Extensive binding of uncharacterized human transcription factors to genomic dark matter [GSE58341 Reanalysis]

Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We determined genomic binding locations of 166 uncharacterized human TFs in living cells. Nearly half of them associated strongly with known regulatory regions such as promoters and enhancers, often at conserved motif matches and co-localizing with each other. Surprisingly, the other half often associated with genomic dark matter, at largely unique sites, via intrinsic sequence recognition. Dozens of these, which we term “Dark TFs” mainly bind within regions of closed chromatin. Dark TF binding sites are rarely under purifying selection, and are enriched for transposable elements. Many Dark TFs are KZNFs, which contain the repressive KRAB domain, but many are not, and may represent potential pioneer TFs: based on compiled literature information, the Dark TFs exert diverse functions ranging from early development to tumor suppression. Thus, a large fraction of previously uncharacterized human TFs may have unappreciated activities within the dark matter genome. This entry describes re-analysis of previously existing datasets in located in SRA entry SRP043061. These datasets have been analyzed previously (GSE52523), but they were re-analyzed here to be consistent with the newly generated ChIP-seq datasets. Previous datasets were mapped into hg19 assembly and analyzed with different computational approaches *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. ***************************************************************