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Indiana University Bloomington

Faculty from several departments participate in our Graduate Program. They are listed according to the following research area.

students in labs

Carl BauerHengyao Niu

Assistant Professor, Molecular and Cellular Biochemistry Department

Office: Simon Hall 400A

Phone: 812/855-8780

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B.S. (1998) Peking University Cell Biology and Genetics
Ph.D. (2007) State University of New York, Stony Brook Molecular and Cellular Biology. Advisor: Nancy Hollingsworth.
Postdoctoral Training (2007-2014) Yale University School of Medicine. Mentor: Patrick Sung.


DNA breaks can arise either from exposure to DNA damaging agents, such as ionizing radiation, genotoxic chemicals, or from injured DNA replication forks. Failure to properly repair these chromosomal lesions may lead to mutagenesis, gross chromosomal rearrangements, and ultimately to cancer. DNA double-strand break (DSB), which may physically break a chromosome, is among the most dangerous DNA lesions and is repaired via two major pathways, Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ). Notably, besides DNA damage repair, DSB processing and repair also play key roles in other pathways of DNA metabolism, e.g. replication fork recovery, telomere maintenance and meiotic chromosome segregation. A long-term interest of our research is to delineate the mechanism of DSB repair and to ascertain its role in various DNA metabolic pathways. In particular, DSB repair takes place within complex organization of chromatin structures. Multiple chromatin modifications, remodelers and histone chaperons either participate directly in the repair process or function indirectly as regulators. Through a multi-disciplinary approach, we will strive to understand the interplay of DSB repair process and chromatin structures.

Representative Publications

Xiangyu Chen, Ray Suhandynata, Rima Suhaney, Beth Rockmill, Neeman Mohibullah, Hengyao Niu, Jason Liang, Hsiao-Chi Lo, Danny E. Miller, Huilin Zhou, Valentin Boerner and Nancy M. Hollingsworth. (2015) Phosphorylation of the synaptonemal complex protein Zip1 regulates crossover formation during meiosis. PLoS Biol. (Accepted)

Hengyao Niu, Catherine J. Potenski, Tamir Danon, Patrick Sung and Hannah Klein. (2015) Specificity of the Srs2-Exo1 interaction at Top1-dependent nicks at ribonucleotides in DNA. Cell Cycle (Accepted)

Danielle S. Krasner, James M. Daley, Patrick Sung* and Hengyao Niu*. (2015) Interplay between Ku and RPA in the restriction of Exo1-mediated DNA break end resection. J. Biol Chem. 290(30): 18806-18816 (*Corresponding authors)

Yupeng Qiu, Hengyao Niu, Lela Vukovic, Patrick Sung and Sua Myong. (2015) Molecular mechanism of resolving trinucleotide repeat hairpin by helicases.  Structure 23(6): 1018-1027

Xiaoyu Xue, Koyi Choi, Jaclyn N. Bonner, Barnabas Szakal, Yu-Hung Chen, Alma Papusha,  Dorina Saro, Hengyao Niu, Grzegorz Ira, Dana Branzei, Patrick Sung and Xiaolan Zhao. (2015) Selective modulation of a DNA motor functions by a histone-fold complex. Genes and Development 29(10): 1000-1005

James M. Daley, Hengyao Niu, Adam S. Miller and Patrick Sung. (2015) Biochemical mechanism of DSB end resection and its regulation.  DNA repair 32: 66-74 (Review)

Fabio Puddu, Tobias Oelschlaegel, Ilaria Guerini, Nicola J Geisler, Hengyao Niu, Mareike Herzog, Israel Salguero, Bernardo Ochoa-Montaño, Emmanuelle Viré, Patrick Sung, David J. Adams, Thomas M Keane and Stephen P. Jackson. (2015) Synthetic-viability genomic screening defines Sae2 function in DNA repair. EMBO J. 34(11): 1509-1522

Zhi Qi, Sy Redding, Ja Y. Lee, Bryan Gibb, YoungHo Kwon, Hengyao Niu, William Gaines, Patrick Sung and Eric C. Greene. (2015) Mechanism of DNA seqeunce alignment during homologous recombination. Cell 160(5): 856-869

Xiaoyu Xue, Koyi Choi, Jaclyn Bonner, Tamara Chiba, YoungHo Kwon, Yuanyuan Xu, Humberto Sanchez, Claire Wyman, Hengyao Niu, Xiaolan Zhao and Patrick Sung. (2014) Restriction of replication fork regression activities by a conserved SMC complex. Molecular Cell 56(3): 436-445

James M. Daley, Tamara Chiba, Xiaoyu Xue, Hengyao Niu and Patrick Sung. (2014) Multifaceted role of the Topo IIIa-RMI1-RMI2 complex and DNA2 in the BLM-dependent pathway of DNA break end resection. Nucleic Acid Research 42(17): 11083-11091

Bryan Gibb, Ling F. Ye, YoungHo Kwon, Hengyao Niu, Patrick Sung and Eric C. Greene. (2014) Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules. Nature Struct. Mol. Biol.  21(10): 893-900

Catherine J. Potenski*, Hengyao Niu*, Patrick Sung and Hannah L. Klein. (2014) Role of Srs2 DNA helicase in limiting mutations arising from misincorporation of ribonucleotides into DNA. (*equal contribution) Nature 511: 251-254

Bryan Gibb, Ling F. Ye, Stephanie C. Gergoudis, YoungHo Kwon, Hengyao Niu, Patrick Sung, and Eric C. Greene. (2014) Concentration-dependent exchange of Replication protein A on single-stranded DNA revealed by single-molecule imaging. PLoS One 9(2): e87922

James M. Daley, Youngho Kwon, Hengyao Niu and Patrick Sung. (2013) Investigation of Homologous Recombination Pathways and Their Regulation. Yale J Biol Med. 86(4):453-461

Marenda A. Wilson, Youngho Kwon, Yuanyuan Xu, Woo-Hyun Chung, Peter Chi, Hengyao Niu, Ryan Mayle, Xuefeng Chen, Anna Malkova, Patrick Sung and Grzegorz Ira. (2013) Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration. Nature 502: 393-396

Nicholas L. Adkins, Hengyao Niu, Patrick Sung and Craig L. Peterson. (2013) Nucleosome dynamics regulate double-strand break processing in homologous recombination. Nature Struct. Mol. Biol. 20(7): 836-842

Ranjith P. Anand, Kartik A. Shah, Hengyao Niu, Patrick Sung, Sergei M. Mirkin and Catherine H. Freudenreich. (2012) Overcoming natural replication barriers: Differential helicase requirements. Nucleic Acid Research 40(3): 1091-1105

Xiao-Feng Zheng, Rohit Prakash, Dorina Saro, Simonne Longerich, Hengyao Niu, Patrick Sung. (2011) Processing of DNA structures via DNA unwinding and branch migration by the S. cerevisiae Mph1 protein. DNA Repair 10(10): 1034-1043

Xuefeng Chen, Henyao Niu, Woo-Hyun Chung, Zhu Zhu, Alma Papusha, Eun Yong Shim, Sang Eun Lee, Patrick Sung and Grzegorz Ira. (2011) Cell cycle regulation of double-strand break end resection by Cdk1-dependent Dna2 phosphorylation. Nature Struct. Mol. Biol. 18(9): 1015-1019

Hengyao Niu, Woo-Hyun Chung, Zhu Zhu, Youngho Kwon, Weixing Zhao, Peter Chi, Rohit Prakash, Changhyun Seong, Dongqing Liu, Lucy Lu, Grzegorz Ira and Patrick Sung. (2010) Mechanism of the ATP-dependent DNA end resection Machinery from Saccharomyces cerevisiae. Nature 467: 108-111

Janine Mok, Philip M. Kim, Hugo Y. K. Lam, Stacy Piccirillo, Xiuqiong Zhou, Grace R. Jeschke, Douglas L. Sheridan, Sirlester A. Parker, Ved Desai, Miri Jwa, Elisabetta Cameroni, Hengyao Niu, Matthew Good, Attila Remenyi, Jia-Lin Nianhan Ma, Yi-Jun Sheu, Holly E. Sassi, Richelle Sopko, Clarence S. M. Chan, Claudio De Virgilio, Nancy M. Hollingsworth, Wendell A. Lim, David F. Stern, Bruce Stillman, Brenda J. Andrews, Mark B. Gerstein, Michael Snyder, and Benjamin E. Turk (2010)  Breaking the protein kinase code through large-scale analysis of yeast phosphorylation motifs.   Science Signaling 3(109): ra12

Hengyao Niu*, Lihong Wan*, Valeria Busygina, Youngho Kwon, Jasmina A. Allen, Xue Li, Ryan C. Kunz, Kazuishi Kubota, Beatrice Wang, Patrick Sung, Kevan M. Shokat, Steven P. Gygi and Nancy M. Hollingsworth. (2009) Mek1 kinase regulates meiotic recombination by phosphorylating Rad54. Molecular Cell 36(3): 393-404 (*equal contribution)

Hengyao Niu*, Steven Raynard* and Patrick Sung. (2009) Mutiplicity of chromosome end processing. Genes and Development 23(13): 1481-1486. (Review) (*equal contribution)

Steven Raynard*, Hengyao Niu* and Patrick Sung. (2008) DNA double-strand break processing: the beginning of the end. Genes and Development 22(21):2903-2907. (Review) (*equal contribution)

Lihong Wan, Hengyao Niu, Bruce Futcher, Chao Zhang, Kevan M. Shokat, Simon J. Boulton and Nancy. M. Hollingsworth, (2008) Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast.  Genes and Development 22: 386-397

Hengyao Niu, Xue Li, Caroline Park, Emily Job, Danesh Moazed, Steven P. Gygi and Nancy M. Hollingsworth, (2007) Mek1 kinase is regulated to suppress double-strand break repair between sister chromatids during budding yeast meiosis. Molecular and Cellular Biology 27(15): 5456-5467 (*equal contribution)

Hengyao Niu*, Lihong Wan*, Bridget Baumgartner, Dana Schaefer, Josef Loidl, and Nancy M. Hollingsworth, (2005) Partner choice during meiosis is regulated by Hop1-promoted dimerization of Mek1. Molecular Biology of the Cell, 16(12): 5804-5818 (*equal contribution)