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We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell.
View Article and Find Full Text PDFFast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations.
PLoS One
January 2025
DIADE, IRD, Cirad, University of Montpellier, Montpellier, France.
Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e.
View Article and Find Full Text PDFDeletion of atypical type II restriction genes in Clostridium cellulovorans using a Cas9-based gene editing system.
Appl Microbiol Biotechnol
January 2025
Chair of Microbiology, Technical University of Munich, TUM School of Life Science, Emil-Ramann-Str. 4, 85354, Freising, Germany.
The anaerobic bacterium Clostridium cellulovorans is a promising candidate for the sustainable production of biofuels and platform chemicals due to its cellulolytic properties. However, the genomic engineering of the species is hampered because of its poor genetic accessibility and the lack of genetic tools. To overcome this limitation, a protocol for triparental conjugation was established that enables the reliable transfer of vectors for markerless chromosomal modification into C.
View Article and Find Full Text PDFGenomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata).
Mol Ecol
January 2025
Department of Biology, Aarhus University, Aarhus C, Denmark.
Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation.
View Article and Find Full Text PDFTranscription near arrested DNA replication forks triggers ribosomal DNA copy number changes.
Nucleic Acids Res
January 2025
Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.
Article Synopsis
- Sir2 is a histone deacetylase that helps maintain the stability of ribosomal RNA genes in budding yeast by preventing DNA breaks from leading to changes in rDNA copy number.
- It does this by suppressing transcription near issues that arise during DNA replication, which can otherwise provoke double-strand breaks (DSBs) and subsequent DNA repair processes.
- When Sir2 is absent, increased transcription can lead to DSBs, resulting in unstable rDNA copy numbers and the formation of extrachromosomal DNA, highlighting the importance of Sir2 in maintaining rDNA integrity.
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