Transcriptional reprogramming of neural stem cells by a PHF6/EphR signalling pathway [ChIP-Seq]

The plant homeodomain zinc finger protein,PHF6, is a transcriptional regulator, with its germline mutations causing the X-linked intellectual disability (XLID), Börjeson-Forssman-Lehmann syndrome (BFLS).The precise mechanisms by whichPHF6regulates transcription and how its mutant forms lead to XLID remain poorly characterized. Here, we show genome-wide binding of PHF6 in the developing cortex, most of which overlap (CA)n-microsatellite repeats near genes involved in central nervous system development and neurogenesis. Mice harbouring BFLS patient mutations exhibit defects in neurogenesis and altered neural stem cell fate. Mechanistically, we find that PHF6 regulatesa panel of Ephrin receptors (EphRs)and that PHF6regulation ofEphRis impaired in BFLS mice and ina conditionalPhf6knock-out mouse model. We report that mice harboring BFLS mutations exhibit an increase in embryonic neural stem cell (eNSC) self-renewal, a significant attenuation of newly born neurons, and thatEphRknockdown phenocopies the PHF6 loss-of-function defects in altering eNSC fate. Our results suggest that alterations in eNSC fate specification via a PHF6/EphRtranscriptional pathway leads to impaired neurogenesis in BFLS Here, we show genome-wide binding of PHF6 in the developing cortex. ChIP-seq data were processed as previously described (Hernandez-Corchado & Najafabadi, 2022). Briefly, raw reads were aligned to the mouse genome assembly version mm10 with bowtie2 (version 2.3.4.1) using the “--very-sensitive-local” mode. Duplicate reads were removed using samtools (version 1.9) (Danecek et al., 2021). ChIP-seq peaks were identified using MACS (version 1.4) (Feng, Liu, Qin, Zhang, & Liu, 2012; Zhang et al., 2008) with a permissive p-value threshold of 0.001, using “--nomodel” option. Fragment size was specified using “--shiftsize” argument, with the fragment length obtained by cross-correlation analysis using phantompeakqualtools (Landt et al., 2012). Peak-TSS distances were calculated using bedtools (Quinlan & Hall, 2010) only for peaks that passed p-value threshold of 10–5, with TSS coordinates obtained from GENCODE (Frankish et al., 2019) (release M9).