尹贻蒙 教授
硕士招生类型：学术型
硕士招生专业：基础医学
博士招生类型：学术型
博士招生专业：临床医学（基础医学方向）
所在院系：医学院
联系方式：yy461@tongji.edu.cn
课题组链接：
研究方向
主要任职
科研业绩

我们团队主要致力于开发和应用前沿的计算生物学、分子生物学方法来探索：（1）生物体内精细复杂的转录调控网络；（2）发育过程中细胞命运决定的分子机制；（3）细胞增殖和分化过程中积累的基因序列改变如何导致了衰老、癌症等人类疾病的发生。

Themission of our group is to develop and apply combined experimental andcomputational techniques to understand the precisely orchestratedtranscriptional programmes in complex organisms, to decipher the underlyingmechanisms by which cell identities are specified during the processes ofcellular differentiation and development, and to dissect how the geneticchanges our cells acquire as we go through life are related to ageing, cancerand other disease processes.



2019年 - ， 同济大学 教授 青年****
2018 - 2019年，剑桥大学 研究助理
2013 - 2018年，卡罗琳斯卡医学院 博士后
2007 - 2012年，中国科学技术大学 博士
2003 - 2007年，河南大学 学士

2019 - present Professor,Tongji University
Young Scholar Thousand Talents Program
2018 - 2019 Research associate, University of Cambridge
2013 - 2018 Postdoctoral researcher, Karolinska Institutet
2007 - 2012 Ph.D.,University of Science and Technology of China
2003 - 2007 A.B.,Henan University



我们主要利用分子生物学和计算生物学的方法，围绕转录因子如何通过特异性识别基因组DNA序列以及不同形式的表观修饰来调控基因表达，进而决定细胞命运这一关键科学问题开展了系统性研究。主要学术成果如下：
v 开发了methylation-sensitive SELEX方法，系统性解析了转录因子结合DNA的序列特异性、并定量评估了DNA的表观遗传修饰对二者结合的影响;
v 首次在全基因组水平揭示了甲基化对转录因子结合DNA的序列特异性的影响，发现了 ~170个与胚胎发育和器官发生相关的转录因子更倾向于结合甲基化的DNA序列；
v 建立了CAP-SELEX方法，通过计算富集DNA库中两个转录因子结合序列在同一DNA分子出现的频率、距离以及方向分布，评估转录因子间结合DNA的协同性。揭示了一种广泛存在转录因子间的、由DNA通过局部结构变化而介导的协同效应。

To understand how cell fates aredetermined by transcription factors (TFs) during the processes of cellulardifferentiation and development, we’ve developed combined experimental andcomputational techniques to explore the binding specificities of human TFs, toevaluate the impact of DNA modifications on the binding specificities of humanTFs, and to characterize the cooperativity of TFs in presence of DNA. Thefollowing is the details of my achievements:
v Established themethylation-sensitive SELEX method to systematically determine the bindingspecificities of TFs and quantify the effect of cytosine methylation on thebinding of TFs to DNA.
v Identified a large numberof previously uncharacterized transcription factor recognition motifs and unveiledmany developmentally important transcription factors showing preference tomethyl-CpG containing subsequences.
v Developed the CAP-SELEXmethod to capture the binding cooperativity of TF pairs in presence of DNA, anduncovered that, rather than through protein-protein interaction, most ofcooperativity between TFs is mediated or facilitated by DNA.

Key publications:
1. Yin, Y., Morgunova,E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja,T., Dave, K., Zhong, F., et al. (2017). Impact of cytosine methylation on DNAbinding specificities of human transcription factors. Science 356.
2. Jolma, A., Yin, Y.,Nitta, K.R., Dave, K., Popov, A., Taipale, M., Enge, M., Kivioja, T.,Morgunova, E., and Taipale, J. (2015). DNA-dependent formation of transcriptionfactor pairs alters their binding specificity. Nature 527,384-388.
3. Morgunova, E., Yin, Y.,Jolma, A., Dave, K., Schmierer, B., Popov, A., Eremina, N., Nilsson, L., andTaipale, J. (2015). Structural insights into the DNA-binding specificity of E2Ffamily transcription factors. Nature communications 6, 10050.
4. Morgunova, E., Yin, Y.,Das, P.K., Jolma, A., Zhu, F., Popov, A., Xu, Y., Nilsson, L., and Taipale, J.(2018). Two distinct DNA sequences recognized by transcription factorsrepresent enthalpy and entropy optima. eLife 7.
5. Lambert, S.A., Jolma, A.,Campitelli, L.F., Das, P.K., Yin, Y., Albu, M., Chen, X.,Taipale, J., Hughes, T.R., and Weirauch, M.T. (2018). The Human TranscriptionFactors. Cell 172, 650-665.
6.Zhu, F., Farnung, L., Kaasinen, E., Sahu, B., Yin, Y., Wei, B.,Dodonova, S.O., Nitta, K.R., Morgunova, E., Taipale, M., et al. (2018). Theinteraction landscape between transcription factors and the nucleosome. Nature562, 76-81.