Chromatin remodeling

We are interested in the regulation of genome structure in eukaryotes by ATP-dependent chromatin remodeling complexes. These highly conserved “remodelers” are the only known factors that can directly alter the positioning of nucleosomes, the basic repeating unit of chromatin, comprising ~150 basepairs of DNA wrapped around a core of histone proteins. This activity is essential for cellular activities such as DNA replication, repair and transcription, which rely on access to functional DNA sequences that are rendered inaccessible within a nucleosome.

Remodelers contain a conserved ATPase domain that catalyzes the disruption of histone-DNA interactions, allowing for the histone core to be repositioned along the DNA. Association with different sets of domains and accessory factors allows remodelers to perform diverse functions, such as sliding or ejecting the histone core. Perhaps the most functionally unique and mechanistically intriguing function is the exchange of histone proteins, which alters the composition of nucleosomes at specific regions. Only two remodelers have been identified to have this function, the highly similar SWR1 and INO80.

SWR1 regulates the global distribution of H2A.Z, an evolutionarily conserved histone variant. This distribution is shared among all eukaryotes. SWR1 is recruited to nucleosomes flanking nucleosome-depleted regions, such as gene promoters, where it replaces the canonical H2A-H2B dimer with the variant H2A.Z-H2B dimer. This activity involves a concerted ejection of the canonical dimer and insertion of the variant dimer. Among chromatin remodelers, dimer exchange by SWR1 is a unique activity that relies on the association of 14 subunits, including the putative hexameric helicases Rvb1 and Rvb2, to form a 1 Mega-Dalton complex. It is not understood how SWR1 has evolved to possess such a different activity from the other remodelers. Using 3 dimensional electron microscopy, I aim to obtain the structure of nucleosome-bound SWR1 and investigate how the enzyme handles its substrates to allow for such a complex and dynamic activity.

 

Publications

* Equal contribution
# Co-corresponding authors

Xu J*, Lahiri I*, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE# and Wang D# (2017). Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Nature 551: 653-7.

Nguyen VQ, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C and Leschziner AE (2013). Molecular architecture of the ATP-dependent chromatin remodeling complex SWR1. Cell, 154:1220-1231. {download PDF}

Leschziner AE (2011). Electron Microscopy studies of nucleosome remodelers. Current Opinion on Structural Biology. 2011 21:709-718 {download PDF}

Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR and Nogales E (2007). Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc. Natl. Acad. Sci. USA 104(12): 4913-8. {download PDF}

Leschziner AE, Lemon B, Tjian R and Nogales E (2005). Structural studies of the human PBAF chromatin-remodeling complex. Structure (Camb) 13(2): 267-75. {download PDF}

 
  Regulation of chromatin structure by ATP-dependent chromatin remodelers.  (1) Eukaryotes package the genome by wrapping DNA around a core of histone proteins, forming nucleosomes. Nucleosomes are packed tightly against each other by specialized remodelers. (2) A promoter is rendered inaccessible while in a nucleosome. Some remodelers are targeted to these regions to reposition the nucleosome. (3) A nucleosome-free region (NFR) is established. The gene requires an active/poised transcriptional state. (4) The SWR1 complex deposits the conserved histone variant H2A.Z into nucleosomes flanking the NFR. This occurs via a unique and concerted reaction involving ejection of the canonical histone dimer (H2A/H2B, green) and insertion of the variant dimer (H2A.Z/H2B, red). (5) The gene now possesses a stable NFR that allows for productive transcription.

Regulation of chromatin structure by ATP-dependent chromatin remodelers. (1) Eukaryotes package the genome by wrapping DNA around a core of histone proteins, forming nucleosomes. Nucleosomes are packed tightly against each other by specialized remodelers. (2) A promoter is rendered inaccessible while in a nucleosome. Some remodelers are targeted to these regions to reposition the nucleosome. (3) A nucleosome-free region (NFR) is established. The gene requires an active/poised transcriptional state. (4) The SWR1 complex deposits the conserved histone variant H2A.Z into nucleosomes flanking the NFR. This occurs via a unique and concerted reaction involving ejection of the canonical histone dimer (H2A/H2B, green) and insertion of the variant dimer (H2A.Z/H2B, red). (5) The gene now possesses a stable NFR that allows for productive transcription.

  Composition of the SWR1 Complex  SWR1 contains 14 subunits. The catalytic ATPase domain resides in Swr1, which serves as a platform for the assembly of the remaining subunits. Bdf1 contains tandem bromodomains that bind acetylated histone tails. Bdf1 may help target the complex to hyperacetylated regions, such as promoters. The H2A.Z/H2B dimer binds specifically to Swc2. We have shown that Rvb1 and Rvb2 associate with the complex as a single heterohexameric ring [Nguyen et al. (2013)  Cell , in press]. The estimated molecular weight of the complex is ~1 MDa.

Composition of the SWR1 Complex
SWR1 contains 14 subunits. The catalytic ATPase domain resides in Swr1, which serves as a platform for the assembly of the remaining subunits. Bdf1 contains tandem bromodomains that bind acetylated histone tails. Bdf1 may help target the complex to hyperacetylated regions, such as promoters. The H2A.Z/H2B dimer binds specifically to Swc2. We have shown that Rvb1 and Rvb2 associate with the complex as a single heterohexameric ring [Nguyen et al. (2013) Cell, in press]. The estimated molecular weight of the complex is ~1 MDa.