Elucidating the molecular architecture of adaptation via evolve and resequence experiments

A Long, G Liti, A Luptak, O Tenaillon - Nature Reviews Genetics, 2015 - nature.com
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations
to a novel environment, then next-generation sequencing to analyse genetic changes. They …

Chemistry and biology of self-cleaving ribozymes

RM Jimenez, JA Polanco, A Lupták - Trends in biochemical sciences, 2015 - cell.com
Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and
catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a …

A widespread self-cleaving ribozyme class is revealed by bioinformatics

A Roth, Z Weinberg, AGY Chen, PB Kim… - Nature chemical …, 2014 - nature.com
Ribozymes are noncoding RNAs that promote chemical transformations with rate
enhancements approaching those of protein enzymes. Although ribozymes are likely to …

Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function

CE Weinberg, Z Weinberg… - Nucleic acids research, 2019 - academic.oup.com
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester
backbone at a specific linkage. The structures of and the reactions catalysed by members of …

The ubiquitous hammerhead ribozyme

C Hammann, A Luptak, J Perreault, M De La Peña - Rna, 2012 - rnajournal.cshlp.org
The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-)
cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three …

Identification of hammerhead ribozymes in all domains of life reveals novel structural variations

J Perreault, Z Weinberg, A Roth… - PLoS computational …, 2011 - journals.plos.org
Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by
internal phosphoester transfer. Comparative sequence analysis was used to identify …

The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme

X Zhan, TJ Wilson, Z Li, J Zhang, Y Yang… - Nature …, 2024 - nature.com
We have determined the crystal structure of a pseudoknot (PK)-containing hammerhead
ribozyme that closely resembles the pistol ribozyme, with essentially identical secondary …

A general design strategy for protein-responsive riboswitches in mammalian cells

S Ausländer, P Stücheli, C Rehm, D Ausländer… - Nature …, 2014 - nature.com
RNAs are ideal for the design of gene switches that can monitor and program cellular
behavior because of their high modularity and predictable structure-function relationship …

HDV-like self-cleaving ribozymes

CHT Webb, A Lupták - RNA biology, 2011 - Taylor & Francis
HDV ribozymes catalyze their own scission from the transcript during rolling circle replication
of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human …

Hovlinc is a recently evolved class of ribozyme found in human lncRNA

Y Chen, F Qi, F Gao, H Cao, D Xu… - Nature chemical …, 2021 - nature.com
Although naturally occurring catalytic RNA molecules—ribozymes—have attracted a great
deal of research interest, very few have been identified in humans. Here, we developed a …