Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Abstract

Pioneer transcription factors are required for stem cell pluripotency, cell differentiation, and cell reprogramming 1,2 . Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. Sox2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells 3 . Here we report cryo-electron microscopy structures of the DNA-binding domains of Sox2 and its close homologue Sox11 bound to nucleosomes. These first structures of pioneer factors in complex with nucleosomes show that Sox factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, and this increases DNA accessibility. Sox factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4, including residue lysine-16. This is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. These results indicate that pioneer transcription factors can use binding energy to contribute to initial chromatin opening and facilitate nucleosome remodelling and transcription.Transcription of the human genome is controlled by ~1,600 transcription factors (TFs) 4 . TFs recognize DNA motifs and recruit protein complexes that enable transcription initiation 5 . Binding of most TFs is restricted to regions of the genome that are not packaged into chromatin 6 . Some TFs can however bind to chromatin via contacts to its fundamental unit, the nucleosome 7 . These 'pioneer' TFs can initiate transcription in silent chromatin regions 8 and are required for embryo development, cell differentiation, and cell reprogramming 9,10 . Sox2 and Oct4 are pioneer factors that are widely used for reprogramming of adult cells to induced pluripotent stem cells 2,11,12 . They can interact with nucleosomes in vitro and in vivo 13,14 . Sox2 alone can direct chromatin opening 15 and bind target DNA sites before Oct4 11 in vivo, indicating that Sox2 makes DNA accessible for binding of other factors. Most Sox family factors show pioneer factor function 7 , are essential for developmental processes 16 , and their mutation can lead to severe developmental defects and cancer 17 . How pioneer TFs such as Sox factors bind to the nucleosome and how they make DNA accessible is unknown. Author contributions S.O.D. designed and carried out all experiments and data analysis. F.Z. supported by J.T. identified the original DNA template used in the study. C.D. assisted with cryo-EM data collection. P.C. designed and supervised research. S.O.D. and P.C. interpreted the data and wrote the manuscript, with input from all authors.

Interaction of the pioneer transcription factor GATA3 with nucleosomes

“…However, in contrast to GATA3, binding of Sox11 on naked DNA and near the nucleosomal dyad leads to local DNA distortion with widening of the minor groove. This DNA distortion, as opposed to steric clash, leads to displacement of DNA away from the octamer surface 40 . It seems reasonable to conclude that the biophysics of protein/DNA interaction, which differs for the various known DNA binding domains, provides key information on mechanisms by which transcription factors interrupt the chromatin fiber, or fail to do so.…”

SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma

“…SOX TFs exhibit the exceptional feature to bind the minor groove of DNA and subsequently bend the DNA, which is essential for the enhanceosome architecture as well as for the distortion of DNA wrapped around histones suggesting putative pioneer factor function 8 . As our current findings also reveal a role for SOX11 in transcriptional regulation of crucial components of several epigenetic protein regulatory complexes, including PRC2 and SWI/SNF, we propose a master epigenetic regulator function of SOX11 in adrenergic NB cells.…”

“…SOX11 belongs to the SoxC subgroup, which also includes SOX4 and SOX12, and the expression of these proteins is of key importance for the survival and development of the neural crest, multipotent neural and mesenchymal progenitors, and the sympathetic nervous system 6,7 . In addition to its presumed canonical transcription factor activity, SOX11 was recently also shown to have pioneering activity and thus can be assumed to direct chromatin accessibility at loci controlling cell fates 8 . Here, we report that SOX11 acts as a lineage-dependency factor in adrenergic NB cells.…”

Structural Basis of Nucleosome Recognition and Modulation

“…The cross‐talk between the transcription factors, RNAP II and chromatin remodeler complexes remains a puzzle to be solved. Certain specific histone methyltransferases, demethylases, ubiquitinases deubiquitinases, as well as a low‐resolution model for Nucleosome acetyltransferase of histone H4 (NuA4), [ 133 ] and transcription regulators [ 134,135 ] have been characterized in complex with the nucleosome; however, the structure of several other families of these enzymes and histone deacetylases in complex with the nucleosome have yet to be explored.…”