人类基因组有大量的DNA被视为基因组垃圾，最近斯坦福大学医学院和圣塔克鲁兹-加州大学（University of California - Santa Cruz）的研究人员发现，这些垃圾DNA也携带重要信息，控制基因的开/关时间。具体研究内容刊登于4月23日《PNAS》。
斯坦福大学发育生物学和计算机科学副教授Gill Bejerano发现人类染色体上点缀着1万多个近似的片段，这些片段大部分位于被称为“基因沙漠”的无基因染色体区。实际上，这些片段携带许多有用的DNA小块，其中就包括被Bejerano等命名为“regulatory jungles”的DNA块。
Bejerano等发现，大多数邻近基因的DNA片段在胚胎发育头几周发挥调节作用，调节基因作用的时间和地点，并且在细胞粘附相关基因的周围含量丰富，帮助细胞迁移到正确位点，正确排列为组织和器官。
Bejerano等研究的10402个片段是转座子的残体。如果一个转座子插入到一个不必要的地方，会慢慢地累积突变直到与原始序列无相似之处，基因组充满了这些“衰败”的转位子。如果一个转座子插入一个需要它的地方，会保持原始序列，为其筛选提供了可能。Bejerano等曾经鉴别出许多似乎对邻近基因有调节作用的转座子，但不知道这种现象发生的频率。Bejerano说转座子也许是推动进化的主动力。
Bejerano的成功受益于两大成果：多个脊椎动物的全基因组测序结果公布和遗传分析软件的技术进步。实际上，Bejerano并不是第一个提出转座子有调节邻近基因作用的人，诺贝尔奖获得者Barbara McClintock博士（转位子的发现者）早在1956年便提出转座子能够帮助邻近基因确定开关时间。
英文原文：
'Junk' DNA Now Looks Like Powerful Regulator, Scientists Find
Science Daily—Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study by researchers at the Stanford University School of Medicine and the University of California-Santa Cruz. The scientists propose that this redeemed DNA plays a role in controlling when genes turn on and off.
Gill Bejerano, PhD, assistant professor of developmental biology and of computer science at Stanford, found more than 10,000 nearly identical genetic snippets dotting the human chromosomes. Many of those snippets were located in gene-free chromosomal expanses once described by geneticists as "gene deserts." These sections are, in fact, so clogged with useful DNA bits - including the ones Bejerano and his colleagues describe - that they've been renamed "regulatory jungles."
"It's funny how quickly the field is now evolving," Bejerano said. His work picking out these snippets and describing why they might exist will be published in the April 23 advance online issue of the Proceedings of the National Academy of Sciences.
It turns out that most of the segments described in the research paper cluster near genes that play a carefully orchestrated role during an animal's first few weeks after conception. Bejerano and his colleagues think that these sequences help in the intricate choreography of when and where those genes flip on as the animal lays out its body plan. In particular, the group found the sequences to be especially abundant near genes that help cells stick together. These genes play a crucial role early in an animal's life, helping cells migrate to the correct location or form. into organs and tissues of the correct shape.
The 10,402 sequences studied by Bejerano, along with David Haussler, PhD, professor of biomolecular engineering at UC-Santa Cruz, are remnants of unusual DNA pieces called transposons that duplicate themselves and hop around the genome. "We used to think they were mostly messing things up. Here is a case where they are actually useful," Bejerano said.
He suspects that when a transposon is plopped down in a region where it wasn't needed, it slowly accumulated mutations until it no longer resembled its original sequence. The genome is littered with these decaying transposons. When a transposon dropped into a location where it was useful, however, it held on to much of the original sequence, making it possible for Bejerano to pick out.
In past work, Bejerano and his co-workers had identified a handful of transposons that seemed to regulate nearby genes. However, it wasn't clear how common the phenomenon might be. "Now we've shown that transposons may be a major vehicle for evolutionary novelty," he said.
The paper's first author, Craig Lowe, a graduate student in Haussler's lab at UC-Santa Cruz, said finding the transposons was just the first step. "Now we are trying to nail down exactly what the elements are doing," he said.
Bejerano's work wouldn't have been possible without two things that became available over the past few years: the complete gene sequence of many vertebrate species, and fast computers running sophisticated new genetic analysis software. "Right now it's like being a kid in a candy warehouse," Bejerano said. Computer-savvy biologists have the tools to ask questions about how genes and chromosomes evolve and change, questions that just a few years ago were unanswerable.
Bejerano and his colleagues aren't the first to suggest that transposons play a role in regulating nearby genes. In fact, Nobel laureate Barbara McClintock, PhD, who first discovered transposons, proposed in 1956 that they could help determine the timing for when nearby genes turn on and off.
Funding for the study came through Haussler, who is a Howard Hughes Medical Institute investigator.
Note: This story has been adapted from a news release issued by Stanford University Medical Center.
