Evolutionary turnover of mammalian transcription start sites
Evolutionary turnover of mammalian transcription start sites
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DOI：
10.1101/gr.5031006
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发表时间：
2006-06-01
期刊：
影响因子：
7
通讯作者：
Sandelin, Albin
中科院分区：
文献类型：
--
作者：
Frith, Martin C.;Ponjavic, Jasmina;Sandelin, Albin
同源基因组序列的比对被广泛用于鉴定功能遗传元件和研究它们的进化。大多数研究默认功能元件的同源性等同于序列同源性。这一假设是违反了营业额的现象，其中功能等同的元素驻留在位置是nonorthopathic在序列水平。周转率已被证明以前的转录因子结合位点。在这里，我们表明，转录起始位点的等效基因并不总是驻留在人类和小鼠基因组中的等效位置。我们还确定了两种类型的部分营业额，说明进化途径，可能导致完全营业额。这些发现表明，编码转录起始位点的信号是高度灵活和可进化的，并具有警示意义的使用序列水平的保守性，以检测基因调控元件。
Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence homology. This assumption is violated by the phenomenon of turnover, in which functionally equivalent elements reside at locations that are nonorthologous at the sequence level. Turnover has been demonstrated previously for transcription-factor-binding sites. Here, we show that transcription start sites of equivalent genes do not always reside at equivalent locations in the human and mouse genomes. We also identify two types of partial turnover, illustrating evolutionary pathways that could lead to complete turnover. These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements.