在人类胰腺癌细胞BxPC3全基因组中受Notch-1胞内结构域和CBF-1转录共调控的靶基因特征分析

Investigation of genes co-regulated by Notch-1 intra-cellular domain and CBF-1 at transcription level in the whole genome of human pancreatic cancer BxPC3 cells

目的在人类胰腺癌细胞BxPC3全基因组水平上寻找受Notch-1胞内结构域和CBF-1共同转录调控的靶基因;分析它们的类型、功能和在基因组中的分布等特征值;并以此为基础预测Notch信号通路的潜在生物学功能和调控模式。方法染色质免疫共沉淀联合基于Illumina/Solexa平台的高通量测序。结果 1)Notch-1胞内结构域和CBF-1两组样本有效read数分别为14 287 722和14 289 280个,与人类参考基因组唯一匹配的read数分别为11 782 027和11 711 920个;2)两组样本的peak数分别为385和492个,peak区域分别为318 344 bp和383 768 bp,都占全基因组的约0.01%;3)两组样本的peak区域几乎集中于基因间区和内含子区,只有不到5%位于外显子区;4)两组样本的peak对应基因数分别为150和287个,其中共有基因93个;5)通过基因聚类分析和数据库比对可以查到这些基因的名称、分类、基本功能和在基因组中的位置等具体信息。结论在人类胰腺癌细胞BxPC3全基因组范围内找到了更多在转录水平上受CBF-1和Notch-1胞内结构域共同调控的未知靶基因;初步明确了它们的类型、分布和功能等特征值;这些数据可以为进一步分析Notch信号通路潜在的生物学功能和调控模式奠定基础。

Objective Looking for the potential genes co-regulated by Notch-1 intra-cellular domain（ NICD） and CBF-1 at transcription level in the whole genome of human pancreatic cancer cell BxPC3 cells; investigating characteristics of those genes such as distribution, functions and classification;suggesting the potential functions and regulatory pattern of Notch signalling pathway based on the data obtained. Methods Chromatin immuno-precipitation（ ChIP） coupled with Illumina/Solexa-platform based high-throughput sequencing was employed to illustrate the profile of synergistic transcription between NICD and CBF-1 at genome-wide level in human pancreatic cancer BxPC3 cells. Results 1） The numbers of qualified reads for NICD and CBF-1 samples are 14 287 722 and 14 289 280, 11 782 027 and 11 711 920 of which are uniquely matched with human reference genome, respectively. 2） The numbers of peaks for NICD and CBF-1 samples are 385 and 492;the peak region covers 318 344 bp and 383 768 bp, each of which accounts for 0. 01% of whole genome. 3） Regardless of NICD or CBF-1 samples, most peaks scatter at intergenic and intronic region and only less than 5% of them locate in exonic region. 4） 150 out of 385 peaks for NICD samples and 287 out of 492 peaks for CBF-1 samples can be uniquely matched with a human gene, 93 of which are the same between two groups. 5） The details of those genes, such as names, locations and functions, were indicated by gene ontology（GO） analysis and gene database mining. Conclusion More unknown genes co-regulated by NICD and CBF-1 at transcription level were discovered in human pancreatic BxPC3 cells;the distribution, functions and classification of them were demonstrated;the potential functions and regulatory pattern of Notch signalling pathway were implied based on the data obtained.