Comparative analysis of sequence features involved in the recognition of tandem splice sites.
Comparative analysis of sequence features involved in the recognition of tandem splice sites.
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DOI：
10.1186/1471-2164-9-202
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发表时间：
2008-04-30
期刊：
影响因子：
4.4
通讯作者：
Holste D
中科院分区：
文献类型：
--
作者：
Bortfeldt R;Schindler S;Szafranski K;Schuster S;Holste D
Pre-mRNAs的剪接明显是可变的，并产生多个选择性剪接(AS)亚型，这些亚型编码来自一个基因座位的不同信息。计算研究发现了一类高度相似的异构体，它们与串联的5‘-剪接位点(5’s)和3‘-剪接位点(3’s)有关，但在实验研究中鲜有轶事证据。为了比较人类不同器官系统和细胞类型中存在的可选串联剪接位点外显子的类型和水平，并研究参与识别和区分相邻剪接位点的已知序列特征，我们进行了大规模、严格的cDNA序列和EST与人类和小鼠基因组的比对，然后进行了实验验证。我们分析了来自转录序列的备选5‘s外显子(A5E)和备选3’s外显子(A3E)，这些转录序列与组装的基因组序列比对，以推断在数千个基因中发生的AS的模式。比较重叠(串联)和非重叠(竞争)A5E和A3E的水平，发现串联受体和供体明显偏爱异构体，分别有四个核苷酸和三到六个核苷酸长外显子延伸。选择了推测的A5E串联外显子的一个子集，并进行了实验验证。我们以A5Es为研究对象，研究了它们的转录覆盖率、序列保守性和与U1单链RNA的碱基配对、近端和远端剪接位点的分类、顺式调控活性的候选基序，并比较了A5Es与A3Es、构成外显子和假外显子在智人和肌肉分枝杆菌中的差异。结果揭示了一组小但真实的丰富的串联剪接位点偏好，在近端和远端5‘s(3’s)之间有特定的距离，这分别显示了A5E和A3E的框内和框外剪接水平之间的明显二分法，识别了一些候选的NMD靶标，并允许根据剪接位点信息粗略估计未检测到的串联供体的数量。这项比较研究区分了串联5‘s和3’s，具有3到6个核苷酸长的延伸，具有异常高的AS比例，在实验上验证了串联供体在一组不同的人类组织中的作用，强调了串联剪接位点发生的AS类型的二分性，并阐明了在重叠的5‘s处剪接的人类可选外显子具有典型剪接变体的特征，这对细胞很有好处。
The splicing of pre-mRNAs is conspicuously often variable and produces multiple alternatively spliced (AS) isoforms that encode different messages from one gene locus. Computational studies uncovered a class of highly similar isoforms, which were related to tandem 5'-splice sites (5'ss) and 3'-splice sites (3'ss), yet with very sparse anecdotal evidence in experimental studies. To compare the types and levels of alternative tandem splice site exons occurring in different human organ systems and cell types, and to study known sequence features involved in the recognition and distinction of neighboring splice sites, we performed large-scale, stringent alignments of cDNA sequences and ESTs to the human and mouse genomes, followed by experimental validation. We analyzed alternative 5'ss exons (A5Es) and alternative 3'ss exons (A3Es), derived from transcript sequences that were aligned to assembled genome sequences to infer patterns of AS occurring in several thousands of genes. Comparing the levels of overlapping (tandem) and non-overlapping (competitive) A5Es and A3Es, a clear preference of isoforms was seen for tandem acceptors and donors, with four nucleotides and three to six nucleotides long exon extensions, respectively. A subset of inferred A5E tandem exons was selected and experimentally validated. With the focus on A5Es, we investigated their transcript coverage, sequence conservation and base-paring to U1 snRNA, proximal and distal splice site classification, candidate motifs for cis-regulatory activity, and compared A5Es with A3Es, constitutive and pseudo-exons, in H. sapiens and M. musculus. The results reveal a small but authentic enriched set of tandem splice site preference, with specific distances between proximal and distal 5'ss (3'ss), which showed a marked dichotomy between the levels of in- and out-of-frame splicing for A5Es and A3Es, respectively, identified a number of candidate NMD targets, and allowed a rough estimation of a number of undetected tandem donors based on splice site information. This comparative study distinguishes tandem 5'ss and 3'ss, with three to six nucleotides long extensions, as having unusually high proportions of AS, experimentally validates tandem donors in a panel of different human tissues, highlights the dichotomy in the types of AS occurring at tandem splice sites, and elucidates that human alternative exons spliced at overlapping 5'ss posses features of typical splice variants that could well be beneficial for the cell.
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影响因子：
4.5
作者：
Borensztajn, Keren;Sobrier, Marie-Laure;Duquesnoy, Philippe;Fischer, Anne-Marie;Tapon-Bretaudiere, Jacqueline;Amselem, Serge
通讯作者：
Amselem, Serge
影响因子：
4.5
作者：
Chern, Tzu-Ming;van Nimwegen, Erik;Kai, Chikatoshi;Kawai, Jun;Carninci, Piero;Hayashizaki, Yoshihide;Zavolan, Mihaela
通讯作者：
Zavolan, Mihaela
影响因子：
11.4
作者：
EPERON, IC;IRELAND, DC;KRAINER, AR
通讯作者：
KRAINER, AR
影响因子：
16.8
作者：
Bühler, M;Steiner, S;Mühlemann, O
通讯作者：
Mühlemann, O
DOI：
10.1073/pnas.0506139102
发表时间：
2005-09-06
影响因子：
11.1
作者：
Baek, D;Green, P
通讯作者：
Green, P