Research interests in the Bowman lab

In all eukaryotes, genomic DNA is extensively packaged into nucleosomes. In general, the locations and patterns of nucleosomes have a strong impact on gene expression. For genes to be expressed, a nucleosome-free region must be maintained in gene promoters to allow the transcription machinery to bind and initiate transcription. Nucleosomes are packed together in evenly spaced arrays in gene bodies, which blocks spurious cryptic transcription (Smolle et al., 2012;). These patterns of nucleosomes are actively controlled by ATP-dependent chromatin remodeling enzymes. There are several distinct families of chromatin remodelers, which appear to have specialized biochemical and biological functions. Chd1 and ISWI-type remodelers can organize nucleosomes into evenly spaced arrays (Lusser et al., 2005; Pointner et al., 2012 ; Ocampo et al., 2016), whereas SWI/SNF-type enzymes disrupt arrays (Kwon et al., 1994; Imbalzano et al., 1994;), both by altering spacing and also evicting histone cores (Dechassa et al., 2010).

cartoon of nucleosome arrays

We are interested in understanding how chromatin remodelers work at the molecular level: how do they manipulate nucleosome structure, and how are they directed to act on particular substrates? All remodelers possess a helicase-like ATPase motor that is the core engine that drives the remodeling reaction. The ATPase motor is regulated by auxiliary domains, which likely confer distinct biochemical characteristics for each remodeler type. We have focused on the Chd1 remodeler as a model system, which is naturally found as a monomer and thus possesses all regulatory elements in a single chain. Chd1 was named for three recognizable domains: a pair of N-terminal chromodomains, a central helicase-like ATPase motor, and a C-terminal DNA-binding domain (Delmas et al., 1993).

Our crystal structure of the chromo-ATPase portion of S. cerevisiae Chd1 revealed that the chromodomains can pack against a DNA-binding surface on the ATPase motor, providing the first example of how a remodeler ATPase motor can be auto-regulated (Hauk et al., 2010). We also showed that the DNA-binding domain was essential for directional sliding (McKnight et al., 2011), even though this domain binds DNA in a sequence-nonspecific manner (Sharma et al., 2011).

Chd1 overview

Using site-specific cross-linking, we discovered a novel organization of remodeler domains on the nucleosome (Nodelman et al., 2017). The same domain organization was observed by cryo-EM in Chd1-nucleosome complexes, solved by Patrick Cramer's and Tom Owen-Hughes' groups (Farnung et al., 2017; Sundaramoorthy et al., 2018). This structural data has stimulated our thinking for how remodeler domains may manipulate nucleosome structure and communicate together. We are currently focused on two core questions regarding the mechanisms of remodeler action and regulation:

     1. How do remodelers sense DNA outside the nucleosome?

     2. How do remodelers mechanically shift DNA past the histone core?