Invited Speakers
Masaki Sasai (Nagoya U, Japan) 笹井理生 （日本名古屋大学）
Yiqin Gao (PKU) 高毅勤 （北京大学）
Yujie Sun (PKU) 孙育杰 （北京大学）
Changbong Hyeon (KIAS, Korea) （韩国高等研究院）
Ping Chen /Guohong Li (CAS Biophysics) 陈平/李国红 （中科院生物物理所）
Ming Li (CAS Physics) 李明 （中科院物理所）
Tan Cheng/Shoji Takada (Kyoto U, Japan) 谭丞／高田彰二 （日本京都大学）
Jin Yu (CSRC) 喻进 （北京计算科学研究中心）
Haiguang Liu (CSRC) 刘海广 （北京计算科学研究中心）
Zhucheng Chen (Tsinghua) 陈柱成 （清华大学）
Bing Zhu (CAS Biophysics) 朱冰 （中科院生物物理所）
Xiaodong Su (PKU) 苏晓东 （北京大学）
Zhihu Zhao (Military Medical Science Institute) 赵志虎 （北京军事医学科学院）
Jianhua Xing (U Pittsburgh, USA) 邢建华 （美国匹兹堡大学）
Program Schedule
July 15 Morning Chromatin folding in the cell
1. 9:00 am -9:40 am Masaki Sasai (Nagoya U): The phase-separation principle of human genome folding
2. 9:45 am -10:25 am Yiqin Gao (PKU): Computer modeling of 3-D chromatin structures
Coffee/Teak Break (10:30 – 11:00 )
3. 11:00 am – 11:40 am Yujie Sun (PKU): Probing 3D genome via genomic loci dynamics
4. 11:45 am – 12:25 pm Changbong Hyeon (KIAS): Chain organization and dynamics of chromatin inside cell nucleus
Lunch Break (12:30 – 2:00 pm)
July 15 Afternoon Nucleosome to chromatin and protein-DNA interaction
5. 2:00 pm – 2:40 pm Ping Chen/Guohong Li (CAS Biophysics): Structure and function of the 30-nm chromatin fiber in gene regulation
6. 2:45 pm – 3: 25 pm Ming Li (CAS Physics): High precision single-molecule techniques for molecular biophysics and membrane biophysics
Coffee/Teak Break (3:30 pm – 3:50 pm )
7. 3:50 pm – 4: 30 pm Tan Cheng/Shoji Takada (Kyoto U): Interplay of nucleosome dynamics and protein target search on DNA
8. 4:30 pm – 5:00 pm Jin Yu (CSRC): RNA polymerase transcription elongation dynamics along DNA
9. 5:00 pm – 5:30 pm Haiguang Liu (CSRC) Posttranslational Modification Effects in nucleosome, studied using all-atom molecular dynamics simulations
Dinner reception (6:30 pm – 9:00 pm)
July 16 Morning Epigenetic regulation
10. 9:00 am – 9:40 am Zhucheng Chen (Tsinghua): Structural basis of chromatin remodeling
11. 9:45 am – 10:25 am Bing Zhu (CAS Biophysics): Establishment and Maintenance of Epigenetic Information
Coffee/Teak Break (10:30 – 10:50 )
12. 10:50 am – 11:30 am Xiaodong Su (PKU): The effects of cytosine methylation on general transcription factors
13. 11:30 am – 12: 10 pm Zhihu Zhao (Military Medical Science Institute): Highly abundant and mitotic retained chromatin associated RNAs bookmark active chromatin domains during the cell cycle
14. 12:10 pm – 12: 50 pm Jianhua Xing (U Pittsburgh) Coupling between epigenetic modification and gene expression
Lunch (1 pm- 2 pm)
Afternoon free discussions and leave
Abstracts
1. The phase-separation principle of human genome folding
Shin Fujishiro and Masaki Sasai, Department of Applied Physics, Nagoya University
Email: sasai@nuap.nagoya-u.ac.jp
The 3D organization of mammalian genome should be closely related to the epigenetic state of chromatins. Although this relation has attracted intense interest, the principle that governs the 3D organization of genomes is still unclear. We developed a computational model of human genome by modeling chromosomes as chains of soft-core beads, whose softness is defined by the epigenetic state of the corresponding part of chromatin, while no specific interaction is assumed among beads. With this physics-based approach of modeling, the experimentally observed contact maps and nuclear lamina interactions were well reproduced, which suggested that a major determinant of the 3D genome organization is the spontaneous phase separation of heterochromatin-like and euchromatin-like regions in the nucleus.
2. Computer modeling of 3-D chromatin structures
Yiqin Gao, College of Chemistry and Molecular Engineering, and Biodynamics Optical Imaging Center, Peking University Email: gaoyq@pku.edu.cn
Chromosome structure is essential in many biological studies. Recent Hi-C experimental studies have been improving our understanding of the 3D chromatin. In this talk, we describe the modelling of the chromatin structure utilizing experimental Hi-C data, which provides the spatial details of chromatin. By mapping a number of genome features onto the chromatin model, we discuss the importance of chromatin architecture for genome function. We find that the colocalization of genome features on a linear map coincides their 3D segregation, and thus the latter provides a mechanism for the regulation of various genome properties. In particular, the overall DNA methylation pattern was found to reflect the 3-D organization of the human chromatin. We will also discuss the simulations of DNA/chromatin structures at different scales and therefore the possible mechanism of the hierarchical chromatin packing.
5. Structure and function of the 30-nm chromatin fiber in gene regulation
Guohong Li, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China Email:liguohong@sun5.ibp.ac.cn
Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus, in which the accessibility of DNA is dependent on the packing density of chromatin. Dynamics of chromatin structures plays a critical role in transcriptional regulation and all other DNA related biological processes. Previously, we reported the 11 Å resolution cryo-electron microscopy (cryo-EM) structures of 30 nm chromatin fibers reconstituted in the presence of linker histone H1, which reveals a left-handed double helix twisted by the repeating tetra-nucleosomal structural units. However, the dynamic organization of chromatin fibers and its regulation mechanisms remain poorly understood. Using single-molecule force spectroscopy, we reveal that the tetranucleosomes-on-a-string appears as a stable secondary structure during hierarchical organization of chromatin fibers. The stability of the tetranucleosomal unit is negatively regulated by the histone chaperone FACT (Facilitates Chromatin Transcription) in vitro. Interestingly, we also demonstrated that formation of 30-nm chromatin fibers greatly facilitates the faithful propagation and maintenance of H2AK119ub1 by RYBP-PRC1. In summary, our study demonstrates that the tetranucleosome is a novel regulatory structural unit of chromatin fibers beyond the nucleosome, and provides crucial mechanistic insights into functions of chromatin fibers in transcriptional regulation and epigenetic inheritance.
6． High precision single-molecule techniques for molecular biophysics and membrane biophysics
Ming Li, Ying Lu, Shu-Xin Hu, Chun-Hua Xu, Shuo-Xing Dou
Institute of Physics, Chinese Academy of Sciences, Haidian, Beijing, 100190, China
Email: mingli@iphy.ac.cn
Fluorescent energy transfer has become an indispensable technique for studying dynamics of molecular motors and membrane proteins. The lack of angstrom resolution made it difficult to correlate the results with computer modeling and electron microscopy. Here, we report on our recent efforts in taking advantage of bending elasticity of double-stranded DNA to exert force on the molecules of interest to improve the resolution of fluorescent resonance energy transfer (FRET) to a few angstroms. We validated the method by applying it to study DNA unwinding kinetics of helicases. The resolution is high enough to uncover the differences in DNA unwinding by yeast Pif1 and E. coli RecQ whose unwinding behaviors cannot be differentiated by currently practiced methods. The method is both simple and efficient, and is expected to find wide applications in smFRET studies of helicases and other molecular motors that interact with nucleic acids. We also developed a single-molecule imaging method termed surface-induced fluorescence attenuation (SIFA) to detect trans-membrane positions of individual proteins in lipid bilayers. The resolution is better than one eighth of the thickness of lipid bilayers. The method was validated by observing the antimicrobial peptide LL-37 to transfer among five transmembrane positions: the surface, the upper leaflet, the centre, the lower leaflet and the bottom of the lipid bilayer. The results demonstrated the power of SIFA to study protein-membrane interactions and provide unprecedented in-depth understanding of molecular mechanisms of insertion and translocation of membrane proteins.
7. Interplay of Nucleosome Dynamics and Protein Target Search on DNA
Cheng Tan, Giovanni Brandani, Toru Niina, Shoji TakadaDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan Email address: takada@biophys.kyoto-u.ac.jp
Nucleosomes serve as general repressors by occluding target sequences for transcription factors (TFs). However, recent experiments suggested that some "pioneer" TFs can bind to the target sequences within nucleosomes, playing crucial roles in early stage of gene activation. Despite recent exper-imental results of high-resolution binding positions of pioneer TFs on nu-cleosomal DNA, a detailed structural and dynamic recognition mechanismis still lacking. Here we employed molecular dynamics simulations to investigate the target search of TFs on both bare and nucleosomal DNA, and spontaneous sliding dynamics of the nucleosome. We first developed a new method of modeling the sequence-speci_c protein-DNA interactions based on Position Weight Matrix (PWM) and PDB structure. With several applications, we illustrated the ability of our model to capture the subtlest features in protein-consensus DNA recognition. On the other side, we introduced a new model for hydrogen bonds between DNA and histone proteins and achieved a general and complete picture of spontaneous nucleosome dynamics. Finally, we combined these models together and studied the binding of pioneer TF Oct4 to a nucleosome in Lin28 gene locus. Our results confirmed the previously proposed mechanism of partial motif recognition and revealed a possible interplay between the TF binding and nucleosome dynamics.
9. Posttranslational Modification Effects in nucleosome, studied using all-atom molecular dynamics simulations
Haiguang Liu, Beijing Computational Science Research Center, Email: hgliu@csrc.ac.cn
Post translational modifications are (PTM) frequently found on the histone proteins. In this work, we applied all-atom molecular dynamics simulation methods to study the PTM effects by mutating the lysine residues to its counterpart after acetylation. The histone protein N-terminal peptide, single nucleosome core particle, and a tetranucleosome system are simulated to compare the structure and dynamics properties. We found that the acetylation in general reduces the interactions between histone tails and the DNA, subsequently may facilitate the access of regulation molecules to activate gene expressions.
11. Establishment and Maintenance of Epigenetic Information
Bing Zhu, Institute of Biophysics, Chinese Academy of Sciences, Email: zhubing@ibp.ac.cn
DNA is unarguably the carrier of genetic information. However, DNA sequence alone cannot explain how hundreds of cell types in a complex multi-cellular organism, such as a human individual can possess distinct transcription programs, while sharing the same genetic information. This is believed to be achieved by fine-tuning our genetic information with a so-called “epigenetic” system. To fulfill the two basic tasks challenging the multi-cellular organisms, epigenetic system must simultaneously offer dual characteristics, “Plasticity & Inheritability”. Plasticity allows the transformation of one genome into hundreds of epigenomes and transcriptomes, whereas inheritability permits the maintenance of every single epigenome and its corresponding transcriptome.
We are interested in several dimensions of the epigenetic system. Primarily, we would like to understand how epigenetic information is inherited during mitotic divisions and how epigenetic information is established during germ cell maturation, stem cell differentiation and development. In this talk, I will highlight some of our recent progresses along these directions.
12. The effects of cytosine methylation on general transcription factors
Jianshi Jin, Tengfei Lian, Chan Gu, Kai Yu, Yi Qin Gao & Xiao-Dong Su
BIOPIC, Peking University, Beijing, 100871 Email: xdsu@pku.edu.cn, gaoyq@pku.edu.cn
DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. Our conclusion is that cytosine methylation can influence binding of most transcription factors to DNA—in some cases negatively and in others positively, which will modulate many important physiology processes.
13. Highly abundant and mitotic retained chromatin associated RNAs bookmark active chromatin domains during the cell cycle
Yan Zhang, Minglei Shi, Ping Li, Wenlong Shen, Chao He, Zhuang Ma, Yifei Jin , Dandan Peng，Zhang Zhang, Huahu Ye, , Michael Q. Zhang, Yang Chen, Zhihu Zhao Email: zhaozh2046@gmail.com
Background: RNAs are important components of eukaryotic chromatin, and increasing evidences suggest their roles in regulation of chromatin state and gene expression. Despite several studies have profiled chromatin associated RNA (CARs) by different methods in interphase or mitotic phase (M-phase) cells, little is known about the dynamics of these CARs in binding to chromatin during mitosis. At the same time, whether the mitotic CARs, especially those retained from interphase chromatin ones, have any functional relevance to chromatin higher-order structure and epigenetic state and cellular processes, particularly the cell-type specificity and its’ relationship to the cell identity remain elusive.
Results: We applied nuclear fractionation method by separating soluble nuclear extracts from those tightly bound to chromatin complex, and further analyzed CARs in both interphase and M-phase of/for different cell types. In this end, we found that chromatin enrichment of CARs in interphase cells is actually correlated with those in M-phase cells, and hence we identified a substantial fraction of CARs to be mitotic retained, we named these interphase and mitotic common CARs as IM_CARs, which are highly abundant and are sustainably transcribed throughout the whole cell cycle. Functional enrichment of IM_CARs indicated that these CARs play housekeeping roles and take part in the mitosis process itself. In addition, we found these IM_CARs, especially most abundant ones tend to be cell type non-specific. We also inferred chromatin targets of most common IM_CARs, and found both these CARs and their cognate targets preferentially located in active chromatin domains. Finally, we confirmed growth arrest effect upon disruption of RMRP, one of the common IM_CARs, by CRISPR technology.
Conclusions: Our findings suggested that tendency of being CARs in interphase is actually remained in M-phase, and that highly abundant, sustainably transcribed IM_CARs tend to be shared by different cell types, locate in active chromatin domains and play active roles in essential biological processes including mitosis and cell proliferation, and hence might have implications in human diseases such as cancers.
14. Coupling between epigenetic modification and gene expression
Jianhua Xing, Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh Email: xing1@pitt.edu
Conventionally chemical physics is a field that mainly investigates physicochemical phenomena at atomic and molecular levels. Noticing the analogy between molecular (especially macromolecular) dynamics and cellular dynamics, in the past few years my lab has focused on understanding cell phenotype transitions from chemical physics perspective. Epigenetics is a major layer of cell phenotype regulation. In this talk I will first present a model study on epigenetic memory, then discuss a long-standing Nobel-Prize winning puzzle on olfaction. Each olfactory sensory neuron stochastically expresses one and only one type of olfactory receptors, but the molecular mechanism remained unanswered for decades. I will show how simple physics taught in introductory physical chemistry textbook explains this seemingly complex problem. Last I will present our recent efforts on developing CRISPR-based knockin technique that allows us to efficiently insert fluorescence protein sequences at the endogenous sites of target genes for subsequent live cell imaging.
