Hong Ye: Professor, Doctoral Supervisor, Independent Principal Investigator (PI), Lab Head. He received his B.S. from Shandong University in 2005 and his Ph.D. from the State Key Laboratory of Microbial Technology at Shandong University in 2011. During his doctoral studies, he conducted joint training at the Max Planck Institute for Terrestrial Microbiology in Germany. After graduation, he worked as a postdoctoral researcher at the Centre for Gene Regulation and Expression at the University of Dundee, UK, and at the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU). He returned to China in 2019 and joined Shandong University as a Qilu Young Scholar. His lab primarily uses the model organism Caenorhabditis elegans to study the molecular mechanisms underlying genome stability maintenance in germ cells and early embryos. As corresponding author, his research has been published in high-impact international journals including Science, Science Advances, PLOS Biology, Nucleic Acids Research, and PLoS Pathogens. His lab also collaborates with experts in environmental science and medicine, such as participating in the development of novel photocatalytic materials for degrading per- and polyfluoroalkyl substances (PFAS) in water (primarily responsible for toxicological evaluation; Nature Water, 2026; Water Research, 2026), and contributing to the analysis of genetic risk factors for human premature ovarian insufficiency (POI) (Fundamental Research, 2025). In addition, he serves as a Young Editorial Board Member for the journal Genome Instability & Disease and acts as a reviewer for multiple prestigious international journals, including Genes & Development and PLOS Biology.

Research

Mechanisms of genome stability maintenance in germ cells and early embryos, and genetic mechanisms underlying gametogenesis failure such as premature ovarian insufficiency (POI) and non-obstructive azoospermia.

1. Identification and Functional Analysis of Novel Replisome Components in Multicellular Animals

DNA replication is one of the most fundamental biological processes, responsible for the faithful transmission of genetic information within cells. Defects caused by DNA replication errors lead to genomic instability, a key factor in major human diseases including aging and cancer. In particular, early embryonic development undergoes a rapid phase of cell proliferation and division, during which DNA replication faces enormous stress. The precise regulation of replication directly determines the quality of early embryos and thus affects the growth and development of the organism later in life. To date, our fundamental understanding of eukaryotic DNA replication has primarily come from the unicellular eukaryote Saccharomyces cerevisiae, while much less is known about DNA replication in multicellular animals.

Using the model organism C. elegans, our lab and collaborators have systematically identified the components of the replisome, the macromolecular machine responsible for DNA replication in multicellular animals. We discovered that the DONSON gene dnsn-1, closely associated with Microcephalic Primordial Dwarfism (MPD), plays an important role in DNA replication initiation. We further elucidated the specific mechanism by which the DNSN-1 protein mediates the assembly of the CMG helicase complex at replication initiation sites, revealing significant differences in DNA replication initiation between multicellular metazoans and unicellular S. cerevisiae. This research compensates for the limitations of the model organism S. cerevisiae in studying replication-defective complex diseases such as MPD, provides new directions for deeper exploration of the molecular mechanisms of metazoan DNA replication initiation, and lays an important foundation for the diagnosis and treatment of related diseases (Science, 2023).

2. Assembly and Disassembly Mechanisms of Pro-crossover Complexes Involved in Crossover Formation during Meiosis

Unlike early embryonic cells, germ cells programmatically induce DNA double-strand breaks (DSBs) during meiosis. Through homologous recombination repair, these DSBs facilitate genetic exchange between homologous chromosomes from paternal and maternal origins, thereby increasing genetic diversity in offspring. They also form transient connections between chromosomes, ensuring accurate chromosome segregation during later stages. The crossover recombination process is complex and tightly regulated by a conserved class of pro-crossover proteins, whose dysfunction leads to genomic instability in germ cells and is a major cause of human infertility. However, the mechanisms by which these pro-crossover proteins function in crossover recombination remain unclear.

Our lab has elucidated the interactions between pro-crossover proteins, identified the critical impact of these protein-protein interactions on meiotic crossover recombination, and revealed the mechanism by which pro-crossover protein complexes promote crossover formation during meiotic prophase (Science Advances, 2026; PLoS Biology, 2026; Nucleic Acids Research, 2024). This research not only enhances our understanding of genome maintenance mechanisms in germ cells but also provides new perspectives on the genetic mechanisms of gametogenesis failure, while offering more theoretical basis for expanding the screening list of infertility-related genes.

Publications (^#First author，*Corresponding author)

           2026

1.  Liu G, Yang Y, Nan W, Xiao T, Guo Z, Zhang M, Wang Y, Wu X, Gartner A, Zhang H*,Hong Y* . COSA-1-SLX-4 interaction directly links crossover designation with Holliday junction resolution. Science Advances. (2026);12(17):eadx9148. 

2. Zhang H, Liang W, Li M, Yang Y, He L, Nan W, Liu G, Wang B, Hong Y*. Ubiquitin-proteasome system regulates pro-crossover protein dynamics during meiosis in Caenorhabditis elegans. PLoS Biology. 2026 Jun 16;24(6):e3003868.

3. Wang S, Han W, Zhao B, Hong Y*, Li J*, Miao J*, Lin Z*. A novel SO2 probe inhibits lysophagy induced by Senecavirus A infection by promoting LAMP1 Cys375 sulfenylation. PLoS Pathogens. (2026);22(2):e1013932.

4. Nan W, Li P, Liu G, He L, Zhang M, Gao H, Wang B, Yu Z, Zhang H, Li A*, Hong Y*. RBPL-1 Promotes Meiotic Homolog Pairing Through Its Conserved DWNN Domain in Caenorhabditis elegans.FASEB Journal. (2026);40(9):e71869.

5. Liu F, Li H, Gao Z, Song Q, Cullen P J, Nie Z, Hong Y, Zhang Y, Yao S, Gu C, Meng F, Zuo Z, Liu R*, Chen Z*, Ma D, Yin Y, Cai Y, Duan X*, Zhang Q*. Steering charge transfer in CuInS2/BiOCl composites to enable sunlight-driven C–F bond cleavage of PFAS in water. Nature Water(2026); 4, 334–347.

6. Song X, Xue H, Li H, Liang J, Ji X, Song Q, Cullen PJ, Hong Y, Liu R, Duan X, Zhang Q, Yin Y, Cai Y. Burstein-Moss band engineering of amine-functionalised In2S3 for visible-light photocatalytic degradation of PFAS. Water Research. 2026 Jul 12;305:126489.

2025

1. Xi Y, Liu J, Zhao Y, Hong Y*. Breaking the stability paradox: mScarlet3-H enables long-term super-resolution and CLEM imaging. The Innovation Life (2025); 3:100174.

2.  Li Y, Cao Z, Gao J, Xu P, Gao Y, He L, Ji W, Qin Y, Hong Y, Guo T*, Wang Y*. Genetic variants in the homologous recombination pathway as common risk for premature ovarian insufficiency and ovarian cancer. Fundamental Research (2025)

3. Song J, Geary P, Salemova K, Rouse J, Hong Y, Rolland SGM, Gartner A. Functional dissection of the conserved C. elegans LEM-3/ANKLE1 nuclease reveals a crucial requirement for the LEM-like and GIY-YIG domains for DNA bridge processing. Nucleic Acids Research. (2025). gkaf265.

2024

1. Yang Y, Wang N, Liu G, Nan W, Wang B, Gartner A, Zhang H*, Hong Y*. COSA-1 mediated pro-crossover complex formation promotes meiotic crossing over in C. elegans. Nucleic Acids Research, (2024). gkae130

2.Odiba AS, Liao G, Ezechukwu CS,Liao G, Hong Y, Fang W,Jin C, Gartner A, Wang B. SMC-5/6 complex subunit NSE-1 plays a crucial role in meiosis and DNA repair in Caenorhabditis elegans. DNA repair.(2024).103669

2023

1.Xia Y, Sonneville R, Jenkyn-Bedford M, Ji L, Alabert C, Hong Y*, Yeeles JTP*, Labib KPM*. DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans. Science. (2023);381(6664):eadi4932.

2.Odiba AS, Liao G, Ezechukwu CS, Zhang L, Hong Y, Fang W, Jin C, Gartner A, Wang B. Caenorhabditis elegansNSE3 homolog (MAGE-1) is involved in genome stability and acts in inter-sister recombination during meiosis. Genetics. (2023);225(2):iyad149. 

Other publications

1. Ji LQ, Hong Y, Tao YX. Melanocortin-5 Receptor: Pharmacology and Its Regulation of Energy Metabolism. International Journal of Molecular Sciences. (2022);23(15):8727.

2. Hong Y*, Zhang H, and Gartner A*. The Last Chance Saloon. Frontiers in Cell and Developmental Biology (2021)9, 671297.

3.Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M, Gartner A. Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation. PLOS One. (2021);16(4):e0250291.

4.Hong Y#,Sonneville R,Wang B,Woglar A,Labib K,Jantsch V,Gartner A*.LEM-3 is a midbody- tethered DNA nuclease that resolves chromatin bridges during late mitosis. Nature Communications (2018),9,728

5.Hong Y# ,Velkova M,Silva N,Jagut M,Scheidt V,Labib K,Jantsch V andGartner A*.Theconserved LEM-3/Ankle1 nuclease is involved in meiotic recombination and chromosome segregation in Caenorhabditis elegans. PLOS Genetics (2018) 14(6): e1007453.

6.Meier B, Volkova N, Hong Y, Schofield P, Campbell PJ, Gerstung M*, Gartner A*.Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers.Genome Research(2018), 28(5):666-675

7. Bertolini S, Wang B, Meier B, Hong Y, Gartner A*. Caenorhabditis elegans BUB-3 and SAN-1/MAD3 Spindle Assembly Checkpoint Components Are Required for Genome Stability in Response to Treatment with Ionizing Radiation. G3 (Bethesda). 2017;7(12):3875-3885. 

8.Hong Y#,Sonneville R,Agostinho A, Meier B, Wang B,Blow J,Gartner A*. TheSMC-5/6 complex and the HIM-6 (BLM) helicase synergistically promote meioticr ecombination intermediate processing and chromosome maturation during C.elegans meiosis.PLOS Genetics(2016) 24;12(3):e1005

9.Shlien A*, Campbell BB, deBorja R, Alexandrov LB, Merico D, Wedge D,VanLoo P, Tarpey PS, Coupland P,Behjati S, Pollett A, Lipman T, Heidari A,Deshmukh S,Avitzur N,Meier B,Gerstung M,Hong Y, Merino DM, Ramakrishna M,Remke M,ArnoldR,PanigrahiGB,Thakkar NP, Hodel KP, Henninger EE,Göksenin AY,Bakry D,Charames GS,Druker H,Lerner-Ellis J, Mistry M,Dvir R,Grant R,Elhasid R,Farah R,Taylor GP,Nathan PC,Alexander S,Ben-Shachar S,Ling SC,Gallinge rS,Constantini S,Dirks P,Huang A,Scherer SW,Grundy RG,Durno C,Aronson M,Gartner A,Meyn MS,Taylor MD,Pursell ZF,Pearson CE,Malkin D,Futreal PA,Stratton MR,Bouffet E,Hawkins C,CampbellPJ,TaboriU; Biallelic Mismatch Repair Deficiency Consortium. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hyper mutated cancers.Nat Genetics.(2015),3,257-262.

10.Hong Y#, Wang Z, Zhang Z, Ma X, Ni J, Sheng D, Shen Y*. Dissection of the functional domains of an archaeal Holliday junction helicase. DNA repair. (2012),2,102-111