...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>PLoS Genetics >Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses
【24h】

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses

机译：从人内源性逆转录病毒源自治疗元素的系统鉴定与表征

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified “HERV/LTR-shared regulatory element (HSRE),” defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.
机译：人类内源性逆转录病毒（HERVS）和其他长末端重复（LTR） - 型转回转移（HERV / LTR）具有可能影响宿主基因的转录的调节元件。我们系统地识别并基于由编码和路线图表观组织项目提供的97个转录因子（TFS）的可公开的Chip-SEQ数据集进行了这些监管元素。我们使用芯片SEQ数据集确定转录因子结合位点（TFBS）并鉴定在HERV / LTR序列（HERV-TFBS）上观察到的TFBS。总体而言，鉴定了794,972个肝病素材。随后，我们鉴定了“Herv / LTR共享的调节元件（HSRE）”，“在HERV-TFBS中定义为TF结合基序，在肝脏/ LTR类型的大部分内共享。 HSRES可能表明Herv / LTR的调控元素在其插入之前存在。我们确定了2,201个HSRES，包括354 Herv / LTR和84个TF的特定关联。聚类分析表明，Herv / LTR可以根据TF结合模式进行分组; HERV / LTR基团涉及多能TFS（例如，SOX2，POU5F1和纳米），胚胎内胚层/中胚层TFS（例如，GATA4 / 6，SOX17和FOXA1 / 2），造血TFS（例如，SPI1（PU1），GATA1 / 2和TAL1），并确定CTCF。 HERV / LTR的监管要素倾向于在附近定位和/或三维地区与参与免疫应答的基因，表明该调节因素在控制免疫调节网络方面发挥着重要作用。此外，我们在LTR7，LTR5B和LTR5_HS内展示了特异性特异性TF结合，表明在HERV / LTR的基因组侵犯期间发生调节元件的增益或损失。最后，我们构建了Dbherv-Res，赫夫/ LTR监管要素的交互式数据库（http://herv-tfbs.com/）。本研究提供了了解HERV / LTRS对宿主转录的影响，提供了对腰患者的转录调制系统和祖先的患者的洞察力。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号