Luca Pinello | Search bioRxiv

bioRxiv2016

Forward genetic screen of human transposase genomic rearrangements

Background. Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. Results. To enable functional analysis of human transposase-derived genes, we combined forward chemical genetic hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) screening with massively parallel paired-end DNA sequencing and structural variant genome assembly and analysis. Here, we report the HPRT1 mutational spectrum induced by the human transposase PGBD5, including PGBD5-specific signal sequences (PSS) that serve as potential genomic rearrangement substrates. Conclusions. The discovered PSS motifs and high-throughput forward chemical genomic screening approach should prove useful for the elucidation of endogenous genome remodeling activities of PGBD5 and other domesticated human DNA transposases and recombinases.

Genomics↗

bioRxiv2015

CRISPResso: sequencing analysis toolbox for CRISPR genome editing

To the Editor To the Editor References Recent progress in genome editing technologies, in particular the CRISPR-Cas9 nuclease system, has provided new opportunities to investigate the biological functions of genomic sequences by targeted mutagenesis [1-4]. Briefly, Cas9 may be directed by a chimeric single guide RNA (sgRNA) to a target genomic sequence upstream of a protospacer adjacent motif (PAM) for cleavage. Double strand breaks (DSBs) resulting from site-specific Cas9 cleavage can be resolved by endogenous DNA repair pathways such as non-homologous end joining (NHEJ) or homology-directed repair (HDR). These repair mechanisms result in a spectrum of diverse outcomes including insertions, deletions, nucleotide substitutions, and, in the case of HDR, recombination of extrachromosomal donor sequences [1-3, 5 ...

Bioinformatics↗