Chip-exo and Chip-seq of human KRAB-ZNFs transduced in HEK 293T cells

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on more than a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation. We transduced HEK 293T cells with doxycyclin-inducible plasmids encoding for human KRAB-ZFPs fused with 3 HA tags at the C-terminus. After verifying the correct integration and expression of the KZFP by Sanger sequencing and Western blot, we performed ChIP-exo and ChIP-seq and prepared a barcoded Illumina library for each sample. For the ChIP-exo, the libraries were pooled and sequenced 12 per lane on an Illumina Hiseq 2500 to a minimum depth of around 15 million 100 bp single-end reads. For the ChIP-seqs, all samples were pooled and sequenced on the same lane on an Hiseq 4000 to a depth of around 30 Million 75 bp paired-end reads. The reads were mapped to the hg19 assembly of the human genomes and peaks were identified using MACS. For the ChIP-exos we used a total input derived from random sampling from all samples in the study, as it was found to perform better than either the standard total input or the exonuclease treated total input. For the ChIP-seqs, either individual inputs or a pooled input for one sequencing lane was sequenced.