Active Motif,
Tools to analyze nuclear function,
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Active Motif

Active Motif Grant Competition

May 16, 2018

We would like to thank all of the researchers that took the time to submit abstracts and we'd also like to congratulate Maha Abdellatif on being selected to receive $20,000 in free services. We were especially excited about Dr. Abdellatif’s research, which connects metabolism and metabolic enzymes directly with chromatin bound complexes, which results in a local supply of cofactors that are required for histone modifying enzyme function. The potential role of this epigenetic and metabolic connection to cardiovascular disease makes this research all the more important and we look forward to participating in this exciting project.

Services Grant Competition Winner

Maha Abdellatif, PhD
Professor, Cell Biology & Molecular Medicine
Rutgers University

Maha
Abdellatif Lab

From left to right: Zhi Yang (Surgeon), Sujung Choi (Graduate Student), Maha Abdellatif (PI), Kathy He (Lab Manager), Yong Heui Jeon (Graduate Student).

Winning Abstract

Our overall goal is to understand the mechanisms that govern transcription in the heart during health and disease.

Transcription is a highly dynamic process that requires metabolic intermediates for its activation or deactivation, these include: acetyl-CoA for histone acetylation, alpha-ketoglutarate as a cofactor for histone and DNA demethylases, and succinyl-CoA for histone succinylation. Since none of the CoA-linked metabolites could be exported out of the mitochondria, the nucleus must acquire its acetyl-CoA (Ac-CoA), mainly, via export of citrate from the mitochondria during substrate abundance, which is then converted to acetyl-CoA in the nucleus via ATP citrate lyase. On the other hand, the nucleus’s source of alpha-ketoglutarate (alpha-KG), succinyl-CoA (Suc-CoA), or other short-chain acyl-CoA is not established. The other unanswered question, is how are histones selectively modified at promoters and how does this influence an organ’s homeostasis? In a recent unbiased screen for discovery of proteins that associated with chromatin-bound histone variant H2A.Z in the heart, we uncovered mitochondrial enzymes of the TCA cycle, beta-oxidation, and branched-chain amino acid catabolism in the nucleus, uniquely localized to the transcription start sites (TSS) of genes. The data have been confirmed by immunostaining and Western blots in mouse heart tissue, isolated adult and neonatal myocytes, human iPSC-derived myocytes, and mouse embryos, and metabolomics that identified the metabolites in the nucleus after inhibiting the respective metabolizing enzyme. Importantly, we also uniquely show, using chromatin immunoprecipitation-sequencing (ChIP-Seq) with anti-acetyl-CoA acyltransferase (ACAA2), that this enzyme localizes selectively to the TSS of genes that have H2A.Z in the heart. Knockdown of ACAA2 in cardiac myocytes reduced histone modifications in those promoters. We are currently focusing our investigation on the nuclear role of 4 enzymes, representatives of the pathways that catabolize glucose and fatty acids. These include isocitrate dehydrogenase 2 (IDH2), which converts isocitrate into alpha-ketoglutarate; OGDH, which converts alpha-KG into Suc-CoA; pyruvate dehydrogenase A1 (PDHA1), which converts pyruvate into Ac-CoA; ACAA2, which converts 3-ketoacyl-CoA into Ac-CoA and acyl-CoA.

We hypothesize that:
1) The nucleus harbors mitochondrial enzymes of the TCA cycle and beta-oxidation of fatty acids, that are specifically localized to H2A.Z-bound chromatin at the TSS of select genes.
2) This allows for the local production of Ac-CoA, Suc-CoA, and the production/consumption of alphaKG, which are required for histone modifications necessary for transcriptional activation or repression. Disruption of the nuclear localization of these genes results in the reduction of histone acetylation and succinylation, or enhances methylation at select gene promoters, dysregulating gene expression, and promoting or inhibiting cardiomyopathy, depending on the genes that are selectively regulated.

Using ChIP-Seq, our aim is to identify the chromatin association sites of the metabolic enzymes PDHA1, IDH2, OGDH, and ACAA2 in the normal and hypertrophied hearts, and the effect of their knockdown on histone modifications.