Manipulating the transcriptome and chromatin accessibility in T cells through CRISPR-induced alternative splicing of IKZF1 (RNAseq)

Genome-wide association studies have identified statistically significant associations between genetic variants in or near the IKZF1 gene and several autoimmune disorders. IKZF1, encoding the transcription factor Ikaros, produces at least 10 distinct transcripts via alternative splicing. To explore the role of alternative splicing of IKZF1 in mature T cells, we generated a panel of Jurkat T-cell clones with various truncating mutations in IKZF1 exon 4, exon 6 or both. Differences among clones in gene expression, chromatin accessibility, and protein abundance were assessed by RNA-seq, ATAC-seq and immunoblotting. Clones with single targeting events in either exon 4 or 6 clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKZF family members. Our results suggest that even modest perturbations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells. Overall design: Exons 4 and 6 of the human IKZF1 gene in Jurkat cell lines were edited using CRISPR/Cas9. Gene expression profiling was performed using RNA-seq of four WT clones, seven clones with edits in IKZF1 exon 4, five clones with edits in IKZF1 exon 6, and eight clones with edits in IKZF1 exons 4 and 6. Analysis of gene expression was performed comparing WT clones to CRISPR-edited clones based on exons edited and protein detection.