Gene duplication and alternative splicing play a role in modulating the functions of the ZNF286A transcription factor

Neurogenesis, and the processes through which neural stem cells and progenitor cells differentiate into neurons, occurs most actively during embryonic development, although neural differentiation continues at lower levels in certain brain regions well into adulthood. A vast regulatory network involving many known and conserved transcription factors regulates these functions. We have identified a novel zinc finger transcription factor (TF), ZNF286A, which is conserved in all eutherians and marsupials and provide evidence that this novel TF plays a role in regulation of mammalian neurogenesis. ZNF286 occurs as a unique gene in most species. However, we demonstrate evidence that a gene duplication event in very recent primate history created a human-specific duplicate of ZNF286A, called ZNF286B. ZNF286B arose as part of a larger duplication in human chromosome 17, approximately 600,000 kb in length, that also includes many surrounding genes. Concomitant with (or shortly after) duplication, a processed and incomplete FOXO3B pseudo-gene was inserted into the ZNF286B genomic sequence and a DNA segment, encompassing a coding exon and regulatory sequences present in the ancestral ZNF286A gene, was deleted. As a result, ZNF286B encodes a protein with significant structural and expression differences relative to the ancestral gene. Most strikingly, the exon deleted in ZNF286B codes for the chromatin-interacting KRAB-domains that are present in the ZNF286A gene; in this respect the new human paralog resembles a natural KRAB-less alternative isoform that we demonstrate to be expressed naturally from the parental ZNF286A gene. Using ChIP and siRNA knockdown, we show that ZNF286A protein binds to DNA at or near genes involved in the networks controlling the differentiation of neurons and the formation of axons during neurogenesis, and that both ZNF286A and ZNF286B directly regulate expression of many of those same genes. The pattern of DNA binding closely parallels binding of well-known neuronal differentiation factor, REST, in the same cell lines; siRNA results suggest that ZNF286 proteins act antagonistically to REST during development. We show that the mouse gene, Zfp286, is expressed at high levels in the developing nervous system and that both mouse and human genes and proteins are up-regulated transiently over the course of neurogenic differentiation in vitro, consistent with the predicted biological role. We hypothesize that the duplication event that gave rise to ZNF286B allowed for independent regulation of the KRAB-less isoform of the ZNF286 protein, permitting this ancient mammalian gene to take on novel functions in the adult human brain