| 引用本文: | 张峰,刘亚军,谢建明,孙啸,刘宏德.Hi-C的干细胞染色质多重相互作用特征分析[J].生物信息学,2017,15(3):137-141. |
| ZHANG Feng,LIU Yajun,XIE Jianming,SUN Xiao,LIU Hongde.Characteristic analysis of chromosome multiple interactions in stemcell based on Hi-C[J].Chinese Journal of Bioinformatics,2017,15(3):137-141. |
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| 摘要: |
| 染色质高级结构是基因转录调节的重要因素,染色质多重相互作用是高级结构中的一种,是多个(≥3)染色质片段在空间上相互接触而形成的紧凑结构。为了解染色质多重相互作用这类高级结构的特征及其在干细胞中分化中起到的作用,通过对Hi-C数据进行相关分析并计算基因的FPKM表达量,研究了染色质多重相互作用。分析发现:多重相互作用约占所有作用的30%,包含近70%的基因；此类作用区域的高表达基因多于低表达基因；且与组蛋白乙酰化相关性高。在分化过程中,多重作用位点数目和比例减少；位于多重作用区域的基因的表达略有降低；组蛋白乙酰化(H3K27ac 和H3K23ac)在多重作用区域的减弱,而组蛋白甲基化(H3K4me3和H3K27me3)倾向于增强。结果表明,染色质多重相互作用是一种广泛存在的染色质高级结构,在干细胞分化中有重要作用,此类结构多具有H3K27ac修饰,调节基因的表达。总之,染色质多重相互作用是一种重要的基因转录调节因素,在细胞分化中具有调控作用。 |
| 关键词: 染色质多重相互作用 Hi-C 基因表达 组蛋白修饰 |
| DOI：10.3969/j.issn.1672-5565.201701008 |
| 分类号:R737.9 |
| 文献标识码:A |
| 基金项目:国家自然科学基金(31371339)；国家重点基础研究发展计划(973计划)(2012CB316501). |
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| Characteristic analysis of chromosome multiple interactions in stemcell based on Hi-C |
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ZHANG Feng, LIU Yajun, XIE Jianming, SUN Xiao, LIU Hongde
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(State Key Laboratory of Bioelectronics(Southeast University), Nanjing 210096, China)
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| Abstract: |
| Higher-order chromatin structure is an important factor for transcriptional regulation. Chromatin multiple interaction (CMI) is a kind of compact high-level structure in which more than three chromatin fragments spatially interconnect together. In order to understand the characteristic of the CMI and its change in stem cell differentiation, the CMI was investigated by both correlation analysis of Hi-C data and gene expression (FPKM). The results show that CMI sites occur in 30% of Hi-C reads, covering nearly 70% of human genes, in which the highly expressed genes are more than those with low expression. Meanwhile, the CMI is highly correlated with histone acetylation. During stem cell differentiation, the number and the proportion of CMI sites decrease,and the expression slightly decreases in the CMI regions. The histone acetylation (H3K27ac and H3K23ac) is weakened in the CMI regions, whereas histone methylation (H3K4me3 and H3K27me3) tends to increase. These results suggest that the CMI is widely distributed,mostly modified with histone H3K27ac and plays a role in differentiation and gene regulation. In conclusion, chromatin multiple interaction is kind of important transcriptional regulator and contributes to cell differentiation regulation. |
| Key words: Chromosome multiple interaction (CMI) Hi-C Gene expression Histone modification |
