNA(Ser) by ∼0.6 kcal/mol relative to wild-type. UV melting experiments confirm that insertion mutations lower mt-tRNA(Ser) melting temperature by 6-9 °C and increase the folding free energy by 0.8-1.7 kcal/mol in a largely sequence- and salt-independent manner, in quantitative agreement with our simulation predictions. Our results show that topological constraints provide a quantitative framework for describing key aspects of RNA folding behavior and also provide the first evidence of a pathogenic mutation that is due to disruption of topological constraints.
View details for DOI 10.1021/ja5130308
View details for Web of Science ID 000351420800028
View details for PubMedID 25705930
A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P
NUCLEIC ACIDS RESEARCH
2014; 42 (20)
Ribonuclease P (RNase P) is an essential endonuclease that catalyzes the 5' end maturation of precursor tRNA (pre-tRNA). Bacterial RNase P is an attractive potential antibacterial target because it is essential for cell survival and has a distinct subunit composition compared to the eukaryal counterparts. To accelerate both structure-function studies and discovery of inhibitors of RNase P, we developed the first real-time RNase P activity assay using fluorescence polarization/anisotropy (FP/FA) with a 5' end fluorescein-labeled pre-tRNAAsp substrate. This FP/FA assay also detects binding of small molecules to pre-tRNA. Neomycin B and kanamycin B bind to pre-tRNAAsp with a Kd value that is comparable to their IC50 value for inhibition of RNase P, suggesting that binding of these antibiotics to the pre-tRNA substrate contributes to the inhibitory activity. This assay was optimized for high-throughput screening (HTS) to identify specific inhibitors of RNase P from a 2880 compound library. A natural product derivative, iriginol hexaacetate, was identified as a new inhibitor of Bacillus subtilis RNase P. The FP/FA methodology and inhibitors reported here will further our understanding of RNase P molecular recognition and facilitate discovery of antibacterial compounds that target RNase P.
View details for DOI 10.1093/nar/gku850
View details for Web of Science ID 000347693200007
View details for PubMedID 25249623
View details for PubMedCentralID PMC4227764
Ligand Concentration Regulates the Pathways of Coupled Protein Folding and Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2014; 136 (3): 822-825
Coupled ligand binding and conformational change plays a central role in biological regulation. Ligands often regulate protein function by modulating conformational dynamics, yet the order in which binding and conformational change occurs are often hotly debated. Here we show that the "conformational selection versus induced fit" distinction on which this debate is based is a false dichotomy because the mechanism depends on ligand concentration. Using the binding of pyrophosphate (PPi) to Bacillus subtilis RNase P protein as a model, we show that coupled reactions are best understood as a change in flux between competing pathways with distinct orders of binding and conformational change. The degree of partitioning through each pathway depends strongly on PPi concentration, with ligand binding redistributing the conformational ensemble toward the folded state by both increasing folding rates and decreasing unfolding rates. These results indicate that ligand binding induces marked and varied changes in protein conformational dynamics, and that the order of binding and conformational change is ligand concentration dependent.
View details for DOI 10.1021/ja4086726
View details for Web of Science ID 000330202300001
View details for PubMedID 24364358
View details for PubMedCentralID PMC3977005
RNase P enzymes Divergent scaffolds for a conserved biological reaction
2013; 10 (6): 909-914
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of precursor-tRNAs (pre-tRNA) and is conserved in all domains of life. However, the composition of RNase P varies from bacteria to archaea and eukarya, making RNase P one of the most diverse enzymes characterized. Most known RNase P enzymes contain a large catalytic RNA subunit that associates with one to 10 proteins. Recently, a protein-only form of RNase P was discovered in mitochondria and chloroplasts of many higher eukaryotes. This proteinaceous RNase P (PRORP) represents a new class of metallonucleases. Here we discuss our recent crystal structure of PRORP1 from Arabidopsis thaliana and speculate on the reasons for the replacement of catalytic RNA by a protein catalyst. We conclude, based on an analysis of the catalytic efficiencies of ribonucleoprotein (RNP) and PRORP enzymes, that the need for greater catalytic efficiency is most likely not the driving force behind the replacement of the RNA with a protein catalyst. The emergence of a protein-based RNase P more likely reflects the increasing complexity of the biological system, including difficulties in importation into organelles and vulnerability of organellar RNAs to cleavage.
View details for DOI 10.4161/rna.24513
View details for Web of Science ID 000327574000002
View details for PubMedID 23595059
View details for PubMedCentralID PMC3904588
Mixed Inhibition of Adenosine Deaminase Activity by 1,3-Dinitrobenzene: A Model for Understanding Cell-Selective Neurotoxicity in Chemically-Induced Energy Deprivation Syndromes in Brain
2012; 125 (2): 509-521
Astrocytes are acutely sensitive to 1,3-dinitrobenzene (1,3-DNB) while adjacent neurons are relatively unaffected, consistent with other chemically-induced energy deprivation syndromes. Previous studies have investigated the role of astrocytes in protecting neurons from hypoxia and chemical injury via adenosine release. Adenosine is considered neuroprotective, but it is rapidly removed by extracellular deaminases such as adenosine deaminase (ADA). The present study tested the hypothesis that ADA is inhibited by 1,3-DNB as a substrate mimic, thereby preventing adenosine catabolism. ADA was inhibited by 1,3-DNB with an IC(50) of 284 μM, Hill slope, n = 4.8 ± 0.4. Native gel electrophoresis showed that 1,3-DNB did not denature ADA. Furthermore, adding Triton X-100 (0.01-0.05%, wt/vol), Nonidet P-40 (0.0015-0.0036%, wt/vol), or bovine serum albumin (0.05 mg/ml or changing [ADA] (0.2 and 2 nM) did not substantially alter the 1,3-DNB IC(50) value. Likewise, dynamic light scattering showed no particle formation over a (1,3-DNB) range of 149-1043 μM. Kinetics revealed mixed inhibition with 1,3-DNB binding to ADA (K(I) = 520 ± 100 μM, n = 1 ± 0.6) and the ADA-adenosine complex (K(IS) = 262 ± 7 μM, n = 6 ± 0.6, indicating positive cooperativity). In accord with the kinetics, docking predicted binding of 1,3-DNB to the active site and three peripheral sites. In addition, exposure of DI TNC-1 astrocytes to 10-500 μM 1,3-DNB produced concentration-dependent increases in extracellular adenosine at 24 h. Overall, the results demonstrate that 1,3-DNB is a mixed inhibitor of ADA and may thus lead to increases in extracellular adenosine. The finding may provide insights to guide future work on chemically-induced energy deprivation.
View details for DOI 10.1093/toxsci/kfr317
View details for Web of Science ID 000299346000018
View details for PubMedID 22106038
View details for PubMedCentralID PMC3262860
Wheat germ agglutinin-modified trifunctional nanospheres for cell recognition
2007; 18 (6): 1749-1755
A simple and convenient strategy has been put forward to fabricate smart fluorescent magnetic wheat germ agglutinin-modified trifunctional nanospheres (WGA-TFNS) for recognition of human prostate carcinoma DU-145 cells which are surface-expressed with sialic acid and N-acetylglucosamine. These TFNS can be easily manipulated, tracked, and conveniently used to capture and separate target cells. The presence of wheat germ agglutinin on the surface of WGA-TFNS was confirmed by FTIR, biorecognition of carboxymethyl chitin-modified quantum dots (CM-CT-QDs), and bacterium Staphylococcus aureus. The success in recognizing DU-145 cells by the WGA-TFNS indicates that WGA-TFNS could be applicable.
View details for DOI 10.1021/bc060387g
View details for Web of Science ID 000251166400010
View details for PubMedID 17894449