As ATF4 (ref. ) and CHOP (ref. ) are basic leucine zipper-containing transcription factors, we reasoned that ATF4 and CHOP target genes that establish the apoptotic program. Therefore, we applied genome-wide chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) and mRNA expression analysis (mRNA-seq) to identify genes directly regulated by ATF4 and CHOP in response to Tm ( and Methods). ChIP-seq found 2,598 peaks for CHOP and 3,023 peaks for ATF4, which are assigned to the nearest transcription start sites (TSSs) of unique genes based on gene annotations of USCS known genes (mm9). Analysis of the ATF4-and CHOP-binding site distribution demonstrated that 10.4% of CHOP- and 12.5% of ATF4-binding sites were located and ). Thus, ATF4 and CHOP preferentially bind to proximal promoter regions of target genes. Conventional ChIP validated the ChIP-seq results (). Strikingly, a total of 218 genes out of 321 CHOP targets and out of 472 ATF4 targets that have binding sites and ). ChIP-seq identified known ATF4 and CHOP target genes, including Atf3 (ref. ), Gadd34 (refs ,) and Trib3 (ref. ), as well as many uncharacterized genes ( and ). To our surprise, the most significantly enriched biological functions of ATF4 and/or CHOP target genes involve protein synthesis including eleven aminoacyl-tRNA synthetases (Aars, Lars, Yars, Sars, Wars, Vars, Nars, Mars, Gars, Iars and Eprs) and four initiation factors (Eif2s2, Eif3c, Eif4g2 and Eif5), and, as expected, the UPR ( and ). It is notable that ATF4 alone targets genes encoding functions in amino acid transport and amino acid biosynthesis ( and ). Most strikingly, we did not find enrichment in cell death-related functions in either ATF4 and/or CHOP target genes.
Alright, back to biology. Oftentimes RNA polymerase can't begin transcription without the assistance of regulatory DNA binding proteins. These proteins bind to the promoter in a special region called an operator. Since these binding proteins activate transcription through the RNA polymerase, they are called positive regulators, working through positive regulation. Alternatively, a different set of proteins, called transcriptional repressors, can bind to the genes preventing their transcription. This is a form of repression, or negative regulation. Regulation that involves the binding of either positive or negative regulatory proteins is called regulation in trans because they involve (trans) factors separate from the DNA sequence. We'll show you a real life example in a minute.
: mRNA binding regulated by phosphorylation of binding proteins
AUTHOR CONTRIBUTIONSJ.H., S.H.B. and R.J.K. designed all experiments and performed most of them. J.H., Y-H.L and M.A.S. performed bioinformatic analysis and contributed to preparation of figures and tables. R.G. performed western blot and cell viability assays using Eif2αA / A and Atf4–/– MEFs and GADD34 overexpression experiments. J.S. and M.S.K. generated and characterized the ATF4 antibody and performed co-immunoprecipitation and sequential ChIP experiments. C.L.Y., D.K. and M.H. measured in vivo protein synthesis using 2H2O. S.W. analysed protein synthesis and western blots. J.H., S.H.B. and R.J.K. prepared the manuscript.
Regulation of Protein Synthesis | S-cool, the revision …
Because mesoderm induction occurs beforethe onset of zygotic transcription, the FGF receptor must be encoded byoogenic messengers, and translation of those messengers must be regulatedto ensure that the receptor is present in the right cells at the right timeand in sufficient amounts.
The XFGFR-1 messenger is present in oocytes and early embryos.
Mechanism and regulation of eukaryotic protein synthesis.
The ER is the organelle essential for calcium storage, lipid synthesis and protein folding and secretion in metazoan cells. The ER has a dynamic capacity to accommodate increases in the demand for protein folding. However, extracellular stimuli and changes in intracellular homeostasis cause protein misfolding in the ER. The ER uses its protein folding status as a signal to orchestrate downstream adaptive or apoptotic responses. The unfolded protein response (UPR) is a cellular adaptive response that evolved to restore protein-folding homeostasis by reducing protein synthesis through phosphorylation of eIF2α and by increasing the ER protein-folding and degradative capacities through transcriptional activation by XBP1 and ATF6α (refs –). If the UPR cannot resolve the protein-folding defect, cells undergo apoptosis. One of the mechanisms of ER stress-induced cell death involves sequential steps of PERK-mediated eIF2α phosphorylation,, preferential translation of ATF4/CREB-2 messenger RNA (refs –) and induction of CHOP/GADD153 (refs –). Studies of Chop deletion in mice show that CHOP is required for ER stress-mediated cell death in response to a variety of pathological conditions–. However, forced expression of CHOP alone does not induce cell death, but sensitizes to ER stress-induced cell death–, suggesting that another yet unidentified signal is required for the apoptotic response, as previously suggested. Analysis of Atf4–/– cells has generated conflicting results as to having a pro-survival– or a pro-apoptotic role–. Here, we identified the roles of ATF4 and CHOP for initiating ER stress-induced cell death.
Regulation of Protein Synthesis by Insulin | Annual …
One possibilityis that the 3' end of RNA can influence the effectiveness of translationinitiation factors in protein synthesis.
The messenger encoding the FGF receptor-1 (XFGFR-1) provides further evidencefor long-range interactions in regulation of translation of oogenic mRNA.