Transcriptional Profiling of Daily Patterns of mRNA Expression in the C57BL/6J Mouse Cornea
Transcriptional Profiling of Daily Patterns of mRNA Expression in the C57BL/6J Mouse Cornea
复制标题
C57BL/6J 小鼠角膜中 mRNA 表达日常模式的转录分析。
DOI：
10.1080/02713683.2019.1625408
复制
发表时间：
2019-06-26
影响因子：
2
通讯作者：
Li, Zhijie
中科院分区：
文献类型：
--
作者：
Jiao, Xinwei;Wu, Mingjuan;Li, Zhijie
目的：本研究的目的是确定小鼠角膜的转录组如何适应生理学的昼夜变化。方法：C57BL/6J 小鼠在 12 小时光照/12 小时黑暗 (LD) 周期下维持两周。在 Zeitgeber 时间 (ZT) 0、3、6、9、12、15、18 和 21 时从安乐死小鼠收集角膜。提取总 RNA 并进行 RNA 测序 (RNA-Seq)。使用 JTK_CYCLE 算法和其他软件工具来分析转录数据，以确定转录本的周期性、节律性和幅度。使用基因本体论（GO）和京都基因和基因组百科全书（KEGG）来分析循环转录本的富集度。结果：小鼠角膜基因组总转录物中约 24% 在 LD 周期内有节奏地表达。 GO分析表明这些循环基因主要参与细胞和代谢过程。 KEGG 通路分析确定了 6 个分支和 44 条通路，它们编码基本细胞功能和过程所需的基因输出。更重要的是，大多数昼夜节律基因除了一些共同的通路外，还丰富了自己独特的通路。此外，大部分节律性基因表达集中在12小时和24小时期间。 GO 和 KEGG 的比较分析显示代谢过程存在巨大差异，但细胞过程没有差异。最后，小鼠角膜还在转录水平上在 LD 周期内有节奏地表达生物钟基因的 11 种典型成分。结论：四分之一的角膜转录组遵循涉及基本分子和细胞机制的节律表达模式。这意味着一天中的时间对角膜转录组的整体时间组织有显着贡献。
Purpose: The purpose of this study was to determine how the transcriptome of the murine cornea adapts to diurnal changes in physiology. Methods: C57BL/6J mice were maintained under a 12-h light/12-h dark (LD) cycle for two weeks. Corneas were collected from euthanized mice at Zeitgeber time (ZT) 0, 3, 6, 9, 12, 15, 18, and 21. Total RNA was extracted and subjected to RNA sequencing (RNA-Seq). A JTK_CYCLE algoithm and other software tools were used to analyze the transcriptional data to determine the periodicity, rhythmicity, and amplitude of the transcripts. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the enrichment of cycling transcripts. Results: Approximately 24% of the total transcripts from the murine corneal genome were rhythmically expressed over an LD cycle. GO analysis showed that these cycling genes are primarily involved in cellular and metabolic processes. A KEGG pathway analysis identified 6 branches and 44 pathways that encode the gene outputs necessary for basic cellular functions and processes. More importantly, most of the rhythmic genes between the day and night are enriched in their own unique pathways in addition to some common pathways. Furthermore, most of the rhythmic gene expression was concentrated in the 12-h and 24-h periods. A comparative analysis of GO and KEGG showed large differences in metabolic processes, but not cellular processes. Finally, the murine cornea also rhythmically expressed 11 canonical components of circadian clock genes over an LD cycle at the transcriptional level. Conclusions: One fourth of the corneal transcriptome follows a rhythmic expression pattern involved in basic molecular and cellular mechanisms. This implies that the time of day contributes significantly to the overall temporal organization of the corneal transcriptome.