In eukaryotes, chromatin is organized into nucleosomes through wrapping double stranded DNA around the histone core. The histone core is composed of eight subunits, two each of histones H2A, H2B, H3, and H4. Histones are rich in lysine residues that undergo several types of acylation including acetylation and novel acylations such as propionylation, butyrylation, crotonylation, malonylation, succinylation, and glutarylation. Sirtuins are a group of histone deacylases that potentially catalyze the removal of both acetylation and novel acylations from chromatin. Previous studies have focused on using acetyl/acyl-peptide substrates for sirtuin studies. However, acetyl/acyl-peptides don't represent the native sirtuin substrates in cells and therefore critical information such as what roles the nucleosome scaffold plays in sirtuin catalyzed nucleosomal deacetylation/deacylation cannot be extracted by using acetyl/acyl-peptide substrates. To characterize fundamental epigenetic roles of sirtuins in regulating chromatin acylations, we have developed strategies for swift preparation of a number of homogenous acetyl/acyl-nucleosomes and used them as substrates for sirtuin studies. Our preliminary data indicates that Sirt1 shows substrate sequence selectivity when catalyzing nucleosomal deacetylation but the nucleosome scaffold inhibits Sirt1 activity. However, Sirt6 displays unique substrate sequence selectivity and the nucleosome scaffold is required for its activation. Encouraged by our exciting preliminary study, we will continue our endeavor of understanding reversible nucleosomal acetylation/acylation by pursuing three specific aims: 1) Study Sirt1 with acetyl/acyl-nucleosome substrates to understand the inhibitory role of the nucleosome scaffold towards Sirt1 activity and regulation of Sirt1 by protein and small molecule factors such as AROS, c-Jun, and resveratrol; 2) Study Sirt6 with acetyl/acyl-nucleosome substrates to understand the activating role of the nucleosome scaffold towards Sirt6 activity, substrate sequence selectivity of Sirt6, and potential indirect regulation of H3K56 acetylation by Sirt6 ; 3) Build methods to synthesize succinyl-nucleosomes for screening Sirt5- targeted nucleosomal deacetylation sites and understanding potentially negative impacts of lysine succinylation on the nucleosome assembly.
The proposed research is relevant to public health because it aims to clarify the fundamental epigenetic roles of reversible nucleosomal acetylation/acylation. Aberrant nucleosomal acetylation/acylation are kin to numerous disorders. The project is relevant to NIH's mission in promoting health and combating diseases because it will assist in understanding functional roles of sirtuins, a group of enzymes that regulate nucleosomal acetylation/acylation and facilitate the discovery of new cures for diseases such as cancers.
|Tharp, Jeffery M; Ehnbom, Andreas; Liu, Wenshe R (2018) tRNAPyl: Structure, function, and applications. RNA Biol 15:441-452|
|Klein, Brianna J; Vann, Kendra R; Andrews, Forest H et al. (2018) Structural insights into the ?-?-? stacking mechanism and DNA-binding activity of the YEATS domain. Nat Commun 9:4574|
|Sharma, Vangmayee; Zeng, Yu; Wang, W Wesley et al. (2018) Evolving the N-Terminal Domain of Pyrrolysyl-tRNA Synthetase for Improved Incorporation of Noncanonical Amino Acids. Chembiochem 19:26-30|
|Wang, Zhipeng A; Liu, Wenshe R (2017) Proteins with Site-Specific Lysine Methylation. Chemistry 23:11732-11737|
|Wang, Zhipeng A; Kurra, Yadagiri; Wang, Xin et al. (2017) A Versatile Approach for Site-Specific Lysine Acylation in Proteins. Angew Chem Int Ed Engl 56:1643-1647|
|Sharma, Vangmayee; Wang, Yane-Shih; Liu, Wenshe R (2016) Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics. ACS Chem Biol 11:3305-3309|