Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [RNA-seq]

Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, a higher primate-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. We combine CARGO with CRISPR activation or interference to, respectively, induce or silence LTR5HS en masse, and demonstrate that this system robustly targets the vast majority of LTR5HS insertions. Remarkably, activation/silencing of LTR5HS is associated with reciprocal up- and down-regulation of hundreds of human genes. These effects require presence of retroviral sequences, but occur over long genomic distances, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in higher primates. Overall design: Identify transcriptional changes of CARGO-CRISPRa/CRISPRi by RNA-seq CRISPR dCas9 fusions to target transposable elements in the genome; 'VPR' and 'KRAB' refer to the name of the dCas9 fusion protein expressed in the given sample. 'Sp' and 'Sa' refer to the gRNA scaffold species for the CRISPR targeting construct, and 'LTR5HS' and 'nontarget' refer to the class of transposable element (or none at all) that the CRISPR targeting construct aims to target.