TrAC Trends in Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 118297 - 118297
Published: May 1, 2025
Language: Английский
Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1076 - 1100
Published: Feb. 1, 2024
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes treat underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency easy programmability, stand at forefront this revolution. In Review, we discuss current state CRISPR gene technologies both research therapy, highlighting limitations that constrain them technological innovations have developed recent years address them. Additionally, examine summarize landscape applications context health therapeutics. Finally, outline potential future developments could shape coming years.
Language: Английский
Citations
159
Science, Journal Year: 2024, Volume and Issue: 386(6723)
Published: Nov. 14, 2024
The genome is a sequence that encodes the DNA, RNA, and proteins orchestrate an organism’s function. We present Evo, long-context genomic foundation model with frontier architecture trained on millions of prokaryotic phage genomes, report scaling laws DNA to complement observations in language vision. Evo generalizes across proteins, enabling zero-shot function prediction competitive domain-specific models generation functional CRISPR-Cas transposon systems, representing first examples protein-RNA protein-DNA codesign model. also learns how small mutations affect whole-organism fitness generates megabase-scale sequences plausible architecture. These capabilities span molecular scales complexity, advancing our understanding control biology.
Language: Английский
Citations
71
Biochemistry, Journal Year: 2023, Volume and Issue: 62(24), P. 3465 - 3487
Published: May 16, 2023
CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms have been repurposed for versatile applications therapeutics diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting interference are mediated by effectors that either components of multisubunit complexes class 1 or multidomain single-effector proteins 2. The compact 2 broadly adopted multiple applications, especially genome editing, leading a transformation the molecular biology biotechnology toolkit. diversity enzymes, initially limited Cas9 nuclease, was substantially expanded via computational metagenome mining include numerous variants Cas12 Cas13, providing substrates development versatile, orthogonal tools. Characterization these uncovered many new features, including distinct protospacer adjacent motifs (PAMs) expand space, improved editing specificity, rather than DNA targeting, smaller crRNAs, staggered blunt end cuts, miniature promiscuous cleavage, etc. These unique properties enabled such as harnessing RNase activity type VI effector, supersensitive nucleic acid detection. well, despite challenge expressing delivering multiprotein effectors. rich enzymes led rapid maturation toolbox, capabilities gene knockout, base prime insertion, imaging, epigenetic modulation, transcriptional editing. Combined rational design engineering associated RNAs, natural related bacterial provides vast resource expanding repertoire tools biotechnology.
Language: Английский
Citations
54
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Feb. 27, 2024
The genome is a sequence that completely encodes the DNA, RNA, and proteins orchestrate function of whole organism. Advances in machine learning combined with massive datasets genomes could enable biological foundation model accelerates mechanistic understanding generative design complex molecular interactions. We report Evo, genomic enables prediction generation tasks from to scale. Using an architecture based on advances deep signal processing, we scale Evo 7 billion parameters context length 131 kilobases (kb) at single-nucleotide, byte resolution. Trained prokaryotic genomes, can generalize across three fundamental modalities central dogma biology perform zero-shot competitive with, or outperforms, leading domain-specific language models. also excels multi-element tasks, which demonstrate by generating synthetic CRISPR-Cas complexes entire transposable systems for first time. information learned over predict gene essentiality nucleotide resolution generate coding-rich sequences up 650 kb length, orders magnitude longer than previous methods. multi-modal multi-scale provides promising path toward improving our control multiple levels complexity.
Language: Английский
Citations
53
Nature Microbiology, Journal Year: 2025, Volume and Issue: 10(1), P. 20 - 27
Published: Jan. 2, 2025
Language: Английский
Citations
3
Science Advances, Journal Year: 2023, Volume and Issue: 9(39)
Published: Sept. 27, 2023
Programmable RNA-guided DNA nucleases perform numerous roles in prokaryotes, but the extent of their spread outside prokaryotes is unclear. Fanzors, eukaryotic homolog prokaryotic TnpB proteins, have been detected genomes eukaryotes and large viruses, activity functions remain unknown. Here, we characterize Fanzors as RNA-programmable endonucleases, using biochemical cellular evidence. We found diverse that frequently associate with various transposases. Reconstruction evolution revealed multiple radiations RuvC-containing homologs eukaryotes. Fanzor genes captured introns proteins acquired nuclear localization signals, indicating extensive, long-term adaptation to functioning cells. contain a rearranged catalytic site RuvC domain, similar distinct subset TnpBs, lack collateral cleavage activity. demonstrate can be harnessed for genome editing human cells, highlighting potential these widespread biotechnology applications.
Language: Английский
Citations
33
Science, Journal Year: 2024, Volume and Issue: 386(6717)
Published: Aug. 8, 2024
Defense-associated reverse transcriptase (DRT) systems perform DNA synthesis to protect bacteria against viral infection, but the identities and functions of their products remain largely unknown. We show that DRT2 encode an unprecedented immune pathway involves de novo gene through rolling circle transcription a noncoding RNA (ncRNA). Programmed template jumping on ncRNA generates concatemeric cDNA, which becomes double-stranded upon infection. This product constitutes protein-coding, nearly endless open reading frame ( neo ) whose expression leads potent cell growth arrest, restricting Our work highlights elegant expansion genome coding potential RNA-templated creation challenges conventional paradigms genetic information encoded along one-dimensional axis genomic DNA.
Language: Английский
Citations
15
The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 926, P. 172115 - 172115
Published: April 1, 2024
Language: Английский
Citations
12
Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)
Published: Jan. 7, 2025
Abstract Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a nuclease (747 amino acids in length) multiple functional states, revealing stepwise process DNA targeting involving conformational switch REC2 domain insertion. Our provide insights into intricately folded guide RNA which acts as structural scaffold to anchor small, flexible protein domains for recognition. The sgRNA can be truncated by up ~25% yet still retain activity vivo. Using ancestral sequence reconstruction, generated capable efficient mammalian cells. Collectively, our results mechanistic evolution and diverse systems, providing blueprint future re-engineering minimal RNA-guided endonucleases.
Language: Английский
Citations
2
Nature Plants, Journal Year: 2025, Volume and Issue: unknown
Published: April 22, 2025
Language: Английский
Citations
2