Hum Genomics:长链非编码RNA(lncRNA)命名规则

2014-08-09 MedSci MedSci原创

对于人类基因命名标准的制定而言,雨果基因命名委员会(HGNC)是唯一官方授权的机构。HGNC的数据库中有38000个基因名称,其中大部分是 编码蛋白基因;但HGNC也命名了8500多个人类非编码基因及假非编码基因,通过与各层次专家们的合作,他们命名了大多数的小非编码RNA。 小非编码RNA一般可根据它们的同源性及相同功能来分类。相比而言,长链非编码RNA则有其完全不同的一系列特点,它们

对于人类基因命名标准的制定而言,雨果基因命名委员会(HGNC)是唯一官方授权的机构。HGNC的数据库中有38000个基因名称,其中大部分是 编码蛋白基因;但HGNC也命名了8500多个人类非编码基因及假非编码基因,通过与各层次专家们的合作,他们命名了大多数的小非编码RNA。

小非编码RNA一般可根据它们的同源性及相同功能来分类。相比而言,长链非编码RNA则有其完全不同的一系列特点,它们的长度超过200个碱基,不具有保守序列的同源性,还有多变的功能属性。就像编码蛋白基因一样,长链非编码RNA也是尽量基于它们产物的已知功能来命名。


为了帮助科研人员能有效地命名lncRNA,让他们的命名更规范,名字更能反映功能,HGNC制作了这么一个命名指导标准,供科研人员参考。
在一个长链非编码RNA要发表之前,研究人员应先得到HGNC的认可。

依据相关预测,人类基因组中有大量的长链非编码RNA(至少几千条),但人类了解其功能的很少。所以,一般用基因组上下文来对未知功能的lncRNA命名。 HGNC希望与研究者们一起把长链非编码RNA命名的工作做好。HGNC的目标是让lncRNA的命名具有唯一性、准确性(让名字最大程度的反映功能)。


lncRNA 命名指导标准
一条lncRNA要命名得合理准确,有一些原则需要去遵循,有许多的因素需要去注意。详细的命名原则及考虑因素如下:

每一条lncRNA的名字应具有唯一性
“名字唯一性”这条原则很重要,不能违反。它能让我们在研究分析某个基因时不会产生问题(不会发生这种事情:一条基因几个名字,存在重名的基因等)。另一 方面,上述问题也不利于HGNC对命名规则的管理及维护。如果一个作者发布一个lncRNA名字,而它已经在别的地方使用过,HGNC将会指定一个新的名 字供选择。例如,一个新的lncRNA,它的功能是维持上皮细胞在非分化状态,本来打算命名为ANCR,但是这个名字已经被使用于“快乐木偶综合症染色体 区,Angelman syndrome chromosome region”,所以与作者达成一致,用DANCR来命名这个lncRNA“differentiation antagonizing non-protein coding RNA”.


lncRNA的名字应是描述基因的缩写
每条lncRNA的标识都应是一个描述该基因的“缩写”或者“首字母简写”。

例如BANCR就是由‘BRAF-activated non-protein coding RNA’短语的首字母排列而成。这样让人们容易理解名字的含义。


lncRNA的名字应仅由拉丁字母和阿拉伯数字组成
每条lncRNA的标识中不应出现标点符号,但可以用字母或者数字来代替标点符号。


连字符仅在特殊场合使用。例如:反义编码蛋白基因可在标识中加连字符(BACE1-AS就是BACE1 antisense RNA的名字)。

lncRNA的名字中的字母应为大写
为了与其它种类物种的基因区别开来(如啮齿动物基因的标识只要求首字母大写,其余小写),人类基因标识中的字母都应为大写。


例如“热气”(HOTAIR)基因,在人类中叫HOTAIR,而在老鼠中写成Hotair。


lncRNA的名字中不应涉及具体的物种类型
例如:如果基因名字中有H/h(代表人类),由于牵涉到同源基因的问题,就会造成一些疑惑和误导。


lncRNA的标识应避免采用一些常用的词汇
基因的名字中出现的常用词汇会带来一些混乱,给分析研究带来很多问题,因此,在命名中应避免出现常见词汇。


例如:“AIRN”基因最初公布时叫‘AIR’,从公共数据库中搜索可得到22万条不相关的信息,而搜索“AIRN”则只有10条信息。可见“AIRN”的搜索效率有效得多。同样的例子很多。

lncRNA的标识应尽可能的反映其功能
例如:'XIST'基因是'X (inactive)-specific transcript'的缩写,该基因的作用是参与沉默一对X染色体的转录。

命名的时候尽量反映基因通常的功能,而不体现其突变表型。基因的命名应简洁明了,不应包含太多信息。

  • 基因的标识中不应具有攻击或轻蔑的色彩。

  • 基因的标识中不应具有个人及地方色彩。

  • 基因的标识中不应含有神化,虚构或历史人物的名字。

  • 基因的标识中不应含有“臆想”和没什么意义的信息。


功能性转录假基因应包含它们假基因的名字
目前,一些数量较少的转录假基因被发现具有功能性,例如PTENP1基因就与“PTEN-targeting”miRNA结合一起参与调节PTEN的表达水平。


具 有功能的转录假基因在命名时应保留它们的假基因名称,并且不应改变其基于功能的名称。为了方便搜索,这个功能应加在标识的最后。PTENP1的命名就是这 方面的例子。PTENP1 是‘phosphatase and tensin homolog pseudogene 1 (functional)’.


如何命名未知功能的基因应遵循如下要求
未知功能的lncRNA应依据基因组上下文来命名,图一中给出如何系统化的命名的规则。

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图一


如 果有一个很接近的蛋白编码基因,lncRNA的名字应该以这个编码基因名字开始,然后制定以后后缀,这个后缀可以下方式分类:反义 (antisense,AS),BACE1-AS;内含子(intronic,IT),例如,SPRY4-IT1;重叠 (overlapping,OT),例如,OSX2-OT;长链基因间lncRNA(Long intergenic lncRNAs,lincRNAs),以LINC为前缀,数字为后缀,例如LINC00485.本质上以上命名原则是以GNECODE的注释目录为基准, 反义RNA,正义内含子,正义重叠和长链基因间非编码RNA(lincRNA).一些新的分类方法也应该考虑,特别对这些lnRNA,它们与编码基因是头 碰头(head to head),因此推断它们拥有双向启动子,HGNC推荐命名这些lncRNA为反义上游(Antisense upstream,AU),例如,GENE2-AU1。大家也应该注意到HGNC并不赞成以剪接变异体来命名,所以两个剪接变异体命名是以其中一个 lncRNA基因来命名,例如,GENE2-AS1;如果一个lncRNA基因编码的转录本跨多于一个蛋白编码基因,用lncRNA的5’末端的第一个蛋 白编码基因来命名,例如GENE-AS2上述命名的基本架构适用于大多数lncRNA,但对于基因密集区域的lncRNA可能就不适用了,这种情况下,你 应该与HGNC沟通来解决。

原始出处:

Wright MW.A short guide to long non-coding RNA gene nomenclature.Hum Genomics. 2014 Apr 9;8:7. doi: 10.1186/1479-7364-8-7.

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    2014-11-10 d830384
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