RNA structures by the thousands

Date:
June 17, 2020
Source:
Ruhr-University Bochum
Summary:
Researchers have developed a new method to determine the structures
of all RNA molecules in a bacterial cell at once. In the past,
this had to be done individually for each molecule. Besides their
exact composition, their structure is crucial for the function
of the RNAs. The team has now described the new high-throughput
structure mapping method.



FULL STORY ========================================================================== Researchers from Bochum and Mu"nster have developed a new method
to determine the structures of all RNA molecules in a bacterial
cell at once. In the past, this had to be done individually for each
molecule. Besides their exact composition, their structure is crucial
for the function of the RNAs. The team describes the new high-throughput structure mapping method, termed Lead-Seq for lead sequencing, in the
journal Nucleic Acids Research, published online on 28 May 2020.


========================================================================== Christian Twittenhoff, Vivian Brandenburg, Francesco Righetti and
Professor Franz Narberhaus from the Chair of Microbial Biology at Ruhr-Universita"t Bochum (RUB) collaborated with the bioinformatics
group headed by Professor Axel Mosig at RUB and the team led by Professor
Petra Dersch at the University of Mu"nster, previously from the Helmholtz Centre for Infection Research in Braunschweig.

No structure -- no function In all living cells, genetic information is
stored in double-stranded DNA and transcribed into single-stranded RNA,
which then serves as a blueprint for proteins. However, RNA is not only
a linear copy of the genetic information, but often folds into complex structures. The combination of single-stranded and partially folded double-stranded regions is of central importance for the function and
stability of RNAs. "If we want to learn something about RNAs, we must
also understand their structure," says Franz Narberhaus.

Lead ions reveal single-stranded RNA positions With lead sequencing, the authors present a method that facilitates the simultaneous analysis of
all RNA structures in a bacterial cell. In the process, the researchers
take advantage of the fact that lead ions cause strand breaks in single-stranded RNA segments; folded RNA structures, i.e. double strands, remain untouched by lead ions.



==========================================================================
By applying lead, the researchers split the single-stranded RNA regions at random locations into smaller fragments, then transcribed them into DNA
and sequenced them. The beginning of each DNA sequence thus corresponded
to a former strand break in the RNA. "This tells us that the corresponding
RNA regions were present as a single strand," explains Narberhaus.

Predicting the structure using bioinformatics Vivian Brandenburg and
Axel Mosig then used bioinformatics to evaluate the information on the single-stranded RNA sections obtained in the experiments.

"We assumed that non-cut RNA regions were present as double strands
and used prediction programs to calculate how the RNA molecules must be folded," elaborates Vivian Brandenburg. "This resulted in more reliable structures with the information from lead sequencing than without this information." This approach enabled the researchers to simultaneously determine the structures of thousands of RNAs of the bacterium Yersinia pseudotuberculosis all at once. The team compared the results obtained
by lead sequencing of some RNA structures with results obtained using traditional methods -- they were both the same.

New RNA thermometers discovered The group carried out their experiments at
25 and 37 degrees Celsius, since some RNA structures change depending on
the temperature. Using what is known as RNA thermometers, bacteria such as
the diarrhoea pathogen Yersinia pseudotuberculosis can detect whether they
are inside the host. Using lead sequencing, the team not only identified already known RNA thermometers, but also discovered several new ones.

Establishing lead sequencing took about five years. "I'm happy to say
that we are now able to map numerous RNA molecules in a bacterium simultaneously," concludes Franz Narberhaus. "One advantage of the
method is that the small lead ions can easily enter living bacterial
cells. We therefore assume that this method can be used universally and
will in future facilitate the detailed structure-function analysis of
bacterial RNAs."

========================================================================== Story Source: Materials provided by Ruhr-University_Bochum. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Franz Narberhaus, Petra Dersch, Axel Mosig, Aaron M Nuss, Francesco
Righetti, Vivian B Brandenburg, Christian Twittenhoff. Lead-seq:
transcriptome-wide structure probing in vivo using lead(II)
ions. Nucleic Acids Research, 2020; DOI: 10.1093/nar/gkaa404 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/06/200617145959.htm

--- up 21 weeks, 1 day, 2 hours, 34 minutes
* Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1337:3/111)