rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.
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DOI：
10.1093/bioinformatics/btt184
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发表时间：
2013-06-15
期刊：
影响因子：
--
通讯作者：
Baranov PV
中科院分区：
文献类型：
--
作者：
O'Connor PB;Li GW;Weissman JS;Atkins JF;Baranov PV
动机：核糖体图谱是一种新技术，它允许在整个转录组水平上监测翻译核糖体在mRNA上的位置。最近的一项核糖体图谱研究表明，Shine-Dalgarno(SD)内部序列对细菌的翻译速率具有重大的全球影响：核糖体在mRNA中的SD位点暂停。因此，了解SD位点如何通过核糖体影响mRNA的移动和核糖体足迹的产生是很重要的。结果：在这里，我们提供了证据，除了暂停效应外，内部SD序列还诱导了mRNA在核糖体空腔中的毛毛虫状移动。一旦SD位点与核糖体结合，当核糖体解码几个后续密码子时，它仍然与核糖体相连。这导致核糖体足迹在3‘端的不对称渐进性延长。内部SD序列很可能不是在单个密码子上而是在几个相邻密码子上引起停顿。这一发现对于我们理解核糖体中的信使核糖核酸的运动是重要的，也应该有助于解释核糖体图谱数据。联系方式：brave.oval.span@gmail.com
Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine–Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3′-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data. Contact: brave.oval.pan@gmail.com
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DOI：
10.1101/sqb.1987.052.01.078
发表时间：
1987-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
WEISS, RB;DUNN, DM;GESTELAND, RF
通讯作者：
GESTELAND, RF
影响因子：
7
作者：
Michel AM;Choudhury KR;Firth AE;Ingolia NT;Atkins JF;Baranov PV
通讯作者：
Baranov PV
影响因子：
3
作者：
Hyatt, Doug;Chen, Gwo-Liang;Hauser, Loren J.
通讯作者：
Hauser, Loren J.
影响因子：
11.4
作者：
WEISS, RB;DUNN, DM;GESTELAND, RF
通讯作者：
GESTELAND, RF
影响因子：
3.2
作者：
LARSEN, B;WILLS, NM;ATKINS, JF
通讯作者：
ATKINS, JF