Research article

Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array

Xingyi Hang^{* 1} , Peiyao Li^{* 1} , Zhifeng Li¹ , Wubin Qu¹ , Ying Yu¹ , Hualing Li¹ , Zhiyong Shen¹ , Hao Zheng² , Yan Gao¹ , Yonghong Wu¹ , Minghua Deng² , Zhixian Sun¹ and Chenggang Zhang¹

¹Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, PR China

²LMAM, School of Mathematical Sciences and Center for Theoretical Biology, Peking University, Beijing 100871, PR China

author email corresponding author email* Contributed equally

BMC Genomics 2009, 10:126doi:10.1186/1471-2164-10-126

Published:	25 March 2009

Abstract

Background

The balance between endothelial cell survival and apoptosis during stress is an important cellular process for vessel integrity and vascular homeostasis, and it is also pivotal in angiogenesis during the development of many vascular diseases. However, the underlying molecular mechanisms remain largely unknown. Although both transcription and alternative splicing are important in regulating gene expression in endothelial cells under stress, the regulatory mechanisms underlying this state and their interactions have not yet been studied on a genome-wide basis.

Results

Human umbilical vein endothelial cells (HUVECs) were treated with cobalt chloride (CoCl₂) both to mimic hypoxia and to induce cell apoptosis and alternative splicing responses. Cell apoptosis rate analysis indicated that HUVECs exposed to 300 μM CoCl₂ for 24 hrs were initially counterbalancing apoptosis with cell survival. We therefore used the Affymetrix exon array system to determine genome-wide transcript- and exon-level differential expression. Other than 1583 differentially expressed transcripts, 342 alternatively spliced exons were detected and classified by different splicing types. Sixteen alternatively spliced exons were validated by RT-PCR. Furthermore, direct evidence for the ongoing balance between HUVEC survival and apoptosis was provided by Gene Ontology (GO) and protein function, as well as protein domain and pathway enrichment analyses of the differentially expressed transcripts. Importantly, a novel molecular module, in which the heat shock protein (HSP) families play a significant role, was found to be activated under mimicked hypoxia conditions. In addition, 46% of the transcripts containing stress-modulated exons were differentially expressed, indicating the possibility of combinatorial regulation of transcription and splicing.

Conclusion

The exon array system effectively profiles gene expression and splicing on the genome-wide scale. Based on this approach, our data suggest that transcription and splicing not only regulate gene expression, but also carry out combinational regulation of the balance between survival and apoptosis of HUVECs under mimicked hypoxia conditions. Since cell survival following the apoptotic challenge is pivotal in angiogenesis during the development of many vascular diseases, our results may advance the knowledge of multilevel gene regulation in endothelial cells under physiological and pathological conditions.