Introduction of the Special Issue Epigenetics
Epigenetics refers to regulate gene expression, DNA replication or DNA repair processes without changing the DNA sequence. The mechanism includes DNA methylation, histone modification, chromatin remodeling, non- coding RNA, chromatin higher order structure and nuclear spatial localization, etc. Epigenetics plays an important role in many physiological and pathological processes such as cell fate determination, stem cell self-replication, cell differentiation, reproductive regulation, ontogenesis, tumorigenesis and development, immune cell activation, etc. It is also an important bridge mechanism that links the external environment influences with internal gene and cellular functions. Moreover, most epigenetic regulatory processes are reversible, which are precisely positive or negative regulated by the enzyme reactions. Therefore, research on epigenetic regulation not only helps us to understand life processes, many epigenetic regulatory factors are also ideal drug targets for tumors, infertility, cardiovascular diseases, nervous system diseases.
Many specific and continuously optimized technical methods in the field of epigenetics promote the development of epigenetics. Such as analyzing the nucleosome localization based on enzymes cleavage (MNase, DNAse, various endonuclease enzymes, etc.), tracing the histone modification locations in the genome wide through Chromatin Immunoprecipitation (ChIP), mapping the open chromatin region by the Transposase- Accessible Chromatin with high-throughput sequencing (ATAC-Seq), and mapping chromatin interaction through the Chromosomal Conformational Capture.
Guest Editors-in-Chief Profile
Guohong Li Professor at the School of Life Sciences, Wuhan University.
Researcher, Institute of Biophysics, Chinese Academy of Sciences.
His main research interests are the epigenetic regulation of chromatin higher order structures during transcription and its biological functions in determining cell fate during programming and reprogramming of embryonic stem cells.
He received his undergraduate degree from Wuhan University in 1995, his master's degree from the Department of Biophysics, Faculty of Medicine, Peking University in 1998, and his PhD degree from the University of Heidelberg/Maple Cell Institute, Germany in 2003. He then completed his postdoctoral training at Medical University of New Jersey/HHMI and New York University School of Medicine/HHMI, USA. Prof. Guohong Li has long been engaged in biological research on chromatin advanced structure and epigenetic regulation, mainly including chromatin advanced structure (30-nm chromatin fiber and heterochromatin) and its epigenetic regulation mechanism; chromatin structural variation and human diseases; mitotic chromatin and artificial chromosome construction, and has achieved a series of research results: resolved the high-precision 30-nm chromatin fiber three-dimensional cryoelectron microscopy The results have been published in several famous international textbooks. In addition, Guohong Li's group has also studied the molecular mechanism of recognition and assembly of a series of important histone variants and their regulation of chromatin high-level structure; revealed the epigenetic regulation mechanism of key steps of human genetic material transmission (Nature 2020), which was selected as one of the top ten advances in science in China in 2020 by the Ministry of Science and Technology and the National 13th Five-Year Plan "Science and Technology Innovation Achievement Exhibition”. Guohong Li's group has published more than 80 research papers in internationally recognized journals such as Science, Nature, Nature Cell Biology, Molecular Cell, Genes & Development and Developmental Cell. He has been selected for the Outstanding Youth Fund of the National Science Foundation of China, the Howard Hughes Medical Institute (HHMI) International Research Fellowship, the Jiazhen Tan Life Science Innovation Award, and the "Young and Middle-aged Science and Technology Innovation Leaders Program" of the Ministry of Science and Technology of China. He is currently on the editorial board of J Biol Chem, BBA-gene regulatory mechanism, JGG, Genome Biol, Nucleus, China Science - Life Sciences, etc. He is also a member of the Board of Directors of the Chinese Biophysical Society, the Executive Director of the Chinese Society of Biochemistry and Molecular Biology, the Executive Director of the Chinese Society of Genetics, and the Director of the Epigenetics Section of the Chinese Society of Genetics. Director of the Epigenetics Branch of the Chinese Society of Genetics.
Wei Xie Professor, School of Life Sciences, Tsinghua University.
His principal research is on epigenetic regulation of mammalian genomic transcription that regulates development and related human diseases.
Dr. Wei Xie is a Professor at School of Life Sciences, Tsinghua University, and an HHMI International Research Scholar. He received his B.S. degree in Molecular Biology at Peking University in China in 2003. He pursued his Ph.D study at UCLA, where he joined the laboratory of Michael Grunstein to study the function of histones and histone modifications. He also obtained a M.S. double degree in statistics at UCLA with Ker-Chau Li. After completing his graduate studies in 2008, he continued research in epigenetics and transcription regulation as a postdoctoral fellow in Bing Ren’s lab at the Ludwig Institute for Cancer Research, UCSD in 2009. After his postdoc training, he joined Tsinghua University, School of Life Sciences, in Beijing as a Principal Investigator in 2013. He is also a member of the Tsinghua-Peking Joint Center for Life Sciences. Using interdisciplinary approaches, Dr. Wei Xie is dedicated to understanding how the epigenome is inherited, reprogrammed, and established in early mammalian development when life just begins. His group established a series of ultra-sensitive technologies to analyze chromatin dynamics using a few hundred cells. He has authored over 80 publications, including those published in Nature, Science, Cell as the first-author/correspondence author. His work has been cited over 18,000 times. He has won numerous awards including Qiushi Excellent Young Scholar Award, HHMI International Research Scholar, Outstanding Young Scholar Award from National Science Foundation of China, C. C. Tan Life Science Innovation Award, Shulan Medical Science Young Scholar Award, China Science and Technology Young Scholar Award, and the 1st Explorer Prize Award and the 1st New Cornerstone Investigator Program.
Cheng Li Senior Researcher, School of Life Sciences, Center for Statistical Sciences, Center for Biological Information, Peking University.
Main focus is on 3D genomics experimental techniques, analytical methods and their application to biological problems.
Dr. Cheng Li studied computer science at Beijing Normal University (BS, 1995) and statistics at University of California, Los Angeles (PhD, 2001). He has worked at Harvard School of Public Health and Dana-Farber Cancer Institute as an Assistant Professor since 2002 and Associate Professor since 2008. Dr. Cheng Li’s group has developed many novel gene expression and SNP microarray analysis and visualization methods, and implemented and maintained highly-cited genomics analysis software such as dChip and batch effect adjustment software ComBat (2600 citations). Since 2013, he has worked at Peking University, School of Life Sciences and focuses on 3D genomics experimental techniques, analysis methods and applications to diseases.
The Hi-C method is widely used to study the functional roles of three-dimensional architecture of genome. Here, we integrate Hi-C, WGS and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the number of TADs increases by 25% in MM and the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid multiple myeloma cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation.
Accepted types of manuscripts:
1. Research review: An in-depth summary of representative research results in the field in the last 5 to 10 years, with a comprehensive review of the scientific significance, current research status and development trends in the field. The content of the review should be based on or directly related to the author's professional research.
2. Research papers: Report the latest scientific research results with theoretical, innovative and important scientific value, such as basic research and core technology research in the field.
3. Protocols: Report the core technical methods and methodological details of the basic research in the field.
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