RLS-associated MEIS transcription factors control distinct processes in human neural stem cells [ChIP-Seq]

MEIS1 and MEIS2 encode highly conserved homeodomain transcription factors crucial for developmental processes in a wide range of tissues, including the brain. They can execute redundant functions when co-expressed in the same cell types, but their roles during early stages of neural differentiation have not been systematically compared. By separate knockout and overexpression of MEIS1 and MEIS2 in human neural stem cells, we find they control specific sets of target genes, associated with distinct biological processes. Integration of DNA binding sites with differential transcriptomics implicates MEIS1 to co-regulate gene expression by interaction with transcription factors of the SOX and FOX families. MEIS1 harbors the strongest risk factor for restless legs syndrome (RLS). Our data suggest that MEIS1 can directly regulate the RLS-associated genes NTNG1, MDGA1 and DACH1, constituting new approaches to study the elusive pathomechanism or RLS. Overall design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for MEIS1/MEIS2 in human neural stem cells (hNSC) from two replicates. Illumina sequencing libraries were generated using the NEBNext Ultra II Library Prep Kit for Illumina (E7645) with NEBNext Multiplex Oligos for Illumina (Dual Index Set1, E7600) according to the manufacturer's protocol. Size selection was performed using a Pippin Prep (Sage Science), using a 2% cassette with size window set to 300–750 bp. Samples were sequenced 36 bp paired-end on an Illumina NextSeq550. Adapters were trimmed from raw reads using cutadapt (v1.16), without quality-based trimming. Reads were mapped to the human genome assembly GRCh37 (hg19) using bowtie2 (v2.3.0) and samtools (v1.2) at a cutoff of mapq?>?=?30. PCR duplicates were removed with Picard tools (v 2.15.0). Peaks were called against input controls by MACS2 in paired-end mode with a P-value cut-off of 0.01, and were used as input for IDR analysis (v.2.0.3), which was used to determine reproducible peaks between the two replicates.