Sun Lab

Lei Sun （孙磊），PI

I started RNA strcuturome lab at Shandong University (Qingdao) in December of 2022. Our lab broadly interested in RNA biology, especially RNA structure biology, RNA vaccine and adaptor design, and anti-RNA virus drug development (such as SARS-CoV-2). Our lab will develop and use a combination of computational and experimental methods to interpret the structural and functional relationships of biological macromolecules, build the interaction network, uncover the regulation mechanism and find the potential therapy for diseases based on high-throughput sequencing, bioinformatics analysis, artificial intelligence (AI) prediction, and experimental validation.

From 2019 to 2022， I was a Postdoc researcher at Tsinghua University, cooperating with Prof. Qiangfeng Cliff Zhang. Before my Postdoc period, I received my Ph.D. degree in the School of Life Science, Tsinghua University in 2019. Before I came to Tsinghua University, I received a bachelor's degree in Taishan College, Shandong University in 2014.

Please feel free to directly contact me via e-mail for formal or informal inquiries: sunlei0227 at sdu.edu.cn.

What's New

[Mar. 2024] Yuning Liu joined our lab, welcome，Yuning！
[Feb. 2024] Dr. Xiaoyu Zhou joined our lab, welcome，Xiaoyu！
[Jan. 2024] Our Review paper "RNA Structure: Implications in Viral Infections and Neurodegenerative Diseases" was accepted at Advanced Biotechnology. This is the first paper produced by Sunlab only. Congratulations to Suiru, Yongkang and Shaozhen!
[Nov. 2023] Shaozhen Yin joined our lab as an intern, welcome，Shaozhen！
[Oct. 2023] Yule Gu joined our lab for graduation design, welcome，Yule！
[Oct. 2023] Long Qian joined our lab, welcome，Long！
[Sep. 2023] Dr. Jindong Sun joined our lab, welcome，Jindong！
[Sep. 2023] Yuancheng Wang joined our lab, welcome，Yuancheng！
[Sep. 2023] Yang Cheng joined our lab, welcome，Yang！
[Aug. 2023] Jingwen Wang joined our lab, welcome，Jingwen！
[Jul. 2023] Junhao Wang joined our lab, welcome，Junhao！
[Jul. 2023] Ziyou Luo joined our lab, welcome，Ziyou！
[Jun. 2023] Dr. Tong Zhou joined our lab, welcome，Tong！
[May 2023] Our PrismNet web server paper "PrismNet: predicting protein–RNA interaction using in vivo RNA structural information" was accepted at Nucleic Acids Research. This is my first paper in Shandong University.
[May 2023] Chen Yan joined our lab, welcome，Chen！
[May 2023] Jiale He joined our lab, welcome，Jiale！
[Apr. 2023] Dr. Sun gave an invited virtual talk to the Daxue Club about RNA structurome and AI improving drug development.
[Apr. 2023] Ruobin Zhao joined our lab, welcome，Ruobin！
[Apr. 2023] Chengqian Wang joined our lab, welcome，Chengqian！
[Mar. 2023] Suiru Lu joined our lab, welcome，Suiru！
[Mar. 2023] Shanghao Dai joined our lab, welcome，Shanghao！
[Feb. 2023] Yongkang Tang joined our lab, welcome，Yongkang！
[Feb. 2023] Lingyun Xu joined our lab, welcome，Lingyun！
[Dec. 2022] Dr.Sun joined the School of Life Science, Shandong University and started the RNA structurome lab.
[Nov. 2022] Our PrismNet method paper win the 2021 Sanofi-Cell Research Outstanding Research Article Award.
[Oct. 2022] Our Review Article paper "Advances and opportunities in RNA structure experimental determination and computational modeling" was online at Nature Methods. congratulations to all the team members.
[Feb. 2022] Our PrismNet method paper was awarded as the Top Ten Advances of 2021 in Bioinformatics in China by Genomics, Proteomics and Bioinformatics (GPB)
[Jan. 2021] Our PrismNet method paper was accepted by Cell Research, congratulations to all the team members.
[Nov. 2020] Our anti-SARS-CoV-2 drugs based on RNA structures paper was accepted by the top journal Cell, congratulations to all the team members.
[Feb. 2019] Our RNA structural dynamics paper in different cell compartments was accepted by Nature Structural & Molecular Biology, congratulations to all the team members.

Research Interest

1. Technology development
Our lab is both interested in experimental and computational methods development. We have taken part in the development of many technologies including subcellular RNA structure determination (Sun et.al., NSMB, 2019 )and RBP-RNA interaction prediction based on artificial intelligence (Sun et.al., Cell Research, 2021). We are also interested in single-cell RNA structure determination, and co-transcriptional transient RNA structure determination in the future.

2. Biological question
RNA structure and RBP-RNA interactions play key roles in post-transcriptional regulation. The regulatory network of viruses can be studied from the perspectives of RNA structure and RNA-protein interaction by icSHAPE, PrismNet, CLIP, and other techniques. Antiviral drugs can be developed by targeting important structural elements of viruses or interacting host proteins (Sun et.al., Cell, 2021). It is important to note that the integration of high-throughput sequencing, deep learning models, and experimental validation provides a viable idea to systematically study the role of RNA-binding proteins. For example, how do RBPs regulate gene expression during zebrafish development?

3. Technical applications
Based on previous work, we have identified a large number of conserved RNA structural elements related to RNA translation, RNA degradation, etc. These RNA structures can be exploited to design RNA molecules that better help the vaccine and RNA targeting drug development. Moreover, the understanding of RNA structure and the application of artificial intelligence can help us to design better gRNA in the RNA therapy field.

Publication

(* co-First authors; # co-Corresponding authors)

11. RNA structure: implications in viral infections and neurodegenerative diseases

Suiru Lu*, Yongkang Tang*, Shaozhen Yin, Lei Sun#

Advanced Biotechnology, 2024 Advanced Biotechnology

10. Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

Pujuan Deng*, Shun-Qing Tan*, Qi-Yu Yang, Liangzheng Fu, Yachao Wu, Han-Zhou Zhu, Lei Sun, Zhangbin Bao, Yi Lin, Qiangfeng Cliff Zhang, Haoyi Wang, Jia Wang#, Jun-Jie Gogo Liu#

Cell 2023 Cell

9. PrismNet: predicting protein–RNA interaction using in vivo RNA structural information

Yiran Xu*, Jianghui Zhu*, Wenze Huang*, Kui Xu, Rui Yang, Qiangfeng cliff Zhang#, Lei Sun#

Nucleic Acids Research, 2023 Nucleic Acids Research Web server

8. Advances and opportunities in RNA structure experimental determination and computational modeling

Jinsong Zhang*, Yuhan Fei*, Lei Sun#, Qiangfeng Cliff Zhang#

Nature Methods 2022 Nature Methods

7. In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs

Lei Sun*, Pan Li*, Xiaohui Ju*, Jian Rao*, Wenze Huang*, Shaojun Zhang, Tuanlin Xiong, Kui Xu, Xiaolin Zhou, Lili Ren, Qiang Ding#, Jianwei Wang# and Qiangfeng Cliff Zhang#

Cell 2021 Cell bioRxiv bibtex

6. Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure

Lei Sun*, Kui Xu*, Wenze Huang*, Yucheng T. Yang*, Pan Li, Lei Tang, Tuanlin Xiong and Qiangfeng Cliff Zhang#

Cell Research 2021 Cell Research bioRxiv code website bibtex

5. Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2.

Shaojun Zhang*, Wenze Huang*, Lili Ren*, Xiaohui Ju*, Mingli Gong*，Jian Rao*, Sun Lei, Pan Li, Qiang Ding#, Jianwei Wang#, Qiangfeng Zhang#

Cell Research 2021 Cell Research

4. RNA structure maps across mammalian cellular compartments.

Lei Sun*, Furqan Fazal*, Pan Li*, James P. Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T. Kool, Howard Y. Chang# and Qiangfeng Cliff Zhang#

Nature Structural & Molecular Biology 2019 NSMB bioRxiv News & Views by NSMB journal

3. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate.

Zhongmin Liu*, Jia Wang*, Hang Cheng*, Xin Ke*, Lei Sun, Qiangfeng Cliff Zhang, Hong-Wei Wang

Cell 2018 Cell

2. Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity.

Pan Li*, Yifan Wei*, Miao Mei*,Lei Tang*, Lei Sun, Wenze Huang, Jianyu Zhou, Chunlin Zou, Shaojun Zhang, Cheng-Feng Qin, Tao Jiang, Jianfeng Dai, Xu Tan#, Qiangfeng Cliff Zhang#

Cell Host & Microbe 2018 Cell Host & Microbe

1. RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing.

Meiling Piao, Lei Sun, Qiangfeng Cliff Zhang#

Genomics Proteomics Bioinformatics 2017 Genomics Proteomics Bioinformatics

Members

Postdoctoral researcher

Tong Zhou （周通),Postdoctoral researcher，Graduated from institute of oceanology, CAS, China. Interested in metagenome, single cell analysis and the third generation sequencing.

Jindong Sun (孙近东),Postdoctoral researcher，Graduated from Shandong University of Science and Technology. Interested in AI model development，especially Deep learning-based multimodal medical image processing.

Xiaoyu Zhou (周晓瑜),Postdoctoral researcher，Graduated from Aarhus University，Denmark. Interested in bioinformatics analysis，especially single cell analysis.

postgraduate students

Welcome to join us！（欢迎你的加入！）

Yongkang Tang (唐永康),research technician，Interested in RNA structome and system analysis

Chengqian Wang (王成前)，Master, Interested in structural analysis and machine learning.

Ruobin Zhao (赵若斌),Master，Interested in RNA structure method development and analysis.

Jingwen Wang(王婧雯),Master，Interested in precision medicine and RNA secondary structure.

Shaozhen Yin(尹绍桢),intern. Interested in structural analysis.

undergraduate students

Jiale He (何嘉乐),undergraduate，Interested in artificial intelligence and RNA structure analysis.

Chen Yan (闫宸),interested in the prediction of RBP and deep learning

Ziyou Luo (罗子游),interested in the bioinformatics analysis expecially ATAC-seq.

Junhao Wang (王峻昊),interested in the bioinformatics analysis expecially CHIP-seq.

Yang Chen (程洋),undergraduate，Interested in RNA editing and gRNA design.

Shanghao Dai (戴尚好),undergraduate，Interested in artificial intelligence，especially RBP-RNA interaction prediction.

Suiru Lu (鲁穗茹),undergraduate，Interested in gRNA design of CRISPR-Cas13 system.

Yuancheng wang (王远铖),interested in analyzing the high-throughput data .

Yuning Liu (刘昱宁),interested in analyzing the high-throughput data.

Yule Gu(谷雨乐),undergraduate，Interested in RNA structures in Archaea.

Alumni

1. Lingyun Xu (许凌云), Class of 2022 undergraduate, 2023.2-2023.6，Change majors to Institute of Frontier and Interdisciplinary Science，Shandong University.
2. Long Qian （钱龙）， Class of 2023 undergraduate, 2023.9-2023.12，Recommended to partner laboratory in Research Center for Mathematics and Interdisciplinary Science, Shandong University.

Join us

We are looking for Master, Ph.D., Postdoctoral, and Research Assistant fellows who are eager to learn about RNA structure, RNA regulation, bioinformatics analysis, and artificial intelligence. We are proud of our work and strive to do rigorous science that matters.

Also, you will have the opportunity to interact with leading experts in viruses, embryonic development, microorganism, and single-cell experimentalists among others. We welcome both experimentalists and computational trainees.

I aim to provide ample supervision, training, and support for trainees to be highly successful in academia or industry. I also encourage trainees to culture a wide range of interests and thus welcome collaborations with other faculty at Shandong University. Overall, I hope to be a great mentor, but also expect you to do your part.

Please feel free to directly contact me via e-mail for formal or informal inquiries: sunlei0227 at hotmail dot com or sunlei0227 at sdu.edu.cn