News 2022
2022
October 26-28, 2022
Congratulation
PI Yang CHEN, MD Student.2019 Qiaoyi SHEN, and MD Student.2019 Zhizhuo CHEN formed the first iGEM competition team PUMC to participate in the competition and won the bronze award.
September 24, 2022
Activity
September 5, 2022
Publication
CASPIAN: A method to identify chromatin topological associated
CASPIAN requires few parameters to call TADs. This method is realized using the hierarchical density-based clustering method HDBSCAN, where the distance of pairwise bins is calculated based on three distance metrics (Euclidean, Manhattan, and Chebyshev distance metric) to adapt to the characteristics of the Hi-C contact matrix generated from simulation experiments or normalized methods. Our results show that, same as standard methods (e.g., Insulation Score, TopDom), CASPIAN can enrich factors related to promoting the gene expression, such as CTCF, H3K4me1, H3K4me3, RAD21, POLR2A, and SMC3. We also calculated the approximate proportion of various factors anchored at the TAD boundaries to observe the distribution of these factors surrounding the TAD boundaries. In conclusion, CASPIAN is an easy method to explore the relationship between transcription factors and TAD boundaries.
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陈阳、张晓彤合作团队发表时空基因组新工具CASPIAN
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September 1, 2022
New members
Welcome Xueyuan LI, Biao SONG， Yurong YANG, and Xueli WU to join our team!
July 2, 2022
Activity
February 22, 2022
PI Yang CHEN joins CANCER INNOVATION as an Editorial Board Member (2022-2024).
January 24, 2022
New member
Welcome Lisha WANG to join our team!
January 11, 2022
Publication
MyoD is a 3D genome structure organizer for muscle cell identity
Here, we analyzed 3D genome structures in muscle cells from mice lacking the muscle lineage transcription factor (TF), MyoD, versus wild-type mice. We show that MyoD functions as a “genome organizer” that specifies 3D genome architecture unique to muscle cell development, and that H3K27ac is insufficient for the establishment of MyoD-induced chromatin loops in muscle cells. Moreover, we present evidence that other cell lineage-specific TFs might also exert functional roles in orchestrating lineage-specific 3D genome organization during development.
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朱大海/张勇/张奇伟／陈阳合作揭示转录因子MyoD在细胞特异性基因组3D结构构建中的新功能
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