Histone modifications regulate pioneer transcription factor cooperativity

Abstract

Pioneer transcription factors have the ability to access DNA in compacted chromatin1. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming2–4. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.

Mechanistic dissection of theCHD4enhancers reveals cooperative functions among the homotypic ZNF410 clustered motifs

“…50,63 A recent study has shown that pioneer factor OCT4 binds to the nucleosome and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites in a nucleosome-dependent manner via biochemistry and structural biology. 64 Compared with OCT4, TF ZNF410 appears to be uncapable to bind to nucleosomal DNA in vitro . Meanwhile, we found that the 3’motif mutation has no obvious effect on the ZNF410 binding to additional sites in the naked DNA by EMSA assays.…”

The human LIN28B nucleosome is inherently pre-positioned for efficient binding of multiple OCT4s without H3 K27 acetylation

“…Illustration of band intensity measurement of OCT4 binding to the LIN28B nucleosome using Sinha et al’s gel (Fig. 3 b in Sinha et al 1 ) and ImageJ (upper panel; the boxes indicate the area used for intensity measurement), and percentage of the intensity ratio of the nucleosome bound to OCT4 over the input.…”

“…In a recent study, Sinha et al 1 showed that OCT4 initially targeted the LIN28B DNA-containing nucleosome by interacting with the linker DNA and the N-terminal tail of histone H4, which led to the repositioning of DNA in the nucleosome that locates at multiple positions in its free form. OCT4 binding at the linker DNA was shown to be required for the efficient binding of two additional OCT4 molecules to the internal sites of the fully wrapped nucleosome using partial motifs.…”

“…However, their precise mechanism for recognizing nucleosomes has remained mystery. Recent structural and biochemical investigations into the binding interactions between the human pioneer factor OCT4 and the LIN28B nucleosome by Sinha et al 1 and Guan et al 2 have yielded conflicting results regarding nucleosome positioning, nucleosomal DNA unwrapping, binding cooperativity, and the role of N-terminal tail of OCT4. In this study, we undertook a comparative analysis of these two research efforts and delved into the factors contributing to the observed discrepancies.…”

NetREm Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation

“…Based on recent studies, it is now understood that TFs may jointly coordinate TG transcription even without direct PPIs (Rao et al 2021;Wang et al 2009). Pioneer TFs, for instance, recognize and bind to their TFBSs even within closed chromatin, inducing local chromatin remodeling (e.g., nucleosome eviction), thereby exposing TFBSs and rendering DNA more amenable to subsequent binding by settler TFs (Sinha et al 2023;Mayran and Drouin 2018).…”