A two-day international scientific symposium to celebrate the 70th anniversary of the discovery of DNA's double helix structure, the most profound biological discovery of the last century, concluded in Beijing on Oct 22, 2023.
The symposium, which also marked the third anniversary of Changping Laboratory, focused on recent advances in life sciences reflecting the living legacy of the DNA double helix. Topics presented and discussed in the symposium included DNA sequencing, gene editing, central dogma, DNA and immunology, epigenetics, genomics, genomic medicine and genomic neurobiology and technology.
Session V: Epigenetics
1.Presentation by Anjana Rao
Mutations in Clonal Hematopoiesis Compromise Heterochromatin Integrity
Professor Rao's study focused on the involvement of proteins related to DNA methylation and active demethylation in clonal hematopoiesis. This condition becomes more prevalent with age and is often accompanied by mutations in critical genes. Through experiments using mouse models with various gene defects, Rao's team uncovered that three common mutations associated with clonal hematopoiesis (DMT3A, TET2, and ASXL1) can result in heterochromatin dysfunction, leading to hematopoietic abnormalities and oncogenesis. This dysfunction is primarily linked to impaired DNA and H3K9 methylation, especially in hematopoietic stem and progenitor cells (HSPC), where the loss of heterochromatin integrity is particularly noticeable. The research suggests that the disrupted function of these three genes may collectively contribute to a range of serious health issues, including cancer, inflammation, and aging.
2.Presentation by Yi Zhang
5mC Oxidation and Beyond
Professor Zhang addressed that the reversibility of DNA methylation had been a long sought-after question in the field of epigenetics. Zhang talked about how his team approached the question and showed how the Tet proteins oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylmethylcytosine (5caC). Importantly, they showed that Tet3 protein is mainly involved in oxidizing paternal 5mC in zygotes, and Tet1 protein can activate meiotic genes during meiosis as well as erase genomic imprinting in primordial germ cells. Zhang also talked about their recent work in the hematopoietic stem cells (HSCs) during aging. They find that old HSCs are heterogeneous and generate more CD150 high population. The CD150 high HSC population is functionally defect in long-term to short-term HSCs differentiation, resulting in a deterioration of the organism's functionality. In summary, CD150 serves as a biomarker, indicating an individual's "epigenetic age”. This observation offers an epigenetic explanation for the phenomenon where older mice can be rejuvenated after receiving HSCs from young mice.
3.Presentation by Guoliang Xu
Biological Modifications of DNA Cytosine Base
Starting with the physiological functions of DNA methylation in gene expression silencing, Professor Xu introduced the findings related to DNA methylation and demethylation during embryonic development. With the discovery of oxidation products of 5mC-modified bases, such as 5hmC and 5caC, the process of oxidative demethylation for DNA methylation modifications was gradually elucidated. Professor Xu then presented the team's research on the regulation of the Lefty-Nodal pathway by Tet3 during mouse embryonic development. The study revealed that Tet3-deficient mouse embryos exhibited abnormal methylation of paternal DNA, leading to a decreased survival rate of the embryos. Tet-mediated DNA demethylation activated the expression of genes silenced by DNMT3 methylation modifications, resulting in the production of Lefty and the regulation of Nodal. This implies that the dynamic alterations in the processes of methylation and demethylation play a vital role in an individual's development. Finally, Professor Xu introduced the new progress in vitamin C-mediated DNA modification discovered by his group, which can epigenetically activate the expression of NPQ genes.
4.Presentation by Yiqin Gao
Relating Cell State Dependent Methylation to the DNA Sequence and 3D Genome
Professor Gao first introduced the effects of DNA deformation and sequence on their distribution in the genome. Based on the analysis of changes in CpG density sites where the transcription initiates, they speculated that the composition and distribution of dinucleotides might influence gene regulation mechanisms. After analyzing dinucleotide sequences around promoters and on gene bodies, they observed different characteristics in CpG density among housekeeping genes, genes of developmental and neural functions, and tissue-specific genes. These sequence differences were found to affect the binding of H1 histones. Subsequently, they examined the hierarchical distribution of CpG in the human genome and the hierarchical chromatin structure, showing that CpG could serve as a better indicator of chromatin segregation than other sequential properties. They also introduced their newly developed CTG method, which was used to analyze changes in chromatin structure during cancer development. This analysis was integrated with genomic mutation information, methylation data, and other epigenetic information to identify differences in copy number variation and chromatin structure among different types of cancer. These analyses suggest that dinucleotides and their distribution may have a broad range of effects. For example, the changes in DNA methylation during carcinogenesis are closely linked to multiscale CpG density and chromatin structure.
Session VI: Genomics
1.Presentation by Fuchou Tang
Single Cell Omics Sequencing Technologies: The Third Generation
Professor Tang introduced various single-cell long-read sequencing technologies developed by his team. To investigate the mechanisms by which multiple genomic elements were involved in the regulation of gene expression through three-dimensional genomic conformational changes, Tang's team used the single molecule sequencing platform to develop a single-cell long-read concatemer sequencing method to reveal high-order chromatin structures within individual cells, scNanoHi-C. The algorithm was optimized according to the unique features of scNanoHi-C data, which can identify enhancer-promoter co-regulatory regions in the whole genome. Professor Tang then introduced the scNanoCOOL-seq technology, which was developed by combining the third-generation sequencing platform and the principle of scCOOL-seq. The technology enabled the simultaneous and precise detection of information at multiple omics levels such as the genome (CNVs), DNA methylome, chromatin accessibility, and transcriptome in a single cell. Using this method, they systematically mapped the dynamics of the epigenome in mouse blastocyst stage embryos at single-cell resolution in multiple omics levels.
2.Presentation by William Greenleaf
Exploring the Physical Genome
Professor Greenleaf delved into the exploration and discussion of the physical structure of the genome by addressing the question of how differentiated cells determine the correct phenotype they should evince from their genome. Each cell, despite sharing the same genome, can express specific proteins through transcription factors that recognize DNA sequences. The recognition allows cells to perform distinct roles. Greenleaf's team actively investigated the transcriptional mechanism of the genome in this process, aiming to determine the compression, folding, and other aspects of gene fragments and peptide chains that were controlled by transcription factors.
The team has developed a method for identifying open chromatin elements using a transposase. This technique identifies regulatory elements responsible for driving changes in gene expression. Neural network models were trained to predict mutations that had a highly disruptive impact on chromatin. They also used molecular footprinting methods to understand the specific molecular states of regulatory elements. Using these data, they developed a quantitative model capable of understanding the relationship between DNA sequences and the concentrations of relevant molecules. The resulting partition function model can be employed to evaluate the states of promoters and understand the detailed states that lead to gene expression.
3.Presentation by Bing Ren
Unlocking the Genome’s Regulatory Code
The human genome is the blueprint of life. Its 3-billion base DNA encodes the information necessary for the development of the human body from fertilized eggs to adults. Tiny changes in this blueprint underlie the phenotypic traits and disease risks of each person. Reading this book of life, however, has been difficult because only a tiny fraction (1.5%) of the genome is functionally annotated as protein coding, yet the majority of disease heritability lies outside of these protein-coding sequences. Professor Ren’s presentation centered on his lab’s journey to provide functional annotation to the non-coding genome. Initially, using the ChIP-chip technology that he developed to study the binding of transcription factors and the states of chromatin modification in the genome, he and colleagues demonstrated the feasibility of a strategy to identify transcriptional regulatory sequences in the genome. They then combined ChIP (chromatin immunoprecipitation) with the next generation DNA sequencing technologies to map the chromatin state and DNA binding proteins across the genome in hundreds of tissues and cell types, and determined millions of transcriptional regulatory elements in the human genome along with their tissue-specific usages. More recently, Ren's team conducted single-cell-level epigenomic analysis of 1.32 million cell nuclei from adult and fetal human tissues and delineated the open chromatin regions in 222 cell types. From these maps, they identified around 1.2 million cis-regulatory elements. These elements can be combined with GWAS (Genome-Wide Association Studies) results to help predict cell types related to diseases or to use deep learning models to predict the impact of risk variants on gene regulation. Their results provide a roadmap to determine the genes, pathways and cell types pertinent to various human traits and diseases, which will ultimately lead to more accurate diagnostics and effective treatment strategies.
4.Presentation by Long Cai
Spatial Genomics
Professor Cai presented his recent findings in spatial transcriptomics technology. Firstly, He introduced the Sequential Fluorescence in situ Hybridization (SeqFISH+) technique, which permitted the identification of more than 10,000 genes through multiple cycles of hybridization using various fluorescent probes, and visualization through confocal microscopy. This technique also enabled the localization of introns. Through spatial transcriptomics analysis, his team discovered a group of "neighboring" cells in an acute kidney injury model that interacted with renal epithelium. They noticed varying gene expression patterns in fibroblast cells depending on their spatial distribution. This approach overcame the drawbacks of traditional single-cell sequencing, where crucial spatial information was lost during cell dissociation.
The Cai lab also noted that single-cell spatial genomics provided crucial insights across DNA, protein, and chromatin epigenetic levels. At the epigenetic level, in situ imaging revealed the distribution of DNA, chromatin, and various modifications within the cell nucleus. Differences in heterochromatin distribution across different cell types were observed, along with the discovery of repositioning of DNA to distinct heterochromatin regions across cell types. In summary, spatial genomics offered a potent tool for studying gene expression, cellular interactions, and epigenetic regulation within their natural spatial context, providing valuable insights into complex biological processes.
