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| RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas | |
Sun, Lina1; Yang, Hongsheng1 ; Chen, Muyan3; Ma, Deyou1,2; Lin, Chenggang1,2; Yang, HS
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| 2013-08-06 | |
| 发表期刊 | PLOS ONE
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| ISSN | 1932-6203 |
| 卷号 | 8期号:8页码:e69441 |
| 文章类型 | Article |
| 摘要 | Background: Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to similar to 30000 ESTs.; Background: Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to similar to 30000 ESTs. Results: We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe). This was compared to profiles obtained from a normally-functioning intestine. Approximately 5 million (M) reads were sequenced in every library. Over 2400 up-regulated genes (>10%) and over 1000 down-regulated genes (similar to 5%) were observed at 3 and 7dpe (log(2)Ratio >= 1, FDR <= 0.001). Specific "Go terms" revealed that the DEGs (Differentially Expressed Genes) performed an important function at every regeneration stage. Besides some expected pathways (for example, Ribosome and Spliceosome pathway term), the "Notch signaling pathway," the "ECM-receptor interaction" and the "Cytokine-cytokine receptor interaction" were significantly enriched. We also investigated the expression profiles of developmental genes, ECM-associated genes and Cytoskeletal genes. Twenty of the most important differentially expressed genes (DEGs) were verified by Real-time PCR, which resulted in a trend concordance of almost 100% between the two techniques. Conclusion: Our studies demonstrated dynamic changes in global gene expression during intestine regeneration and presented a series of candidate genes and enriched pathways that contribute to intestine regeneration in sea cucumbers. This provides a foundation for future studies on the genetics/molecular mechanisms associated with intestine regeneration. |
| 学科领域 | Science & Technology - Other Topics |
| DOI | 10.1371/journal.pone.0069441 |
| URL | 查看原文 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS研究方向 | Science & Technology - Other Topics |
| WOS类目 | Multidisciplinary Sciences |
| WOS记录号 | WOS:000324401500009 |
| WOS关键词 | RAT-LIVER REGENERATION ; HOLOTHURIA-GLABERRIMA ; EXTRACELLULAR-MATRIX ; SKELETAL-MUSCLE ; AXON REGENERATION ; SIGNALING PATHWAY ; MOLECULAR-CLONING ; FIN REGENERATION ; LIMB MYOGENESIS ; SATELLITE CELLS |
| WOS标题词 | Science & Technology |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/16490 |
| 专题 | 海洋生态与环境科学重点实验室 |
| 通讯作者 | Yang, HS |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Qingdao, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Ocean Univ China, Qingdao, Peoples R China |
| 第一作者单位 | 中国科学院海洋研究所 |
| 推荐引用方式 GB/T 7714 | Sun, Lina,Yang, Hongsheng,Chen, Muyan,et al. RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas[J]. PLOS ONE,2013,8(8):e69441. |
| APA | Sun, Lina,Yang, Hongsheng,Chen, Muyan,Ma, Deyou,Lin, Chenggang,&Yang, HS.(2013).RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas.PLOS ONE,8(8),e69441. |
| MLA | Sun, Lina,et al."RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas".PLOS ONE 8.8(2013):e69441. |
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| RNA-Seq Reveals Dyna（1628KB） | 限制开放 | CC BY-NC-SA | 浏览 | |||
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