Global identification of transcription start sites in the genome of Apis mellifera using 5'LongSAGE.
Global identification of transcription start sites in the genome of Apis mellifera using 5'LongSAGE.
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DOI：
10.1002/jez.b.21421
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发表时间：
2011-11
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通讯作者：
Huajun Zheng;Liangxian Sun;W. Peng;Yan Shen;Yuezhu Wang;Baohua Xu;Wenyi Gu;Shuting Chen;Zhouying Huang;Shengyue Wang
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文献类型：
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作者：
Huajun Zheng;Liangxian Sun;W. Peng;Yan Shen;Yuezhu Wang;Baohua Xu;Wenyi Gu;Shuting Chen;Zhouying Huang;Shengyue Wang
蜜蜂基因组中基因转录起始位点的精确鉴定将有助于推断起始密码子和确定启动子元件。5 'SAGE方法为鉴定测序基因组中的TSS提供了强有力的工具。本研究的主要目的是鉴定表达基因的实际TSS以及不同TSS在意大利蜜蜂基因组中的使用。我们对雄蜂成虫头部进行了5 'LongSAGE（5' LS）分析，并通过将5 'LS标签序列定位到蜜蜂基因组来确定表达基因的TSS。总共鉴定了8，280个独特的19 bp 5 'LS标签序列，其对应于3，655个预测基因。在这些标签中，4，998个标签（60.4%）定位于2，301个参考编码序列的起始密码子的-1，000 bp至+100 bp的区域。值得注意的是，我们观察到3，655个蜜蜂基因中的28-47%从替代TSS开始转录。蜜蜂基因的TSS共有模式，DT（rich）PyPu（G（rich））（T/A）（T（rich））（3），通过比对5 'LS-TSS侧翼的序列获得。我们还在5 'LS标签的下游区域鉴定了三个新基因，并使用RT-PCR扩增验证了21个TSS。此外，由5 'LS标签识别的17个基因与基因本体论术语“行为”相关。“基因组上5 'LS标签的定位不仅为计算机预测的基因表达提供了直接证据，而且还允许识别以前未被识别的新外显子和替代TSS。
The precise identification of the transcription start sites (TSSs) of genes in the honeybee genome will be helpful for inferring start codons and for determining promoter elements. The 5'SAGE approach provides a powerful tool for identifying TSSs in the sequenced genome. The main purpose of this study is to identify the actual TSSs of expressed genes as well as the usage of different TSSs in the Apis mellifera genome. We performed a 5'LongSAGE (5'LS) analysis for the adult drone head, and the TSSs of the expressed genes were determined by mapping the 5'LS tag sequences to the honeybee genome. A total of 8,280 unique 19 bp 5'LS tag sequences were identified that corresponded to 3,655 predicted genes. Out of these tags, 4,998 tags (60.4%) were mapped to a region from -1,000 bp to +100 bp of the start codon of 2,301 reference coding sequences. Notably, we observed that 28-47% of the 3,655 honeybee genes initiated transcription from alternative TSSs. The TSS consensus pattern of the honeybee genes, DT(rich) PyPu(G(rich))(T/A)(T(rich))(3), was obtained by aligning the sequences flanking the 5'LS-TSSs. We also identified three new genes in the regions downstream of 5'LS tags and validated 21 TSSs using RT-PCR amplification. Additionally, 17 genes identified by the 5'LS tags were associated with the Gene Ontology term "behavior." Mapping of the 5'LS tags on the genome not only provided direct evidence of expression for in silico predicted genes but also allowed for the identification of previously unrecognized, novel exons and alternative TSSs.