Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

Transcriptome dynamics is governed by two opposing processes, mRNA production and degradation. Recent studies found that changes in these processes are frequently coordinated and that the relationship between them shapes transcriptome kinetics. Specifically, when transcription changes are counter-acted with changes in mRNA stability, transient fast-relaxing transcriptome kinetics is observed. A possible molecular mechanism underlying such coordinated regulation might lay in two RNA polymerase (Pol II) subunits, Rpb4 and Rpb7, which are recruited to mRNAs during transcription and later affect their degradation in the cytoplasm. Here we used a yeast strain carrying a mutant Pol II which poorly recruits these subunits. We show that this mutant strain is impaired in its ability to modulate mRNA stability in response to stress. The normal negative coordinated regulation is lost in the mutant, resulting in abnormal transcriptome profiles both with respect to magnitude and kinetics of responses. These results reveal an important role for Pol II, in regulation of both mRNA synthesis and degradation, and also in coordinating between them. We propose a simple model for production-degradation coupling that accounts for our observations. The model shows how a simple manipulation of the rates of co-transcriptional mRNA imprinting by Pol II may govern genome-wide transcriptome kinetics in response to environmental changes

Mammalian-Membrane-Two-Hybrid (MaMTH): a novel split-ubiquitin assay for investigation of signaling pathways in human cells

Cell signaling, one of the key processes involved in human health and disease, is coordinated by numerous membrane protein-protein interactions (PPIs) that change in response to stimuli. Currently, there is a lack of assays that can detect these changes in stimuli- and disease-related contexts. Here, we present a novel split-ubiquitin-method for the detection of integral membrane PPIs in human cells, termed Mammalian-Membrane-Two-Hybrid (MaMTH). We highlight the strength of this technology by showing that it detects stimuli (hormone/agonist)- and phosphorylationdependent PPIs. Importantly, it can detect changes in PPIs conferred by mutations such as those in oncogenic ErbB-receptor variants or by treatment with drugs like the tyrosine-kinase inhibitor erlotinib. Using MaMTH as a screening assay, we identified CRKII as an interactor of oncogenic EGFRL858R, promoting persistent activation of aberrant signaling. In conclusion, our study illustrates that MaMTH is a powerful tool for investigating dynamic interactomes of human integral membrane proteins.The work was supported by grants from the Ontario Genomics Institute (303547), Canadian Institutes of Health Research (Catalyst - NHG99091; ppp-125785), Canadian Foundation for Innovation (IOF-LOF), Natural Sciences and Engineering Research Council of Canada (RGPIN 372393-12), Canadian Cystic Fibrosis Foundation (300348), Canadian Cancer Society (2010-700406), Novartis, UNiversity Health Network (GL2-01-018), FWF-Erwin Schrödinger Fellowship progra

Mannose Trimming Is Required for Delivery of a Glycoprotein from EDEM1 to XTP3-B and to Late Endoplasmic Reticulum-associated Degradation Steps*

Although the trimming of α1,2-mannose residues from precursor N-linked oligosaccharides is an essential step in the delivery of misfolded glycoproteins to endoplasmic reticulum (ER)-associated degradation (ERAD), the exact role of this trimming is unclear. EDEM1 was initially suggested to bind N-glycans after mannose trimming, a role presently ascribed to the lectins OS9 and XTP3-B, because of their in vitro affinities for trimmed oligosaccharides. We have shown before that ER mannosidase I (ERManI) is required for the trimming and concentrates together with the ERAD substrate and ERAD machinery in the pericentriolar ER-derived quality control compartment (ERQC). Inhibition of mannose trimming prevents substrate accumulation in the ERQC. Here, we show that the mannosidase inhibitor kifunensine or ERManI knockdown do not affect binding of an ERAD substrate glycoprotein to EDEM1. In contrast, substrate association with XTP3-B and with the E3 ubiquitin ligases HRD1 and SCFFbs2 was inhibited. Consistently, whereas the ERAD substrate partially colocalized upon proteasomal inhibition with EDEM1, HRD1, and Fbs2 at the ERQC, colocalization was repressed by mannosidase inhibition in the case of the E3 ligases but not for EDEM1. Interestingly, association and colocalization of the substrate with Derlin-1 was independent of mannose trimming. The HRD1 adaptor protein SEL1L had been suggested to play a role in N-glycan-dependent substrate delivery to OS9 and XTP3-B. However, substrate association with XTP3-B was still dependent on mannose trimming upon SEL1L knockdown. Our results suggest that mannose trimming enables delivery of a substrate glycoprotein from EDEM1 to late ERAD steps through association with XTP3-B

Bypass of glycan-dependent glycoprotein delivery to ERAD by up-regulated EDEM1

Extensive trimming of mannose residues targets a misfolded glycoprotein for endoplasmic reticulum–associated degradation (ERAD). Surprisingly, overexpression of EDEM1 or its up-regulation by the unfolded protein response bypasses this requirement. Delivery to OS9 in the ER-derived quality control compartment and ERAD becomes mannose trimming–independent, accelerating glycoprotein disposal

The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells

Cell signaling, one of the key processes involved in human health and disease, is coordinated by numerous membrane protein-protein interactions (PPIs) that change in response to stimuli. Currently, there is a lack of assays that can detect these changes in stimuli- and disease-related contexts. Here, we present a novel split-ubiquitin-method for the detection of integral membrane PPIs in human cells, termed Mammalian-Membrane-Two-Hybrid (MaMTH). We highlight the strength of this technology by showing that it detects stimuli (hormone/agonist)- and phosphorylationdependent PPIs. Importantly, it can detect changes in PPIs conferred by mutations such as those in oncogenic ErbB-receptor variants or by treatment with drugs like the tyrosine-kinase inhibitor erlotinib. Using MaMTH as a screening assay, we identified CRKII as an interactor of oncogenic EGFRL858R, promoting persistent activation of aberrant signaling. In conclusion, our study illustrates that MaMTH is a powerful tool for investigating dynamic interactomes of human integral membrane proteins.The work was supported by grants from the Ontario Genomics Institute (303547), Canadian Institutes of Health Research (Catalyst - NHG99091; ppp-125785), Canadian Foundation for Innovation (IOF-LOF), Natural Sciences and Engineering Research Council of Canada (RGPIN 372393-12), Canadian Cystic Fibrosis Foundation (300348), Canadian Cancer Society (2010-700406), Novartis, UNiversity Health Network (GL2-01-018), FWF-Erwin Schrödinger Fellowship progra