TALENSeek: A validated program for identifying genomic engineering sites
Saturday, Nov 09, 2013, 2:00 PM - 3:00 PM
*J. L. STEIN
, J. S. GRIMLEY
, V. MENON
, D. H. GESCHWIND
, A. KAYKAS
Neurol., UCLA, Los Angeles, CA;
Allen Inst. for Brain Sci., Seattle, WA
Transcription activator-like effector (TALE) proteins can be designed to efficiently and selectively bind to desired sequences in the genome of any species. TALE proteins are often combined with nucleases (TALENs) to cut the genome and insert desired sequences, creating the possibility of genome editing and engineering.
We developed automated software, entitled TALENSeek, to identify unique TALEN binding sites of a user-specified gene or genomic locus. The program is outlined in Figure 1, where (a) automated annotation of genetic regions are used to identify start and end sites of a gene using the farthest protein coding regions across all isoforms (b) potential TALEN binding sites are identified; (c) TALEN binding sites are evaluated for uniqueness across the genome; (d) if a binding site is non-unique, the binding sites are shifted into the coding region of the gene and the algorithm iterates from step (b). Chromosomal locations and genomic sequences of the TALEN binding site are output. In addition, chromosomal locations of TALEN binding sites can be visualized in genome browsers. Homology arms to generate gene knock-outs, knock-ins or correction are also output by the program and can be used to generate donor constructs to direct homologous dependent repair.
The TALENSeek program has been applied to generate genome-wide TALEN binding sites for each isoform of each gene in the human genome (hg19; 509,262 unique binding sites generated). Eight TALEN pairs were assembled and demonstrated activity in K562 cells; one of these eight has been used in human embryonic stem cells to generate hetero- and homozygously targeted cell lines. TALENSeek can be easily modified to any species with an available genome sequence. An application of the program to mouse (mTALENSeek) is also currently available.
TALENSeek is a user-friendly bioinformatics tool that allows for the design of unique TALEN binding sites in the genome. TALENs are efficient genome editing tools, which create the possibility of direct modeling of disease-associated mutations in developing human stem cells.
Broad Stem Cell Research Center Innovation Award
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