2D структура РНК
Sep. 29th, 2010 02:51 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
imbgВ лаборатории Эрана Сигала (Институт им. Вайцманна, Реховот, Израиль) предложен новый экспериментальный метод установления 2В структуры РНК. Интересующую РНК синтезировали in vitro, и параллельно расщепляли двумя структуро-специфичными РНКазами. После этого фрагменты сиквенировали, и компьютерная программа на основе этих данных могла точно определить структуру исходной РНК, соотнося полученные отрезки.
На сколько я знаю - это первый не-компьютерный метод установления вторичной структуры РНК. Все компьютерные методы более просты, но менее надежны. Поэтому значеия данных работ сложно переоценить.
Текст и ссылка на английскую статью:
Genome-wide Measurement of RNA Secondary Structure in Yeast
Michael Kertesz, Yue Wan, Elad Mazor, John L. Rinn, Robert C. Nutter, Howard Y. Chang, Eran Segal
The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
Link
На сколько я знаю - это первый не-компьютерный метод установления вторичной структуры РНК. Все компьютерные методы более просты, но менее надежны. Поэтому значеия данных работ сложно переоценить.
Текст и ссылка на английскую статью:
Genome-wide Measurement of RNA Secondary Structure in Yeast
Michael Kertesz, Yue Wan, Elad Mazor, John L. Rinn, Robert C. Nutter, Howard Y. Chang, Eran Segal
The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
Link
