The authors describe the structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. They demonstrate that this engineered complex can activate multiple genes simultaneously and upregulate long intergenic non-coding RNA (lincRNA) transcripts. The authors also synthesize a library of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that confer resistance to a BRAF inhibitor when activated. The results show that the top hits are enriched in genes that are validated using individual sgRNA and cDNA overexpression. The authors conclude that the CRISPR-based gain-of-function screening approach is a powerful tool for functional genomics research.The authors describe the structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. They demonstrate that this engineered complex can activate multiple genes simultaneously and upregulate long intergenic non-coding RNA (lincRNA) transcripts. The authors also synthesize a library of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that confer resistance to a BRAF inhibitor when activated. The results show that the top hits are enriched in genes that are validated using individual sgRNA and cDNA overexpression. The authors conclude that the CRISPR-based gain-of-function screening approach is a powerful tool for functional genomics research.