正常來講，看懂以下圖片冲呢，就已經(jīng)可以明了關(guān)于miRNA命名的大部分問題了。
（圖片來源于網(wǎng)絡(luò)招狸，鏈接已迷失~~~）
以下內(nèi)容選自miRBase命名法說明，翻譯不當(dāng)邻薯，敬請諒解裙戏。
What’s in a name?
名字有什么含義了？
As I briefly mentioned in a previous post, miRBase 17 included two conceptual changes in the miRNA nomenclature scheme, which deserve further detail and clarification.
正如我在之前的一則公告中提到的厕诡，miRNA17版本在命名規(guī)則上有了兩個概念上的變化累榜，在這里需要要做進一步的說明。
The name of a miRNA contains some human-readable information. If you stop reading this post halfway, you’ll likely think this is a good thing. Which of course it is, as long as we recognise the limitations. Hold on to the end and hopefully you’ll see that names can create some issues.
關(guān)于miRNA命名的可讀性灵嫌，如果你讀這篇文章的時候半途而廢壹罚，那該慶幸是一件好事。當(dāng)然如果你堅持讀下去了寿羞，你會發(fā)現(xiàn)有很多的問題猖凛。
Take for example, hsa-mir-20b. The “hsa” tells us it is a human miRNA. The “20″ tells us that was discovered early — it’s only the 20th family that was named. “20b” tells us that it is related to another miRNA that we can guess is probably called hsa-mir-20a. We can go further — the (lack of) capitalisation of “mir” tells us we’re talking about the miRNA precursor. Or maybe the genomic locus, or maybe the primary transcript, or maybe the extended hairpin that includes the precursor. So that’s already less useful.
比如hsa-mir-20b，hsa表示這是一個人類的miRNA绪穆，20代表第20個家族（排在第20位辨泳，可能發(fā)現(xiàn)的比較早），20b告訴我們它與另外一個miRNA有關(guān)玖院，那個miRNA可能是hsa-mir-20a菠红，mir表示miRNA前體，或者可能是基因組的位置难菌，或者可能是初級轉(zhuǎn)錄物试溯，或者是包括前體的發(fā)夾結(jié)構(gòu)的延伸。
hsa-mir-20b has two mature products, named hsa-miR-20b and hsa-miR-20b* (as of this moment — as you’ll see below, this will change). “miR” tells us we’re talking about a mature sequence. In this case miR-20b arises from the 5′ arm of the mir-20b hairpin, and miR-20b* arises from the 3′ arm. The “” tells us that miR-20b is considered a “minor” product. That means miR-20b* is found in the cell at lower concentration than miR-20b. It is often inferred that miR-20b* is non-functional, and you’ve probably noticed that miR* sequences in general magically disappear in most pictures of miRNA biogenesis, while the dominant arm is magically incorporated into the RISC complex.
hsa-mir-20b有兩個成熟體產(chǎn)物郊酒，分別是hsa-miR-20b 和 hsa-miR-20b* （現(xiàn)在是這樣遇绞，但是后文會說到這個會改的）。這樣的話猎塞，“miR”表示一個成熟體序列试读。miR-20b 來自于mir-20b發(fā)夾結(jié)構(gòu)的5'臂，而miR-20b* 則來自于3'臂荠耽，帶 “ * ” 的被認為是未成熟的產(chǎn)物钩骇，也就是說，miR-20b* 在細胞中的濃度比miR-20b 要低，一直以來人們推測 miR-20b* 是無作用的倘屹。你可能發(fā)現(xiàn)miR* 的序列經(jīng)常在很多miRNA起源的圖片中神奇的消失了银亲，然而居然只有優(yōu)勢臂會和RISC結(jié)合。
But hang on a minute, a bunch of papers now tell us that miR* sequences can be functional (eg Yang et al. 2011), perhaps through binding different Agonaute proteins (a glut of papers in the past couple of years nicely reviewed by Czech and Hannon, 2011). And, of course, the miR* sequence from one hairpin might be expressed at orders of magnitude higher level than the dominant miR sequence from another hairpin. Perhaps the arm that makes the dominant product can change in different tissues, stages and species (G-J et al. 2011). Should we rename miR and miR* sequences every time someone produces an ever deeper sequencing dataset? To cap it all, the “*” character causes problems for database searches and the like.
但是請再想一下纽匙，一些文獻中告訴我們miR* 序列可能是有作用的( Yang et al. 2011)务蝠，作用途徑可能是通過結(jié)合不同的Ago蛋白（過去的兩年里有大量的文獻都提到了，Czech and Hannon, 2011）烛缔。當(dāng)然馏段，從發(fā)夾結(jié)構(gòu)中的一條miR* 序列可能比另一條優(yōu)勢序列的表達量還要高一個水平，也有可能在不同組織践瓷、不同時期院喜、不同物種中，優(yōu)勢序列的表達量也會不一樣(G-J et al. 2011)晕翠，那在產(chǎn)生一個深度測序數(shù)據(jù)中就要改變一下miR和miR* 序列的名字嗎喷舀？那么加不加“*”就會對數(shù)據(jù)庫的檢索等操作帶來麻煩。
We therefore intend to retire the miR/miR* nomenclature, in favour of the -5p/-3p nomenclature (the latter has been used in parallel for mature products of approximately equal expression, and will in future be applied to all sequences). We will make this transition in phases, as we can make companion data available to show the expression of mature products from each arm. In miRBase 17, all Drosophila melanogaster mature sequences are renamed as -5p/-3p, and many previously missing second mature products have been added. The available deep sequencing data makes clear which of the potential mature products is dominant. Other species will follow suit in due course.
所以為了解決miR/miR*的命名問題淋肾，我們提出了用 -5p/-3p的命名法（后者可以同時表示兩個成熟產(chǎn)物而不考慮他們的表達量水平的高低硫麻，未來可能會應(yīng)用在所有的序列上），我們會分階段進行轉(zhuǎn)換樊卓，并且會提供兩個成熟體相關(guān)的表達量數(shù)據(jù)拿愧，在miRBase17版本中，所有的果蠅黑腹菌屬成熟序列都用-5p/-3p來命名碌尔，還有很多之前沒有的第二成熟體也增加進去了「弦矗現(xiàn)在的深度測序可以測到哪個成熟體可能是占優(yōu)勢的，后面我們也會按照這種個方式更新其他的物種七扰。
The second change in miRBase 17 concerns the small number of pairs of miRNA sequences that are transcribed from the same locus in opposite directions — that is, sense/antisense pairs. For example, the dme-mir-307 locus has been shown to be transcribed in both directions, and both transcripts are processed to produce mature miRNAs. These miRNAs were previously named dme-mir-307 and dme-mir-307-as in miRBase. The -as is confusing, because it is similar to the suffixes used to denote families of related miRNAs. The classification of sense and antisense is arbitrary. To confuse matters further, -as and -s were used in early miRNA literature to refer to mature products produced from the 5′ and 3′ arms of a hairpin precursor. From miRBase 17 onwards, the -as nomenclature is retired. Sense and antisense miRNAs will be named independently and in the same way as all other sequences: If the sequences are similar then they get a, b suffixes (eg dme-mir-307a and dme-mir-307b), and if they are not deemed similar enough then they get different numbers (eg rno-mir-151 and rno-mir-3586).
miRBase17版本的第二個變化也涉及到了在基因組相對的位置上轉(zhuǎn)錄成的小的成對的miRNA序列-也就是正反義鏈奢赂，比如dme-mir-307 在位置上可以從兩個方向上轉(zhuǎn)錄，這兩個轉(zhuǎn)錄本經(jīng)過轉(zhuǎn)錄后處理產(chǎn)生兩個成熟的miRNA颈走，這些miRNA在miRBase上之前叫做dme-mir-307 and dme-mir-307-as膳灶，“-as”會有點難解釋清楚，因為這個后綴和表示miRNA家族的方法很像立由，這種正反義鏈的分類的方式是隨意的轧钓。在更早以前， 早期的文獻中锐膜，-as 和-s也用來表示從一個發(fā)夾前體上產(chǎn)生的5’和3‘的兩個成熟體毕箍。不過在miRBase17版本之前，就沒有用-as命名的方式了道盏。我們現(xiàn)在把來自同一個DNA正反義鏈的兩條序列用自己單獨的名字來命名：如果序列是相似的而柑，會在后面加一個a或者b的后綴（比如dme-mir-307a 和 dme-mir-307b）文捶，如果序列的相似度不高就用不同的數(shù)字來表示（比如 rno-mir-151 and rno-mir-3586）。
The combined result of these changes is that the name of a miRNA contains less information than previously. This may seem like a retrograde step. However, the problem with encoding information in the name is that people are tempted to use it. MicroRNA names are often pragmatic compromises, and have been overloaded with relatively complex meaning, for example, regarding family relationships and expression levels. Names should be useful, but should never be used in place of the correct analysis, for example, of sequence relationships or expression. We therefore suggest that you’ll find your miRNA life easier if you bear in mind some simple concepts:
這一系列的改變導(dǎo)致的結(jié)果就是miRNA的命名所展示的信息會比以前更少媒咳，這看上去好像是退步了粹排。但是人們更傾向于使用名字的編碼信息。miRNA命名在實際用法上就妥協(xié)了涩澡，因為以前超載了太多的復(fù)雜意義顽耳，比如把家族和表達水平也考慮進去了。命名規(guī)則確實是需要一些用處的妙同，卻不應(yīng)該用來替代精確的分析射富，比如給一些序列相關(guān)性或者表達量做排序。我們相信如果記住了以下幾點粥帚，你會在miRNA的工作中進行地更加順利：
1. Be explicit. If you are referring to the mature miR-20b sequence, you could rely on the capitalisation in miR-20b to say that for you. But it is much better to say “the mature miR-20b sequence”. Even better, show the sequence along with the name; names are not formally stable, but quoting the specific sequence you’ve used in your paper will ensure the entity is traceable forever.
1.確切地說辉浦，如果你要表示成熟體 miR-20b序列，你可以用大寫的 miR-20b來表示茎辐。這比用“the mature miR-20b sequence”要好的多〉嗨。或者有更好的辦法拖陆，用序列和名字一起來表示；由于名字還沒有正式固定下來懊亡，所以在文章中用特定的序列可以在以后更能追本溯源依啰。
2. Never use the name to encode or derive complex meaning. If you are interested in sequence relationships, you should do some sequence analysis. If you care about expression levels of alternate mature miRNAs, look at expression data. If you derive all your information about miRNA sequence relationships from the name, you will miss a great deal. If you rely on the name to tell you about relative expression then all hope is lost.
2.不讓命名去編碼或者得到什么復(fù)雜的含義。如果對序列的相關(guān)性有興趣店枣，你可以做一些序列的分析速警。如果想關(guān)注成熟miRNA的表達量水平，你可以分析表達量數(shù)據(jù)鸯两。如果從miRNA的名字中得到序列的相關(guān)性闷旧，那可能會不如你所愿，如果想讓名字告訴你相關(guān)的表達量钧唐，你會大失所望的忙灼。
參考：（以上內(nèi)容節(jié)選自）http://www.mirbase.org/blog/category/nomenclature/
翻譯內(nèi)容為原創(chuàng)，轉(zhuǎn)載請注明出處钝侠。
