Junk or functional DNA? ENCODE and the function controversy
Junk or functional DNA? ENCODE and the function controversy
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DOI：
10.1007/s10539-014-9441-3
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发表时间：
2014-11-01
影响因子：
2.5
通讯作者：
Boem, Federico
中科院分区：
文献类型：
--
作者：
Germain, Pierre-Luc;Ratti, Emanuele;Boem, Federico
在2012年9月出版的上一轮出版物中，《DNA元素百科全书》(ENCODE)为大多数人类基因组赋予了一种生化功能，媒体将其视为“垃圾DNA”的终结。这激起了进化生物学家的激烈反应，他们声称，ENCODE采用了错误的、过于包容的功能概念，使其对垃圾DNA的否定只是口头上的。我们认为，这种批评是基于对ENCODE项目的性质、相关的功能概念以及我们大部分基因组是垃圾的说法的误解。我们认为，对功能的进化描述将功能预设为“因果角色”，而选择只是相关功能的有用代理，这很可能不适合生物医学研究。仔细观察ENCODE参与的发现过程，我们认为ENCODE的生化签名策略成功地识别了DNA元素的活动，着眼于生物医学研究感兴趣的因果作用。我们认为，ENCODE有争议的功能声明应该被解释为80%的基因组正在参与相关的生化活动，并且很可能在被认为与生物医学研究相关的现象中起到因果作用。最后，我们讨论了垃圾DNA的含糊不清的含义以及对其流行提出的主要论点之一，并评估了ENCODE的结果对我们大部分基因组是垃圾的说法的影响。
In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of 'Junk DNA'. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as 'causal roles', and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE's strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE's controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE's results on the claim that most of our genome is junk.