scholarly journals CRISPR-mediated biocontainment

2020 ◽  
Author(s):  
Oscar Castanon ◽  
Cory J. Smith ◽  
Parastoo Khoshakhlagh ◽  
Raphael Ferreira ◽  
Marc Güell ◽  
...  
Keyword(s):  
Cell Death ◽  
Transposable Elements ◽  
Human Genome ◽  
Genome Editing ◽  
Copy Number ◽  
Proof Of Concept ◽  
Defense System ◽  
Dna Breaks ◽  
Repetitive Nature ◽  
Mammalian Genomes

AbstractWe have exploited the repetitive nature of transposable elements of the human genome to generate synthetic circuits. Transposable elements such as LINE-1 and Alu have successfully replicated in mammalian genomes throughout evolution to reach a copy number ranging from thousands to more than a million. Targeting these repetitive elements with programmable DNA nucleases such as CRISPR-Cas9 rapidly induce extremely high levels of cell death. We use this genotoxic feature to build synthetic biocontainment circuits: CRISPR defense system (CRISPR-DS) capable of preventing CRISPR genome editing, and we introduce the proof-of-concept of CRISPR Safety-Switch, an inducible, stringent and non-leaky kill-switch capable of clearing out cell lines resistant to DNA breaks.

scholarly journals Paired-end Mappability of Transposable Elements in the Human Genome

2019 ◽  
Author(s):  
Corinne E Sexton ◽  
Mira V Han
Keyword(s):  
Transposable Elements ◽  
Human Genome ◽  
Read Length ◽  
Sequencing Technology ◽  
Repetitive Nature ◽  
Specific Mapping ◽  
Conventional Sequencing

AbstractThough transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50bp, 76bp and 100bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68%, 85%, and 88% of all transposable elements in the RepeatMasker database are uniquely mappable, suggesting that accurate locus-specific mapping of older transposable elements is well within reach.

scholarly journals An improved method for precise genome editing in zebrafish using CRISPR-Cas9 technique

2021 ◽  
Author(s):  
Eugene V. Gasanov ◽  
Justyna Jędrychowska ◽  
Michal Pastor ◽  
Malgorzata Wiweger ◽  
Axel Methner ◽  
...  
Keyword(s):  
Genome Editing ◽  
High Efficiency ◽  
Target Site ◽  
Proof Of Concept ◽  
Intervention Site ◽  
End Joining ◽  
Guide Rna ◽  
Guide Rnas ◽  
Cas9 Nuclease ◽  
Non Homologous End Joining

AbstractCurrent methods of CRISPR-Cas9-mediated site-specific mutagenesis create deletions and small insertions at the target site which are repaired by imprecise non-homologous end-joining. Targeting of the Cas9 nuclease relies on a short guide RNA (gRNA) corresponding to the genome sequence approximately at the intended site of intervention. We here propose an improved version of CRISPR-Cas9 genome editing that relies on two complementary guide RNAs instead of one. Two guide RNAs delimit the intervention site and allow the precise deletion of several nucleotides at the target site. As proof of concept, we generated heterozygous deletion mutants of the kcng4b, gdap1, and ghitm genes in the zebrafish Danio rerio using this method. A further analysis by high-resolution DNA melting demonstrated a high efficiency and a low background of unpredicted mutations. The use of two complementary gRNAs improves CRISPR-Cas9 specificity and allows the creation of predictable and precise mutations in the genome of D. rerio.

scholarly journals Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PLoS Genetics ◽  
2014 ◽  
Vol 10 (4) ◽  
pp. e1004298 ◽  
Author(s):  
Concepcion M. Diez ◽  
Esteban Meca ◽  
Maud I. Tenaillon ◽  
Brandon S. Gaut
Keyword(s):  
Zea Mays ◽  
Transposable Elements ◽  
Copy Number ◽  
Host Responses ◽  
Number Dynamics

scholarly journals The Human Genome Puzzle — the Role of Copy Number Variation in Somatic Mosaicism

2010 ◽  
Vol 11 (6) ◽  
pp. 426-431 ◽  
Author(s):  
Hasmik Mkrtchyan ◽  
Madeleine Gross ◽  
Sophie Hinreiner ◽  
Anna Polytiko ◽  
Marina Manvelyan ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Human Genome ◽  
Copy Number ◽  
Somatic Mosaicism ◽  
Number Variation
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