Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation [ATAC-seq]

Transcriptional enhancers are non-coding DNA elements that regulate gene transcription in a temporal and tissue-specific manner. Despite advances in computational and experimental methods, identifying enhancers and their target genes essential for specific biological processes remains challenging. Determining target genes for enhancers is also complex and often relies on indirect, low-resolution, and/or assumptive methodologies. To identify and functionally perturb enhancers at their endogenous sites without altering their sequence, we performed a pooled tiling CRISPR activation (CRISPRa) screen surrounding PHOX2B, a master regulator of neuronal cell fate and a key player in neuroblastoma development. This screen allowed the identification of CRISPRa- responsive elements (CaREs) that alter cellular growth within the 2 Mb genomic region. To determine CaRE target genes, we developed TESLA-seq (TargEted- SingLe- cell- Activation), which combines CRISPRa screening with targeted single-cell RNA-sequencing, and identified functional CaRE-target gene pairs. While most TESLA-revealed CaRE-gene relationships involved neuroblastoma-related regulatory elements already active in the system, we found many CaREs and target connections normally active only in other tissue types or with no previous evidence and induced out of context by CRISPRa. This highlights the power of TESLA-seq to reveal gene regulatory networks active outside of a given experimental system. Overall design: ATAC-seq experiments were performed in the SH-SY5Y, CLB-Ga, IMR-5, Kelly and NGP neuroblastoma cell lines using 100,000 cells according to the protocol (Buenrostro et al., 2015) with the following modifications: transposition time was increased from 30?min to 1?h and the cell pellets were taken directly to the transposition reaction omitting the lysis step as described in (Karabacak Calviello et al., 2019). For all samples, 12 PCR cycles were performed, and the libraries were sequenced (2x75nt) on a NextSeq 500/550 using a HighOutput v2 Kit for 150 cycles (Illumina #FC-404-2002, discontinued).