The Yeast Splice Site Revisited: New Exon Consensus from Genomic Analysis
The Yeast Splice Site Revisited: New Exon Consensus from Genomic Analysis
复制标题
重新审视酵母剪接位点：基因组分析的新外显子共识
DOI：
10.1016/s0092-8674(00)80462-6
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发表时间：
1997
期刊：
影响因子：
64.5
通讯作者：
W. Gilbert
中科院分区：
文献类型：
--
作者：
M. Long;S. J. Souza;W. Gilbert
Rosbash，1992）。然而，mation：酵母内含子的不同编译产生了冲突的外显子共有模式（Csunk等人，1990; Rymond and Rosbash，Rs（i）2 fblog2（fb）e（n），1992）.酵母基因组的整个序列（Goffeau et al.，1996）现在允许检查所有的其中fb和e（n）是核苷酸的频率和样品大小（n）的校正项（Schneider等，关于这个生物体的信息在这样做的过程中，我们发现了一个迄今为止未被注意到的共识模式（1986）。在外显子（外显子的位置1至aries，并且表明这种模式是外显子序列与10相互作用的结果）至剪接位点的3侧中没有保守性。然而，显着的保守性出现在第5外显子的位置2，小核RNA（snRNA）。在参与剪接的几个snRNAs中，3和4在信息含量和频率上都很明显。为了鉴定共有序列，我们认为U 5与5个外显子序列相互作用，以帮助定义5个剪接位点（根据单个碱基应占总数至少40%的标准进行审查）。因此，我们定义一个S。酿酒酵母外显子Steitz，1992; Horowitz和Krainer，1994）。Wyatt等人（1992）证明哺乳动物U 5 snRNA可以共有剪接位点为A47 A53 A44 N N（下标显示碱基的实际百分比，并交联到5个剪接位点的上游区域，Watson-Crick配对到5个外显子，条形“”显示内含子位置）。这种共识显然不同于以前得出的共识，使用较小的不需要。然而，在S.酿酒酵母，纽曼和诺曼（1992）发现了这样的配对之间的U 5和样品：T44 G50 N在Csunt等人。Rymond和Rosbash（1992）从54个外显子的第2和第3个位置上获得了74个N（G/A）。最近，O 'Keefe et al.（1996）在体外表明，涉及环内含子的突变。该共有序列的生物学作用是在U 5的I区不消除内含子剪接反应的第一催化步骤，但影响5外显子序列与snRNA的第二催化配对。纽曼和诺曼（1992）证明，核苷酸5和步骤。此外，他们的体内实验表明，所有这些突变都是致命的。Sontheimer和Steitz 6在U 5 snRNA的高度保守环I中与mRNA的5外显子序列中的碱基2和3配对，（1993）证明U 5在整个剪接反应中继续保持5外显子。因此，奥基夫基于抑制点突变。环I的序列是（从位置1至9）-GCCUUUUAC。因此，外显子中具有共有AA的2和3位可以形成Watson-Crick碱基配对取向，用于在第二催化步骤中在3剪接位点处的亲核攻击。然而，核苷酸5和6的情况尚不清楚。4外显子共有A也与环中的核苷酸7互补，尽管U 5的环I和5外显子的末端之间如何发生相互作用，因为环的序列实际配对必须通过实验来证明。I是高度保守的，而外显子序列是可变的。通过对酵母基因组数据库的扫描，我们构建了一个包含所有内含子的内含子/外显子子数据库，满足了U 5与外显子序列部分配对的生物学模型。酿酒酵母，使用程序dom匹配的几个碱基在每个网站或可能涉及特定的序列。因此，我们问是否有来自龙...
Rosbash, 1992). However, different compilations of mation: yeast introns have yielded conflicting exon consensus patterns (Csank et al., 1990; Rymond and Rosbash, Rs (i) 2 fblog2 (fb) e (n), 1992). The entire sequence of the yeast genome (Goffeau et al., 1996) now permits one to examine all the where fb and e (n) are the frequency of nucleotides and a correction term for sample size (n)(Schneider et al., information for this organism. In doing so, we find a hitherto unnoticed consensus pattern near the bound- 1986). There is no conservation in the exon (positions 1 to aries of the exons and suggest that this pattern is the result of the interaction of the exon sequence with a 10) to the 3 side of the splice site. However, significant conservation appears in the 5 exon at positions 2, small nuclear RNA (snRNA). Among the several snRNAs involved in the splicing 3, and 4, evident both in the information content and in the frequencies. To identify a consensus, we take as process, U5 is thought to interact with 5 exon sequences to help define 5 splice sites (reviewed by a criterion that a single base should represent at least 40% of the total. Thus, we define an S. cerevisiae exon Steitz, 1992; Horowitz and Krainer, 1994). Wyatt et al.(1992) demonstrated that the mammalian U5 snRNA can consensus for the splice site as A47A53A44N N (the subscripts show the actual percentages of the bases and be cross-linked to the region upstream of the 5 splice sites and that Watson–Crick pairing to the 5 exon is the bar “” shows the intron position). This consensus is clearly different from those derived before, using smaller not required. However, in S. cerevisiae, Newman and Norman (1992) found such a pairing between U5 and samples: T44G50 N in Csank et al.(1990) from 18 introns, and (G/A) 74 N in Rymond and Rosbash (1992) from 54 the 2 and 3 exon positions. Recently, O’Keefe et al.(1996) showed in vitro that mutations involving the loop introns. A biological role for this consensus would be in a I region of U5 do not abolish the first catalytic step of intron splicing reaction but affect the second catalytic pairing of the 5 exon sequence to an snRNA. Newman and Norman (1992) demonstrated that nucleotides 5 and step. Furthermore, their in vivo experiments showed that all such mutations are lethal. Sontheimer and Steitz 6 in the highly conserved loop I of U5 snRNA pair with bases 2 and 3 in the 5 exon sequence of the mRNA,(1993) demonstrated that U5 continues to hold the 5 exon throughout the splicing reaction. Hence, O’Keefe based on the suppression of point mutations. The sequence of loop I is (from positions 1 to 9)-GCCUUUUAC. et al. argue that the role of the loop I of U5 is to tether the free 5 exon after the first splicing step in the correct Thus, the 2 and 3 positions in the exon, which have a consensus AA, could form Watson–Crick base-pairings orientation for a nucleophilic attack at the 3 splice site in the second catalytic step. Nonetheless, it is not clear with nucleotides 5 and 6. The 4 exon consensus A is also complementary to nucleotide 7 in the loop, although how an interaction between loop I of U5 and the end of the 5 exon could occur, because the sequence of loop an actual pairing would have to be proved by experiment. I is highly conserved while exon sequences are variable. By scanning the Saccharomyces Genome Database, This biological model of partial pairing between U5 and the exon sequences could be satisfied through ranwe constructed an intron/exon subdatabase that contains all the introns for S. cerevisiae, using programs dom matching of a few bases at each site or could involvespecificsequences. Thus, weaskediftherewere from Long …
影响因子：
5.6
作者：
SCHNEIDER, TD;STORMO, GD;EHRENFEUCHT, A
通讯作者：
EHRENFEUCHT, A
DOI：
10.1073/pnas.92.26.12495
发表时间：
1995-12-19
影响因子：
11.1
作者：
Long, MY;Rosenberg, C;Gilbert, W
通讯作者：
Gilbert, W