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一文教会你查找基因的启动子、UTR、TSS等区域以及预测转录因子结合位点

发布: 2017-03-12 1,359阅读 195评论

基础知识

首先我们了解一些基础知识启动子（promoter）：与RNA聚合酶结合并能起始mRNA合成的序列。
转录起始点（TSS）：转录时，mRNA链第一个核苷酸相对应DNA链上的碱基，通常为一个嘌呤。UTR（Untranslated Regions)：即非翻译区，是信使RNA（mRNA）分子两端的非编码片段。
5′-UTR从mRNA起点的甲基化鸟嘌呤核苷酸帽延伸至AUG起始密码子，3′-UTR从编码区末端的终止密码子延伸至多聚A尾巴（Poly-A）的末端。

查找基因的启动子区域-NCBI

1. 打开PubMed：https://www.ncbi.nlm.nih.gov/pubmed

 

2. 选择Gene，输入IL17A，点击search，结果如下图，点击第一个：

 

3. 下拉到下图位置，可以看到该基因的以下信息：

 

点击Tools，选择Sequence Text View：

 

还可以看到如下序列信息：

 

4. 以上只是该基因的一些信息，可以用于查找相应的UTR等区域，下面进入正题，寻找promoter区域。还是拉到如下图位置，点击FASTA：

 

5. 基因位置信息如下图：

 

6. 一般认为基因上游2 kb区域为该基因的promoter区域，所以将基因上游2 kb序列调出来：

 

7. 复制上述序列就是基因的启动子序列了。

查找基因的启动子区域-UCSC

1. 打开UCSC：http://www.genome.ucsc.edu/，点击Table Browser：
2. 按照下图所示填好基因相关信息，点击get output：
3.选择genomic：
4. 勾选Promoter/Upstream by选项，并将其改为2000 bases，然后点击get sequence：

5. 得到下面的序列信息，开头直到第一个大写字母前面的所有小写字母序列即为该基因的promoter序列，你可以跟NCBI上得到的序列比对一下，看看是不是一样的呢？

 

6. 当然查找promoter的网站有很多，比如UCSC，在这里就不介绍了，大家可以自行探索，或者加小编微信amateur_1988交流。

 

转录因子结合位点的预测

1. 打开http://jaspar.genereg.net/（我这边这个网址暂时打不开了，所以我登录了这个网址：http://jaspardev.genereg.net/），输入转录因子NFAT，点击Quick Search：

 

2. 将promoter序列粘贴进入右下角的框中，选中左侧转录因子，点击SCAN：

 

3. 得到28条转录因子NFAT与IL17A的结合位点，其中Strand -1没有特殊意义，只需选择Strand 1即可。

 

4. 好了，转录因子与promoter结合位点已经有了，接下来就是愉快的通过实验验证了！Luciferase、点突变、截短、ChIP等统统拉上来就可以了！

 

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