Arc Institute Scientists Discover Next-Generation System for Programmable Genome Design
2024年6月27日 - 12:00AM
ビジネスワイヤ(英語)
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Using a novel bispecific guide RNA, the bridge recombinase
mechanism enables modular and programmable DNA insertion, excision,
and inversion in bacteria
In a leap forward for genetic engineering, a team of researchers
from the Arc Institute has discovered the bridge recombinase
mechanism, a precise and powerful tool to recombine and rearrange
DNA in a programmable way.
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Credit: Visual Science
The study published today in Nature reports their discovery of
the first DNA recombinase that uses a non-coding RNA for
sequence-specific selection of target and donor DNA molecules. This
bridge RNA is programmable, allowing the user to specify any
desired genomic target sequence and any donor DNA molecule to be
inserted.
"The bridge RNA system is a fundamentally new mechanism for
biological programming," said Dr. Patrick Hsu, senior author of the
study and an Arc Institute Core Investigator and University of
California, Berkeley Assistant Professor of Bioengineering. "Bridge
recombination can universally modify genetic material through
sequence-specific insertion, excision, inversion, and more,
enabling a word processor for the living genome beyond CRISPR."
Arc senior scientist Dr. Matthew Durrant and UC Berkeley
bioengineering graduate student Nick Perry were the lead authors of
the discovery. The research was developed in collaboration with the
labs of Dr. Silvana Konermann, Arc Institute Core Investigator and
Stanford University Assistant Professor of Biochemistry, and Dr.
Hiroshi Nishimasu, Professor of Structural Biology at the
University of Tokyo.
Programmable RNA
The bridge recombination system hails from insertion sequence
110 (IS110) elements, one of countless types of transposable
elements—or “jumping genes”—that cut and paste themselves to move
within and between microbial genomes. Transposable elements are
found across all life forms and have evolved into professional DNA
manipulation machines in order to survive. The IS110 elements are
very minimal, consisting only of a gene encoding the recombinase
enzyme, plus flanking DNA segments that have, until now, remained a
mystery.
The Hsu lab found that when IS110 excises itself from a genome,
the non-coding DNA ends are joined together to produce an RNA
molecule – the bridge RNA – that folds into two loops. One loop
binds to the IS110 element itself, while the other loop binds to
the target DNA where the element will be inserted. The bridge RNA
is the first example of a bispecific guide molecule, specifying the
sequence of both target and donor DNA through base-pairing
interactions.
Each loop of the bridge RNA is independently programmable,
allowing researchers to mix and match any target and donor DNA
sequences of interest. This means the system can go far beyond its
natural role that inserts the IS110 element itself, instead
enabling insertion of any desirable genetic cargo—like a functional
copy of a faulty, disease-causing gene—into any genomic location.
In this work, the team demonstrated over 60% insertion efficiency
of a desired gene in E. coli with over 94% specificity for the
correct genomic location.
“These programmable bridge RNAs distinguish IS110 from other
known recombinases, which lack an RNA component and cannot be
programmed,” said Perry. “It’s as if the bridge RNA were a
universal power adapter that makes IS110 compatible with any
outlet.”
The Hsu lab’s discovery is complemented by their collaboration
with the lab of Dr. Hiroshi Nishimasu at the University of Tokyo,
also published today in Nature. The Nishimasu lab used
cryo-electron microscopy to determine the molecular structures of
the recombinase-bridge RNA complex bound to target and donor DNA,
sequentially progressing through the key steps of the recombination
process.
With further exploration and development, the bridge mechanism
promises to usher in a third generation of RNA-guided systems,
expanding beyond the DNA and RNA cutting mechanisms of CRISPR and
RNA interference (RNAi) to offer a unified mechanism for
programmable DNA rearrangements. Critical for the further
development of the bridge recombination system for mammalian genome
design, the bridge recombinase joins both DNA strands without
releasing cut DNA fragments—sidestepping a key limitation of
current state-of-the-art genome editing technologies.
“The bridge recombination mechanism solves some of the most
fundamental challenges facing other methods of genome editing,”
said research co-lead Durrant. “The ability to programmably
rearrange any two DNA molecules opens the door to breakthroughs in
genome design.”
Read the papers in Nature here and here. A short video of the
discovery, developed in collaboration with Visual Science, is
available here.
Other co-authors include James Pai and Aditya Jangid (Arc
Institute and University of California, Berkeley); Januka
Athukoralage, John McSpedon and April Pawluk (Arc Institute); and
Masahiro Hiraizumi (University of Tokyo). This work was supported
by the Arc Institute, the NIH Biology and Biotechnology of Cell and
Gene Therapy Training Program, JSPS KAKENHI Grant Numbers 21H05281
and 22H00403; Takeda Medical Research Foundation; the Inamori
Research Institute for Science, Rainwater Foundation, Curci
Foundation, Rose Hill Innovators Program, S. Altman, V. and N.
Khosla, and anonymous gifts to the Hsu Lab.
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Jessica Adkins jessica@arcinstitute.org