染色质三维构象新型调控因子的机制研究

Study of 3D chromatin organization plays essential role in deep understanding the mechanism of gene transcriptional regulation. However, except a few well-known factors such as CTCF, Cohesin and YY1, it is still unclear whether other regulatory factor exists and how it is involved in transcriptional regulation through 3D chromatin interactions. Based on previous analysis on large amount of omics data, we identified potentially TRIM22 as a novel regulator of chromatin organization. In this project, we will use CRISPR system to knockout TRIM22 in GM12878 cells. Then we will utilize different high-throughput sequencing-based methods to compare the mutant and wild-type cells on multiple levels, including 3D chromatin organization, chromatin openness, TRIM22 DNA binding sites, DNA replication timing and RNA expression. By integrating these data we will be able to determine whether TRIM22 is indeed involved in chromatin organization; reconstruct the multi-level regulatory network mediated by TRIM22 and identify the underling molecular mechanism. This mechanistic analysis on TRIM22 proposed in this study will further expand our understanding of the relationship between 3D chromatin organization and gene transcriptional regulation.

染色质三维构象的研究，对于深入理解基因转录调控的机制具有重要意义。然而，除了少数研究较多的诸如CTCF、Cohesin和YY1之外，其它调控因子是否存在，以及如何通过染色质三维构象来调控基因转录，仍然很不清楚。基于前期大量组学数据的分析，我们发现TRIM22是一个潜在的染色质三维构象的新型调控因子。本项目将利用CRISPR系统在GM12878细胞中敲除TRIM22，然后通过高通量测序技术对基因敲除前后状态进行多组学测量。通过整合染色质三维构象、开放程度、TRIM22蛋白的DNA结合位点、DNA复制时间和基因转录水平等多层面的组学数据，进行生物信息学分析，我们将检验TRIM22是否直接参与了染色质三维构象的调控过程，并重构TRIM22参与的基因调控网络，阐明相关分子机制。本项目关于TRIM22的机制研究，将促进人们进一步认识染色质三维构象与基因转录调控的关系。

染色质三维构象的研究，对于深入理解基因转录调控的机制具有重要意义。然而，除了少数研究较多的诸如CTCF、Cohesin和YY1之外，其它调控因子如何通过染色质三维构象来调控基因转录，仍然很不清楚。基于前期大量组学数据的分析，我们探究了TRIM22染色质构象的关系以及它们参与的基因调控网络。本项目通过CRISPR系统获得了TRIM22 KO 的HAP1细胞，并通过高通量测序技术对基因敲除前后状态进行RNA-seq,ATAC-seq和ChIP-seq多组学测量，通过整合染色质开放程度、TRIM22蛋白的DNA结合位点和基因转录水平等多层面的组学数据，进行生物信息学分析，构建了TRIM22参与的基因调控网络。此外，我们还开展了关于等位基因特异性的染色质构象与基因表达调控的关系研究，并在单细胞水平研究了干扰素刺激下染色质可及性与基因表达的动态关系。本项目的研究，将促进人们进一步了解染色质构象与基因调控网络的关系。