DNA is the template for DNA replication and RNA transcription, making the maintenance of genome integrity extremely important. The Wu laboratory focuses on understanding mechanisms of genome instability in physiological and pathological processes. By developing bioinformatic approaches and sequencing techniques to probe repair associated DNA synthesis (SAR-seq) and DNA breaks (ENDseq), we aim to explore:
Project
By developing two novel sequencing-based approaches to map single strand breaks (SSBs) and repair synthesis in post-mitotic neurons, we discovered that neuronal enhancers are hotspots of endogenous SSBs and are repaired by both short- and long-patch base excision repair. Furthermore, the SSBs are associated with TET-mediated active DNA demethylation. (Wu, W. et al. Nature, 2021;Wang, D.*,Wu, W*,Callen,E*. et al. Science, 2022).
By utilizing genome-wide DNA double strand break detection assay ENDseq, we have directly probed murine meiotic double strand breaks and end resection. Also, we demonstrated the roles of multiple key regulatory factors in meiotic DSB processing such as ATM, DMC1, PRDM9, and identified a novel SPO11-bound recombination intermediate. (Paiano, J.*, Wu, W.*, et al. Nature communications, 2020).
Repetitive sequence is a major source of DNA damage. They usually are unstable and can form various secondary structures in vivo, including G4 quadruplex, triplex-DNA, cruciform, especially in the absence of mismatch repair. By applying ENDseq and its variants, we have discovered several types of fragile repeats in replication and cancers. (Matos-Rodrigues, G., et al. Molecular Cell, 2022; van Wietmarschen, N., et al Nature, 2020; Tubbs, A., et al. Cell, 2018)
About the PI
Dr. Wu received her B.E. in bioinformatics from Huazhong University of Science and Technology in 2012 and obtained her Ph.D. from the institute of biophysics of the Chinese Academy of Sciences in 2017, where she studied long non-coding RNA in cancer and noncoding RNA associated database development at the laboratory of Prof. Runsheng Chen. As a postdoctoral fellow in the laboratory of Dr. André Nussenzweig at the National Cancer Institute, she focused on studying mechanisms of DNA damage and repair by utilizing various novel sequencing technologies and bioinformatics analysis. She is a recipient of NIH Fellows Award for Research Excellence, NCI Director’s Innovation Award, Shanghai Rising Star Program and Career Development Fund for Young Women Scientists in Life Sciences (Category B) from the Chinese Society of Cell Biology.
Lab members
Jingyang Li, Nanjing Agricultural University, Intern, 2024.7-2024.8
Yichao Zhao, University of Toronto, Intern, 2024.5-2024.6
Ximilan Luo, Hunan University, Intern, 2024.3-2024.4
Fangyi Chen, Northeast Normal University, Intern, 2023.10-2024.5
Hanyu Bai, University of Toronto, Intern, 2023.6-2023.8
Xiaopeng Wu, Tsinghua university, Intern, 2023.2-2023.6
Publications
DNA Damage Atlas: an atlas of DNA damage and repair.
Yu Liang*, Qingqing Yuan*, Qijie Zheng, Zilv Mei, Yawei Song, Huan Yan, Jiajie Yang, Shuheng Wu, Jiao Yuan#, Wei Wu#.
Nucleic Acids Research, 2024, gkad845
Lihui Liu*, Ziyang Liu*, Qinghua Liu*, Wei Wu*, Peng Lin*, Xing Liu*, Yuechuan Zhang, Dongpeng Wang, Briana C Prager, Ryan C Gimple, Jichuan Yu, Weixi Zhao, Qiulian Wu, Wei Zhang, Erzhong Wu, Xiaomin Chen, Jianjun Luo, Jeremy N Rich#, Qi Xie#, TaoJiang#, Runsheng Chen#.
Nature Communications.14(1),7526, 2023.
Active DNA demethylation promotes cell fate specification and the DNA damage response.
Dongpeng Wang*, Wei Wu*#, Elsa Callen*, Raphael Pavani, Nicholas Zolnerowich, Srikanth Kodali, Dali Zong, Nancy Wong, Santiago Noriega, William J. Nathan, Gabriel Matos-Rodrigues, Raj Chari, Michael J. Kruhlak, Ferenc Livak, Michael Ward, Keith Caldecott, Bruno Di Stefano, André Nussenzweig#.
Science. 378(6623):983-989, 2022.
Neuronal enhancers are hotspots for DNA single-strand break repair.
Wei Wu*, Sarah E Hill*, William J Nathan*, Jacob Paiano, Elsa Callen, Dongpeng Wang, Kenta Shinoda, Niek van Wietmarschen, Jennifer M Colón-Mercado, Dali Zong, Raffaella De Pace, Han-Yu Shih, Steve Coon, Maia Parsadanian, Raphael Pavani, Hana Hanzlikova, Solji Park, Seol Kyoung Jung, Peter J McHugh, Andres Canela, Chongyi Chen, Rafael Casellas, Keith W Caldecott#, Michael E Ward#, André Nussenzweig#.
Nature. 593(7859):440-4, 2021.
ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis.
Jacob Paiano*, Wei Wu*, Shintaro Yamada, Nicholas Sciascia, Elsa Callen, Ana Paola Cotrim, Rajashree A Deshpande, Yaakov Maman, Amanda Day, Tanya T Paull, André Nussenzweig#
Nature communications. 12;11(1):1-5, 2020.
Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing.
Zhuo Zhang*, Amanda E Jones*, Wei Wu*, Jinman Kim, Yue Kang, Xiaobao Bi, Yue Gu, Ivan K Popov, Matthew B Renfrow, Marina N Vassylyeva, Dmitry G Vassylyev, Keith E Giles, Dongquan Chen, Ashwath Kumar, Yuhong Fan, Yufeng Tong, Chuan-Fa Liu, Woojin An, Chenbei Chang, Jianjun Luo#, Louise T Chow#, Hengbin Wang#
Proceedings of the National Academy of Sciences. 114 (38), E7949-E7958, 2017.
Y Sun*, G Wei*, H Luo*, W Wu*, G Skogerbø, J Luo, R Chen#
Oncogene. 36 (49), 6774-6783, 2017.
NPInter v3. 0: an upgraded database of noncoding RNA-associated interactions.
Yajing Hao*, Wei Wu*, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao#, Runsheng Chen#
Database. 2016
Jiao Yuan*, Wei Wu*, Chaoyong Xie, Guoguang Zhao, Yi Zhao#, Runsheng Chen#
Nucleic acids research. 42 (D1), D104-D108, 2014.
Resources
DNA Damage Atlas (DDA) is an open access and comprehensive database that collects all publicly available datasets generated by genomic technologies probing for DNA damage and repair intermediates.
NPInter is a database that collects interactions between noncoding RNAs and biomolecules.
News
2024 Oct, Our collaboration paper is accepted in Nature and Shuheng is the co-first author! Huge congrats to Shuheng!
2024 Oct, Yu received the National Scholarship, so proud of you!
2024 Aug, Welcome Zhuo Yu!
2024 July, Welcome our new intern Lang Zhou and Jingyang! Welcome back Wenhan!
2024 Apr, Wei has recieved Career Development Fund for Young Women Scientists in Life Sciences (Category B) from the Chinese Society of Cell Biology!
2024 Mar, Welcome our new intern Ximilan Luo!
2023 Nov, Wei's collabration work about functions of the lncRNA INHEG in Glioma is online in Nature Communications!
2023 Oct, Welcome our new intern Fangyi Chen!
2023 Sep, the first paper in Wu lab has been accepted in Nucleic Acids Research! Big congrats to Yu and Qingqing!
2023 Aug, Welcome our new graduate student Jiaqi!
2023 Jun, Welcome our new intern student Wenhan and Hanyu!
2023 May, Welcome our new graduate student Zilv Mei!
2023 Feb, Welcome our new intern student Xiaopeng Wu!
2023 Jan, Qingqing joined us as a graduate student. Welcome Qingqing!
2022 Oct, Wei's collaboration paper(with Wang, D., and Callen, E. and Nussenzweig, A.) is accepted in Science! Congrats Wei!
2022 Aug, Welcome our first postdoc, Shuheng!
2022 Aug, Jiajie, Yawei and Yu joined as graduate students. Welcome!
2022 Aug, Welcome our lab manager Qijie Zheng!
2022 Aug, The collaboration paper (with Matos-Rodrigues, G., van Wietmarschen, N. and Nussenzweig, A.) on triplex DNA detection by S1-ENDseq is accepted in Molecular Cell.
2022 Aug, Wei gave a virtual talk at Shangdong university.
2022 Jul, Wei gave a talk at HMS-CSSA Frontiers Symposium.
2022 May, We started hiring!
Contact
We are looking for passionate researchers of all stages (graduate students and postdocs to develop together. Please do not hesitate to contact me (wuw@sibcb.ac.cn) directly if you are interested in bioinformatics or DNA damage and repair.
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