Increased Transcription of the Seryl‐tRNA Synthetase (SARS) Gene in Response to Amino Acid Limitation is Mediated by an Intronic C/EBP‐ATF Response Element (CARE) that Functions as an Distal Enhancer

Abstract

Amino acid (AA) limitation activates transcription from 16 of the 20 genes encoding cytoplasmic‐localized aminoacyl‐tRNA synthetase (ARS) genes via action of activating transcription factor 4 (ATF4) binding at C/EBP‐ATF‐Response‐Element (CARE) enhancers. Most of the activated genes have a functional CARE near the transcription start site (TSS), but for some the CARE is located downstream within the first intron. For all ARS genes, regardless of the CARE location, there is constitutive association of RNA polymerase II (Pol II) and the general transcription machinery (GTM) near the TSS. For those genes with a downstream CARE, during AA limitation there is enhanced recruitment of ATF4, Pol II, and the GTM to the CARE, not the TSS region. The AAR‐induced expression of ARS genes results from modulation of transcription elongation. Using the seryl‐tRNA synthetase (SARS) gene as a model, the goal of the present research was to further characterize the mechanism by which an intronic CARE enhancer, about 1 kb downstream of the TSS, functions to increase transcription in response to AA limitation. Using CRISPR‐CAS9 technology and HepG2 hepatoma cells, the SARS CARE was deleted and then the wild type and SARS‐CARE−/− cells were subjected to AA limitation. Analysis at both the promoter and the CARE regions of the SARS gene revealed significant changes in association of the GTM, transcription elongation factors, and enhancer binding proteins, in a CARE‐specific manner. Likewise, the absence of the CARE caused changes in localized histone modification within the SARS genomic locus. Collectively, the results indicate that intronic CARE enhancers, such as those contained within the ARS gene family, modulate transcription from the corresponding promoter through changes in histone modification and recruitment of specific factors that control elongation.Support or Funding Informationthis work was supported by a grant to MSK from The National Cancer Institute, CA203565.