Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression -: art. no. e163
Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression -: art. no. e163
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DOI：
10.1093/nar/gnh161
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Marti, J
中科院分区：
文献类型：
--
作者：
Quéré, R;Manchon, L;Marti, J
随着在真核生物中发现越来越多的互补转录物，其易于发挥各种调节功能，需要高通量分析方法来研究它们在多种生物样品中的表达。基因表达系列分析（SAGE），基于定向可靠的短cDNA序列（标签）的计数，能够揭示反义转录本。我们最初通过观察映射到已知mRNA反向互补序列的标签来检测它们。这些标签在单个SAGE文库中的存在表明SAGE数据集包含反义转录物的潜在信息。我们提出了一个虚拟标签的集合来挖掘这些数据。通过搜索24-nt长序列之间的互补性来组装标签对，所述24-nt长序列集中在良好注释的人表达序列的潜在SAGE锚定位点上。分析他们的存在在一个大的集合中公布的SAGE库显示转录本表达水平高，从两个相邻的，相反方向的，转录单位的两条链。在其他情况下，这些顺式定向基因的各自转录物显示互斥的表达模式或在少量文库中共表达。其他标签对揭示了反式编码的独特基因的重叠转录本。最后，我们分离出一组由多个转录本共享的标签。它们中的大多数映射到逆转录元件上，在人类中基本上由以相反方向插入在其他不同mRNA的3 'UTR中的Alu序列表示。将这些标记注册到单独的文件中，使得集中于独特的有义-反义对的计算搜索成为可能。本工作中开发的方法表明，SAGE数据集构成了一个主要的资源，快速调查与高灵敏度的反义转录本的表达，使一个单一的标签可以在一个库中检测时，筛选大量的生物样品。
As a growing number of complementary transcripts, susceptible to exert various regulatory functions, are being found in eukaryotes, high throughput analytical methods are needed to investigate their expression in multiple biological samples. Serial Analysis of Gene Expression (SAGE), based on the enumeration of directionally reliable short cDNA sequences (tags), is capable of revealing antisense transcripts. We initially detected them by observing tags that mapped on to the reverse complement of known mRNAs. The presence of such tags in individual SAGE libraries suggested that SAGE datasets contain latent information on antisense transcripts. We raised a collection of virtual tags for mining these data. Tag pairs were assembled by searching for complementarities between 24-nt long sequences centered on the potential SAGE-anchoring sites of well-annotated human expressed sequences. An analysis of their presence in a large collection of published SAGE libraries revealed transcripts expressed at high levels from both strands of two adjacent, oppositely oriented, transcription units. In other cases, the respective transcripts of such cis-oriented genes displayed a mutually exclusive expression pattern or were co-expressed in a small number of libraries. Other tag pairs revealed overlapping transcripts of trans-encoded unique genes. Finally, we isolated a group of tags shared by multiple transcripts. Most of them mapped on to retroelements, essentially represented in humans by Alu sequences inserted in opposite orientations in the 3'UTR of otherwise different mRNAs. Registering these tags in separate files makes possible computational searches focused on unique sense-antisense pairs. The method developed in the present work shows that SAGE datasets constitute a major resource of rapidly investigating with high sensitivity the expression of antisense transcripts, so that a single tag may be detected in one library when screening a large number of biological samples.