A complex interplay between SAM synthetase and the epigenetic regulator SIN3 controls metabolism and transcription

Mengying Liu,Nirmalya Saha,Ambikai Gajan,Nadia Saadat,Smiti V Gupta,Lori A Pile

doi:10.1074/jbc.ra119.010032

Abstract

The SIN3 histone-modifying complex regulates the expression of multiple methionine catabolic genes, including SAM synthetase (Sam-S), as well as SAM levels. To further dissect the relationship between methionine catabolism and epigenetic regulation by SIN3, we sought to identify genes and metabolic pathways controlled by SIN3 and SAM synthetase (SAM-S) in Drosophila melanogaster Using several approaches, including RNAi-mediated gene silencing, RNA-Seq- and quantitative RT-PCR-based transcriptomics, and ultra-high-performance LC-MS/MS- and GC/MS-based metabolomics, we found that, as a global transcriptional regulator, SIN3 impacted a wide range of genes and pathways. In contrast, SAM-S affected only a narrow range of genes and pathways. The expression and levels of additional genes and metabolites, however, were altered in Sin3A+Sam-S dual knockdown cells. This analysis revealed that SIN3 and SAM-S regulate overlapping pathways, many of which involve one-carbon and central carbon metabolisms. In some cases, the factors acted independently; in some others, redundantly; and for a third set, in opposition. Together, these results, obtained from experiments with the chromatin regulator SIN3 and the metabolic enzyme SAM-S, uncover a complex relationship between metabolism and epigenetic regulation.

Highlights

The SIN3 histone-modifying complex regulates the expression of multiple methionine catabolic genes, including SAM synthetase (SamS), as well as S-adenosyl-methionine (SAM) levels
In addition to affecting expression of genes encoding metabolic enzymes, we recently demonstrated that SIN3 links epigenetic regulation and metabolism, as related to methionine catabolism and global histone methylation [20]
To investigate the underlying transcriptional network regulated by SIN3 and SAM synthetase (SAM-S), we performed a RNA-seq experiment to identify genome-wide changes in gene expression upon RNA interference (RNAi) mediated reduction of Sin3A or Sam-S or both in Drosophila Schneider cell line 2 (S2) cells

Summary

Introduction

The SIN3 histone-modifying complex regulates the expression of multiple methionine catabolic genes, including SAM synthetase (SamS), as well as S-adenosyl-methionine (SAM) levels. The data indicate that there are a number of common genes regulated by SIN3 and SAM-S in which the presence of either factor facilitates control levels of expression and that a measurable change in expression occurs only when both factors are reduced by RNAi. Evaluation of the specific gene targets indicates that there are shared and unique misregulated genes upon individual knockdown of Sin3A or Sam-S (Fig. 2).

Results

Conclusion