Hundreds of putatively functional small open reading frames in Drosophila.
Hundreds of putatively functional small open reading frames in Drosophila.
复制标题
果蝇中数百个被认为具有功能的小型开放阅读框。
DOI：
10.1186/gb-2011-12-11-r118
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发表时间：
2011-11-25
期刊：
影响因子：
12.3
通讯作者：
Couso JP
中科院分区：
文献类型：
--
作者：
Ladoukakis E;Pereira V;Magny EG;Eyre-Walker A;Couso JP
DNA序列与编码信息之间的关系至今仍是一个未解之谜。基因组计划在高等真核生物中发现的蛋白质编码基因的数量比预期的要少，而在高等真核生物中却发现了相当数量的蛋白质非编码转录。已知功能性小开放阅读框（smORF）存在于几种生物体中。然而，编码序列检测方法偏向于检测这种非常短的开放阅读帧。因此，编码短肽的大量非规范编码区可能等待表征。利用生物信息学方法，我们在果蝇的pupirin非编码常染色质DNA中搜索了小于100个氨基酸的smORF，并初步鉴定了其中近60万个。我们研究了这些smORF作为编码实体在D.黑腹果蝇和拟暗果蝇，它们在基因组的同线和转录区域中的存在，以及它们的保守与非保守核苷酸变化的比率。对于阴性对照，我们将结果与使用随机短序列获得的结果进行比较，而阳性对照由蛋白质组学数据验证的smORF提供。这些分析的结合使我们假设果蝇中至少存在401个功能性smORF，可能存在多达4，561个这样的功能性smORF。
The relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization. Using bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data. The combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist.
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影响因子：
7
作者：
Brent, MR
通讯作者：
Brent, MR
影响因子：
12.3
作者：
Brachat, Sophie;Dietrich, Fred S;Voegeli, Sylvia;Zhang, Zhihong;Stuart, Larissa;Lerch, Anita;Gates, Krista;Gaffney, Tom;Philippsen, Peter
通讯作者：
Philippsen, Peter
影响因子：
7
作者：
Hanada, Kousuke;Zhang, Xu;Shiu, Shin-Han
通讯作者：
Shiu, Shin-Han
DOI：
10.1089/cmb.1995.2.117
发表时间：
1995-01-01
期刊：
Journal of computational biology : a journal of computational molecular cell biology
影响因子：
--
作者：
Fickett, J W
通讯作者：
Fickett, J W
影响因子：
5.4
作者：
Hayden CA;Jorgensen RA
通讯作者：
Jorgensen RA