Krüppel-like-factor 1 (KLF1) is a transcription factor (TF) expressed uniquely within the red blood cell lineage. KLF1 binds to the promoters and/or enhancers of many genes critical to erythropoiesis and activates their expression. Pioneer factors are a class of TFs that are able to interact with ‘closed’ DNA that is wound around nucleosomes. They ‘pioneer’ the way for other factors to bind by re-positioning nucleosomes, exposing the hitherto occluded DNA. The relative permissiveness of DNA loci can be measured using ATAC-seq (Assay for Transposase-Accessible Chromatin) which relies on the DNA being accessible (i.e. nucleosome free) to a Tn5 transposase loaded with next-generation sequencing adaptors.
Using a tamoxifen inducible version of mouse KLF1 (Gillinder et al., 2017), we demonstrate that the KLF1 protein possesses pioneering activity. Upon induction we find KLF1 occupies ~3800 genomic regions. The majority show an increase in chromatin accessibility over the parental KLF1 null cell line, although many are already ‘open’ prior to KLF1 induction. Many of the induced sites are at well-known erythroid enhancers such as the -26kb enhancer of the alpha-globin LCR (Hay et al., 2016). The zinc finger DNA-binding domain (DBD) of KLF1 binds DNA well in vitro and in vivo but is unable to alter chromatin in vivo, suggesting the latter function is encoded in the non-DBD. The mechanism by which KLF1 opens chromatin is an active area of investigation and likely relies upon interaction with components of the chromatin-remodelling SWI/SNF complex.
This work establishes KLF1 as a bone fide pioneer TF and begins to dissect the mechanism of its action. As KLF1 is the founding member of the KLF/SP superfamily, this work is likely to establish a paradigm for the function of this TF family in gene regulation and reprograming.