Chromatin replication and human diseases
Project Description
In eukaryotes, DNA is packaged into chromatin with nucleosomes as the fundamental repeating unit comprising ~147 base pairs of DNA wrapped around an octamer of histone proteins (two H2A-H2B dimers and one H3-H4 tetramer). Post-translational modifications (PTMs) on histones serve as critical epigenetic marks, defining chromatin states and regulating transcriptional programs essential for cell differentiation and identity.
During cell division, both genetic and epigenetic information must be faithfully transmitted to progeny cells. As DNA replication forks progress along chromatin templates, parental nucleosomes are disassembled. To maintain the epigenetic landscape, evicted histones, along with their PTMs, must be efficiently recycled and reassembled onto newly synthesized DNA, a process termed chromatin replication. Owing to the large size of the genome, chromatin replication is initiated from multiple sites along each chromosome. Each initiation event is carefully controlled.
When this process is not properly regulated, it can lead to either under- or over-replication of chromosomal DNA with catastrophic consequences such as DNA strand breaks, chromosomal rearrangement, and genome instability. It is not surprising that DNA/chromatin replication defects have serious consequences for human health, such as cancer development and even death. Therefore, gaining fundamental knowledge of chromatin replication is crucial for understanding replication-related diseases and developing effective strategies for their treatment.
Despite years of effort, the mechanisms regulating DNA and chromatin replication are not well understood, particularly at a molecular level. To unravel the molecular mechanisms of these processes in detail, high-resolution structures of the relevant protein complexes must be determined at atomic or near atomic resolution. Cryo-EM technology provides exciting opportunities for structural studies of large replication complexes that are rich in flexible motifs and extensions. To date, using cryo-EM approach, we have determined a series of structures of DNA replication complexes, including yeast ORC (yORC, Nature 2018, PNAS2025), human ORC2-5/1-5 (hORC, Cell Discov 2020), yMcm2-7/Cdt1-Mcm2-7 (NSMB 2017), yMCM-DH (Nature 2015), hMCM-DH (Cell 2023), yMCM-DH-DDK (Dbf4-dependent kinase) (Nat Commun 2022), a leading-strand replisome (Nat Commun, 2023), replisome-FACT-histones (Nature 2024), as well as the structure of Menin in complex with H3K79me2 nucleosome (Science 2023). The information derived from these structures provides significant insights into the regulation of replication initiation and epigenetic control in eukaryotes.
Building on these advances, in this project, we aim to investigate the structure and function of other replication complexes related to chromatin replication. The outcomes of this study are expected to provide novel insights into the regulation of genetic and epigenetic inheritance during the cell division cycle.
During cell division, both genetic and epigenetic information must be faithfully transmitted to progeny cells. As DNA replication forks progress along chromatin templates, parental nucleosomes are disassembled. To maintain the epigenetic landscape, evicted histones, along with their PTMs, must be efficiently recycled and reassembled onto newly synthesized DNA, a process termed chromatin replication. Owing to the large size of the genome, chromatin replication is initiated from multiple sites along each chromosome. Each initiation event is carefully controlled.
When this process is not properly regulated, it can lead to either under- or over-replication of chromosomal DNA with catastrophic consequences such as DNA strand breaks, chromosomal rearrangement, and genome instability. It is not surprising that DNA/chromatin replication defects have serious consequences for human health, such as cancer development and even death. Therefore, gaining fundamental knowledge of chromatin replication is crucial for understanding replication-related diseases and developing effective strategies for their treatment.
Despite years of effort, the mechanisms regulating DNA and chromatin replication are not well understood, particularly at a molecular level. To unravel the molecular mechanisms of these processes in detail, high-resolution structures of the relevant protein complexes must be determined at atomic or near atomic resolution. Cryo-EM technology provides exciting opportunities for structural studies of large replication complexes that are rich in flexible motifs and extensions. To date, using cryo-EM approach, we have determined a series of structures of DNA replication complexes, including yeast ORC (yORC, Nature 2018, PNAS2025), human ORC2-5/1-5 (hORC, Cell Discov 2020), yMcm2-7/Cdt1-Mcm2-7 (NSMB 2017), yMCM-DH (Nature 2015), hMCM-DH (Cell 2023), yMCM-DH-DDK (Dbf4-dependent kinase) (Nat Commun 2022), a leading-strand replisome (Nat Commun, 2023), replisome-FACT-histones (Nature 2024), as well as the structure of Menin in complex with H3K79me2 nucleosome (Science 2023). The information derived from these structures provides significant insights into the regulation of replication initiation and epigenetic control in eukaryotes.
Building on these advances, in this project, we aim to investigate the structure and function of other replication complexes related to chromatin replication. The outcomes of this study are expected to provide novel insights into the regulation of genetic and epigenetic inheritance during the cell division cycle.
Supervisor
ZHAI, Yuanliang
Quota
2
Course type
UROP1000
UROP1100
UROP2100
UROP3100
UROP4100
Applicant's Roles
As a UROP researcher in this project, the applicant will:
Conduct Literature Review – Survey current research on epigenetic inheritance, histone recycling, and DNA replication to identify key knowledge gaps.
Perform Experimental Techniques – Gain hands-on experience in:
Molecular biology techniques (DNA cloning, protein expression/purification)
Assist in Data Analysis
Collaborate with Lab Members – Work alongside graduate students/postdocs to troubleshoot experiments and refine methodologies.
Present Findings – Summarize results in lab meetings and contribute to manuscript preparation if applicable.
Conduct Literature Review – Survey current research on epigenetic inheritance, histone recycling, and DNA replication to identify key knowledge gaps.
Perform Experimental Techniques – Gain hands-on experience in:
Molecular biology techniques (DNA cloning, protein expression/purification)
Assist in Data Analysis
Collaborate with Lab Members – Work alongside graduate students/postdocs to troubleshoot experiments and refine methodologies.
Present Findings – Summarize results in lab meetings and contribute to manuscript preparation if applicable.
Applicant's Learning Objectives
Applicant’s Learning Objectives:
Through this UROP experience, the applicant will:
Develop Technical Skills – Master foundational and advanced techniques in chromatin biology and DNA replication.
Understand Epigenetic Mechanisms – Gain a deep conceptual understanding of how histone modifications are inherited during cell division.
Enhance Critical Thinking – Learn to design controlled experiments, interpret complex data, and refine hypotheses.
Improve Scientific Communication – Practice presenting research findings clearly in written and oral formats.
Cultivate Problem-Solving Abilities – Adapt to experimental challenges and contribute to troubleshooting efforts.
Through this UROP experience, the applicant will:
Develop Technical Skills – Master foundational and advanced techniques in chromatin biology and DNA replication.
Understand Epigenetic Mechanisms – Gain a deep conceptual understanding of how histone modifications are inherited during cell division.
Enhance Critical Thinking – Learn to design controlled experiments, interpret complex data, and refine hypotheses.
Improve Scientific Communication – Practice presenting research findings clearly in written and oral formats.
Cultivate Problem-Solving Abilities – Adapt to experimental challenges and contribute to troubleshooting efforts.
Complexity of the project
Moderate