Work from the Lu lab at USC
Velema WA* and Lu Z* (2023). Chemical RNA crosslinking: mechanisms, computational analysis, and biological applications. JACS Au, in press.
Lee WH and Lu Z* (2023). Integrated analysis of crosslink-ligation data for the detection of RNA 2D/3D conformations in vivo. Methods in Molecular Biology, in press.
Lee WH and Lu Z* (2023). Chemical crosslinking and ligation methods for in vivo analysis of RNA structures and interactions. Methods in Enzymology, in press.
Van Damme R, Li K, Zhang M, Bai J, Lee WH, Yesselman JD, Lu Z* and Velema WA* (2022) (Lu lab members underlined) Chemical Reversible Crosslinking Enables Measurement of RNA 3D Distances and Alternative Conformations in Cells. Nature Communications, 13:911. Recommended by Faculty Opinions, Dr. Janusz Bujnicki (https://facultyopinions.com/article/741670636).
Zhang M, Hwang IT, Li K, Bai J, Chen JF, Weissman T, Zou JY and Lu Z* (2022) Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers. Genome Research, 32: 1-18.
Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z* (2021) Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells and virus infections, Nature Communications, 12:2344.
Zhang W, Ma L, Yang M, Shao Q, Xu J, Lu Z, Zhao Z, Chen R, Chai Y, Chen JF (2020). Cerebral organoid and mouse models reveal a RAB39b–PI3K–mTOR pathway-dependent dysregulation of cortical development leading to macrocephaly/autism phenotypes. Genes & Development 34, 580-597.
Lu Z*, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY (2020). Structural modularity of the XIST ribonucleoprotein complex. Nature Communications, 11:6163
Zhou J, Li P, Zeng W, Ma W, Lu Z, Jiang R, Zhang QC, Jiang T (2020). IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. Quantitative Biology, 1-13
Zhang W, Yang SL, Yang M, Herrlinger S, Shao Q, Collar JL, Fierro E, Shi Y, Liu A, Lu H, Herring BE, Guo ML, Buch S, Zhao Z, Xu J, Lu Z, Chen JF. (2019) Modeling microcephaly with cerebral organoids reveals a WDR62-CEP170-KIF2A pathway promoting cilium disassembly in neural progenitors. Nature Communications. 10:2612
Postdoc work at Stanford University
Lu Z and Chang HY (2018) The RNA Base-pairing Problem and Base-pairing Solutions. Cold Spring Harbor Perspectives in Biology. Also as a book chapter in RNA Worlds: New tools for deep exploration, fifth edition. PDF
Lu Z, Gong J and Zhang QC (2018) PARIS: psoralen analysis of RNA interactions and structures with high throughput and resolution. Methods in Molecular Biology: RNA Detection, 59-84. PDF
Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT and Zhang QC (2017) RISE: a database of RNA Interactome from Sequencing Experiments. Nucleic Acid Research, gkx864. PDF
Lu Z, Carter AC and Chang HY (2017) Mechanistic insights in X chromosome inactivation. Philosophical Transactions of the Royal Society B, 372(1733). PDF
Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY (2016) RNA duplex map in living cells reveals higher order transcriptome structure. Cell, 165 (5): 1267-1279. PDF. Featured on the cover and in a paperclip of Cell (Youtube video: Get an Eye-full (Eiffel)), on the cover of Best of Cell 2016. Highlighted in Nature Methods, Nature Chemical Biology, Molecular Cell and Trends in Biochemical Sciences.
Lu Z, Chang HY (2016) Decoding the RNA structurome. Current Opinion in Structural Biology 36:142- 148. PDF
PhD work at UNC Chapel Hill
Lu Z, Filonov GS, Noto JJ, Schmidt CA, Hatkevich T,Wen Y, Jaffrey SR andMatera AG, (2015) Metazoan tRNA introns generate stable circular RNAs in vivo. RNA 21:1-12. PDF
Lu Z and Matera AG, (2015) Developmental Analysis of Spliceosomal snRNA Isoform Expression. G3: Genes|Genomes|Genetics 5 (1), 103-110. PDF
Lu Z, Guan X, Schmidt CA and Matera AG, (2014) RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins. Genome Biology 15(1):R7. PDF
Lu Z and Matera AG, (2014) Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments. Nucleic Acid Research doi: 10.1093/nar/gku207. PDF
Garcia EL, Lu Z, Meers MP, Praveen K and Matera AG, (2013) Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. RNA 19 (11), 1510-1516. PDF
Undergrad work at Fudan University
Wang H, Zhang SY, Wang S, Lu J, Wu W, Weng L, Chen D, Zhang Y, Lu Z, Yang J, Chen Y, Zhang X, Chen X, Xi C, Lu D, Zhao S, (2009) REV3L confers chemoresistance to cisplatin in human gliomas: The potential of its RNAi for synergistic therapy. Neuro-Oncology 11: 790-802. PDF
Jiang M, Fei J, Lan MS, Lu Z, Liu M, Fan W, Gao X and Lu D, (2008). Hypermethylation of hepatic Gck promoter in ageing rats contributes to diabetogenic potential. Diabetologia, 51: 1525-1533. PDF
Zhipeng Lu Lab @ USC 