scholarly journals Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation

2021 ◽  
Author(s):  
Yang S Chen ◽  
Sharon Tracy ◽  
Vince Harjono ◽  
Fan Xu ◽  
James J Moresco ◽  
...  

During times of unpredictable stress, organisms must adapt their gene expression to maximize survival. Along with changes in transcription, one conserved means of gene regulation during conditions that quickly represses translation is the formation of cytoplasmic phase-separated mRNP granules such as P-bodies and stress granules. Previously, we identified that distinct steps in gene expression can be coupled during glucose starvation as promoter sequences in the nucleus are able to direct the subcellular localization and translatability of mRNAs in the cytosol. Here, we report that Rvb1 and Rvb2, conserved ATPase proteins implicated as protein assembly chaperones and chromatin remodelers, were enriched at the promoters and mRNAs of genes involved in alternative glucose metabolism pathways that we previously found to be transcriptionally upregulated but translationally downregulated during glucose starvation in yeast. Engineered Rvb1/Rvb2-binding on mRNAs was sufficient to sequester the mRNAs into phase-separated granules and repress their translation. Additionally, this Rvb-tethering to the mRNA drove further transcriptional upregulation of the target genes. Overall, our results point to Rvb1/Rvb2 coupling transcription, mRNA granular localization, and translatability of mRNAs during glucose starvation. This Rvb-mediated rapid gene regulation could potentially serve as an efficient recovery plan for cells after stress removal.

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu-Chan Zhang ◽  
Meng-Qi Lei ◽  
Yan-Fei Zhou ◽  
Yu-Wei Yang ◽  
Jian-Ping Lian ◽  
...  

AbstractPlant spermatogenesis is a complex process that directly affects crop breeding. A rapid change in gene abundance occurs at early meiosis prophase, when gene regulation is selective. However, how these genes are regulated remains unknown. Here, we show that rice reproductive phasiRNAs are essential for the elimination of a specific set of RNAs during meiotic prophase I. These phasiRNAs cleave target mRNAs in a regulatory manner such that one phasiRNA can target more than one gene, and/or a single gene can be targeted by more than one phasiRNA to efficiently silence target genes. Our investigation of phasiRNA-knockdown and PHAS-edited transgenic plants demonstrates that phasiRNAs and their nucleotide variations are required for meiosis progression and fertility. This study highlights the importance of reproductive phasiRNAs for the reprogramming of gene expression during meiotic progression and establishes a basis for future studies on the roles of phasiRNAs with a goal of crop improvement.


2019 ◽  
Vol 47 (W1) ◽  
pp. W206-W211 ◽  
Author(s):  
Shaojuan Li ◽  
Changxin Wan ◽  
Rongbin Zheng ◽  
Jingyu Fan ◽  
Xin Dong ◽  
...  

AbstractCharacterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/.


2018 ◽  
Author(s):  
Katherine E. Savell ◽  
Svitlana V. Bach ◽  
Morgan E. Zipperly ◽  
Jasmin S. Revanna ◽  
Nicholas A. Goska ◽  
...  

Recent developments in CRISPR-based gene editing have provided new avenues to interrogate gene function. However, application of these tools in the central nervous system has been delayed due to difficulties in transgene expression in post-mitotic neurons. Here, we present a highly efficient, neuron-optimized dual lentiviral CRISPR-based transcriptional activation (CRISPRa) system to drive gene expression in primary neuronal cultures and the adult brain of rodent model systems. We demonstrate robust, modular, and tunable induction of endogenous target genes as well as multiplexed gene regulation necessary for investigation of complex transcriptional programs. CRISPRa targeting unique promoters in the complex multi-transcript gene Brain-derived neurotrophic factor (Bdnf) revealed both transcript- and genome-level selectivity of this approach, in addition to highlighting downstream transcriptional and physiological consequences of Bdnf regulation. Finally, we illustrate that CRISPRa is highly efficient in vivo, resulting in increased protein levels of a target gene in diverse brain structures. Taken together, these results demonstrate that CRISPRa is an efficient and selective method to study gene expression programs in brain health and disease.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kun Li ◽  
Ziqiang Wang

AbstractHistone crotonylation is a recently described post-translational modification that occurs at multiple identified histone lysine crotonylation sites. An increasing number of studies have demonstrated that histone crotonylation at DNA regulatory elements plays an important role in the activation of gene transcription. However, among others, we have shown that elevated cellular crotonylation levels result in the inhibition of endocytosis-related gene expression and pro-growth gene expression, implicating the complexity of histone crotonylation in gene regulation. Therefore, it is important to understand how histone crotonylation is regulated and how it, in turn, regulates the expression of its target genes. In this review, we summarize the regulatory factors that control histone crotonylation and discuss the role of different histone crotonylation sites in regulating gene expression, while providing novel insights into the central role of histone crotonylation in gene regulation.


2003 ◽  
Vol 23 (24) ◽  
pp. 9361-9374 ◽  
Author(s):  
Cheng-Jun Hu ◽  
Li-Yi Wang ◽  
Lewis A. Chodosh ◽  
Brian Keith ◽  
M. Celeste Simon

ABSTRACT Transcriptional responses to hypoxia are primarily mediated by hypoxia-inducible factor (HIF), a heterodimer of HIF-α and the aryl hydrocarbon receptor nuclear translocator subunits. The HIF-1α and HIF-2α subunits are structurally similar in their DNA binding and dimerization domains but differ in their transactivation domains, implying they may have unique target genes. Previous studies using Hif-1α−/− embryonic stem and mouse embryonic fibroblast cells show that loss of HIF-1α eliminates all oxygen-regulated transcriptional responses analyzed, suggesting that HIF-2α is dispensable for hypoxic gene regulation. In contrast, HIF-2α has been shown to regulate some hypoxia-inducible genes in transient transfection assays and during embryonic development in the lung and other tissues. To address this discrepancy, and to identify specific HIF-2α target genes, we used DNA microarray analysis to evaluate hypoxic gene induction in cells expressing HIF-2α but not HIF-1α. In addition, we engineered HEK293 cells to express stabilized forms of HIF-1α or HIF-2α via a tetracycline-regulated promoter. In this first comparative study of HIF-1α and HIF-2α target genes, we demonstrate that HIF-2α does regulate a variety of broadly expressed hypoxia-inducible genes, suggesting that its function is not restricted, as initially thought, to endothelial cell-specific gene expression. Importantly, HIF-1α (and not HIF-2α) stimulates glycolytic gene expression in both types of cells, clearly showing for the first time that HIF-1α and HIF-2α have unique targets.


2017 ◽  
Vol 121 (suppl_1) ◽  
Author(s):  
Junco S Warren ◽  
Amira Sabry ◽  
Keiko Cawley ◽  
Aman Makaju ◽  
Marta W Szulik ◽  
...  

Smyd1, a muscle-specific histone methyltransferase, has been implicated in global metabolic remodeling in cardiac hypertrophy and failure. We previously showed that cardiac-specific ablation of Smyd1 in mice led to metabolic perturbations prior to overt cardiac dysfunction, suggesting that Smyd1 positively regulates cardiac metabolism. However, the role of Smyd1 in adaptive response to nutritional stress (NS) in cardiomyocytes is largely unknown. Here, we found that glucose deprivation-induced NS led to upregulation of Smyd1 in cultured rat neonatal ventricular myocytes (NRVMs) (FC=1.87, p<0.05), which was associated with the increased mRNA level of PGC-1α, a key regulator of mitochondrial energetics (FC=2.71, p<0.05). Strikingly, siRNA-mediated knockdown of Smyd1 (Smyd1-KD) in NRVM prior to glucose starvation led to extensive cell death not observed in control NRVMs (scrambled siRNA), suggesting that Smyd1 is required for cell survival in NS. To elucidate the mechanism how Smyd1 is involved in adaptive response to NS, we performed unbiased proteomic and metabolomic screening of Smyd1-KD NRVMs. Bioinformatic analysis of proteins and metabolites that were differentially expressed in Smyd1-KD NRVM revealed that oxidative phosphorylation was the most perturbed metabolic pathway in Smyd1-KD NRVMs, concomitant with a reduction in mitochondrial substrates (BCAAs; pyruvate; lactate, all p<0.05). Gene expression analyses using RT-PCR and RNA-seq in Smyd1-KD NRVMs further identified PGC-1α and Perm1 (the muscle-specific PGC-1α and ESRR induced regulator) as potential downstream targets of Smyd1 in regulation of cardiac energetics (FC=-1.92 and -1.66, respectively, both p<0.05). Consistent with downregulation of Perm1, the known Perm1-target genes (Tfb1m; Ctp1b; Glut4; Myl2) were all downregulated at the mRNA levels in Smyd1-KD NRVMs (p<0.05). Lastly, Smyd1-KD NRVMs exhibited accelerated loss of mitochondrial membrane potential during hypoxia, revealing an increased vulnerability to metabolic stress. Taken together, these results show that Smyd1 is an essential regulator of adaptive response and cell survival during metabolic insults, presumably through regulating PGC-1α/Perm1 gene expression.


2017 ◽  
Author(s):  
Jan Krefting ◽  
Miguel A. Andrade-Navarro ◽  
Jonas Ibn-Salem

AbstractBackgroundThe human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts. TADs contribute to gene regulation by restricting chromatin interactions of regulatory sequences, such as enhancers, with their target genes. Disruption of TADs can result in altered gene expression and is associated to genetic diseases and cancers. However, it is not clear to which extent TAD regions are conserved in evolution and whether disruption of TADs by evolutionary rearrangements can alter gene expression.ResultsHere, we hypothesize that TADs represent essential functional units of genomes, which are selected against rearrangements during evolution. We investigate this using whole-genome alignments to identify evolutionary rearrangement breakpoints of different vertebrate species. Rearrangement breakpoints are strongly enriched at TAD boundaries and depleted within TADs across species. Furthermore, using gene expression data across many tissues in mouse and human, we show that genes within TADs have more conserved expression patterns. Disruption of TADs by evolutionary rearrangements is associated with changes in gene expression profiles, consistent with a functional role of TADs in gene expression regulation.ConclusionsTogether, these results indicate that TADs are conserved building blocks of genomes with regulatory functions that are often reshuffled as a whole instead of being disrupted by rearrangements.


2014 ◽  
Author(s):  
Ελευθερία Γαλάτου

Cardiovascular diseases are one of the major causes of morbidity and mortality in the modern world. They are characterized by molecular, cellular and pathophysiological changes in the myocardium, a condition known as cardiac remodeling. While short-term cardiac remodeling is an adaptive response that contributes to the maintenance of cardiac function the long term remodeling leads to contractile dysfunction and eventually heart failure while it is also associated with sudden death from arrhythmias. The energy metabolism of the heart and the utilization of various substrates are modified in various pathological conditions, including cardiac hypertrophy, which is associated with an increase in the catabolism of glucose and reduction of the oxidation of fatty acids, while diabetes mellitus is characterized by increased by enhanced fatty acid metabolism and reduced glucose and lactate metabolism. Given that peroxisome proliferator activated receptors (PPARs) are key transcriptional regulators of energy metabolism and lipid homeostasis, the aim of this thesis was to investigate the role of PPARα/δ activation in cardiac hypertrophy, diabetes mellitus and ischaemia.Primary cultures of cardiomyocytes were exposed to the specific PPARα/δ agonist, GW0742, and then they were treated with a1 adrenergic agonist, phenylephrine (PE). GW0742 inhibited PE- induced increase in cell area and expression of ANP and BNP. The inhibitory effect of GW0742 on cell growth and gene expression was abolished in the presence of GSK0660, a PPARα/δ antagonist. Furthermore, gene expression levels of PPARα/δ and the target genes of the receptor involved in the oxidation of fatty acids (mCPT-1, UCP3) and glucose metabolism (PDK4, GLUT4) were determined. PE- induced down- regulation of PPARα/δ and target genes, was reversed in the presence of GW0742. These results show that activation of PPARα/δ probably compensates for the metabolic dysfunction that characterizes cardiac hypertrophy, by adjusting fatty acids oxidation and glucose metabolism.The molecular mechanisms that contribute to the development of cardiac hypertrophy include, among others, kinase signaling pathways, (MAPK, PI3K/Akt), and reactive oxygen species (ROS). GW0742 inhibited PE -induced ROS production modulating signaling and redox mechanisms that are involved in cardiac hypertrophy. The non genomic role of GW0742 was confirmed by using the antagonist GSK0660. Furthermore, a second aim was to evaluate whether the administration of GW0742, improves cardiac dysfunction in diabetes and to explore the underlying molecular mechanisms of cardioprotection. For this purpose we used the experimental model of streptozotocin (65mg/kg) induced diabetes in rats with total duration of six weeks. GW0742 was found to reduce glucose, cholesterol and triglyceride levels in blood plasma, improve impairment of cardiac contractility, decrease the diabetes-induced fibrosis and inhibits hypertrophy. Additionally, in order to assess the changes in myocardial metabolism both in streptozotocin-induced diabetes and after administration of GW0742, we determined gene expression of PPARα/δ and of the target genes involved in glucose metabolism (GLUT4) and fatty acids (MCAD and mCPT-1). The results showed that PPARα/δ, MCAD and mCPT-1 expression increased in the diabetic myocardium and remained elevated in the presence of GW0742 but at lower levels. Furthermore, GW0742 administration in diabetic animals restored the decreased expression levels of GLUT4 in the control group. These results suggest that glucose metabolism could be compensated in these animals. In parallel, we investigated whether autophagy mechanisms are involved in this experimental model of diabetes mellitus and assessed the effect of GW0742 on them. For this purpose, expression levels of autophagy marker proteins LC3II, p62 and Beclin-1 were determined. We showed that autophagy levels were reduced by diabetes, but were restored to basal levels in the presence of GW0742. Finally, it was determined the infarct size and the effect of GW0742 on ischemia-induced ventricular arrhythmias and on physiological pressure parameters (LVDP) in normal and diabetic animals. The results indicate that GW0742 and WY14643 reduce infarct size and arrhythmias in both normal and diabetic model, via activation of transcription factors PPARα/δ and PPARα, respectively. Furthermore, expression of PPARα/δ and target gene GLUT4 was determined. GLUT4 expression levels are reduced after ischemia/ reperfusion (I/R) in both normal and diabetic myocardium, which is reversed in the presence of GW0742. In contrast, administration of WY14643 in normal animals restores expression of GLUT4 after I/ R. These results suggest that PPARα ηαζ PPARα/δ regulate the expression of GLUT4 differently, although the latter is a target gene of both.


2020 ◽  
Vol 20 (18) ◽  
pp. 2274-2284
Author(s):  
Faroogh Marofi ◽  
Jalal Choupani ◽  
Saeed Solali ◽  
Ghasem Vahedi ◽  
Ali Hassanzadeh ◽  
...  

Objective: Zoledronic Acid (ZA) is one of the common treatment choices used in various boneassociated conditions. Also, many studies have investigated the effect of ZA on Osteoblastic-Differentiation (OSD) of Mesenchymal Stem Cells (MSCs), but its clear molecular mechanism(s) has remained to be understood. It seems that the methylation of the promoter region of key genes might be an important factor involved in the regulation of genes responsible for OSD. The present study aimed to evaluate the changes in the mRNA expression and promoter methylation of central Transcription Factors (TFs) during OSD of MSCs under treatment with ZA. Materials and Methods: MSCs were induced to be differentiated into the osteoblastic cell lineage using routine protocols. MSCs received ZA during OSD and then the methylation and mRNA expression levels of target genes were measured by Methylation Specific-quantitative Polymerase Chain Reaction (MS-qPCR) and real.time PCR, respectively. The osteoblastic differentiation was confirmed by Alizarin Red Staining and the related markers to this stage. Results: Gene expression and promoter methylation level for DLX3, FRA1, ATF4, MSX2, C/EBPζ, and C/EBPa were up or down-regulated in both ZA-treated and untreated cells during the osteodifferentiation process on days 0 to 21. ATF4, DLX3, and FRA1 genes were significantly up-regulated during the OSD processes, while the result for MSX2, C/EBPζ, and C/EBPa was reverse. On the other hand, ATF4 and DLX3 methylation levels gradually reduced in both ZA-treated and untreated cells during the osteodifferentiation process on days 0 to 21, while the pattern was increasing for MSX2 and C/EBPa. The methylation pattern of C/EBPζ was upward in untreated groups while it had a downward pattern in ZA-treated groups at the same scheduled time. The result for FRA1 was not significant in both groups at the same scheduled time (days 0-21). Conclusion: The results indicated that promoter-hypomethylation of ATF4, DLX3, and FRA1 genes might be one of the mechanism(s) controlling their gene expression. Moreover, we found that promoter-hypermethylation led to the down-regulation of MSX2, C/EBP-ζ and C/EBP-α. The results implicate that ATF4, DLX3 and FRA1 may act as inducers of OSD while MSX2, C/EBP-ζ and C/EBP-α could act as the inhibitor ones. We also determined that promoter-methylation is an important process in the regulation of OSD. However, yet there was no significant difference in the promoter-methylation level of selected TFs in ZA-treated and control cells, a methylation- independent pathway might be involved in the regulation of target genes during OSD of MSCs.


2020 ◽  
Vol 17 (2) ◽  
pp. 133-147
Author(s):  
Mina Zafarpiran ◽  
Roya Sharifi ◽  
Zeinab Shirvani-Farsani

Background: Multiple Sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system, and genetic factors play an important role in its susceptibility. The expressions of many inflammatory genes implicated in MS are regulated by microRNA (miRNAs), whose function is to suppress the translation by pairing with miRNA Recognition Elements (MREs) present in the 3' untranslated region (3'UTR) of target mRNA. Recently, it has been shown that the Single Nucleotide Polymorphism (SNPs) present within the 3'UTR of mRNAs can affect the miRNA-mediated gene regulation and susceptibility to a variety of human diseases. Objective: The aim of this study was to analyze the SNPs within the 3'UTR of miRNA inflammatory target genes related to multiple sclerosis. Methods: By DisGeNET, dbGaP, Ovid, DAVID, Web of knowledge, and SNPs databases, 3'UTR genetic variants were identified in all inflammatory genes associated with MS. Also, miRNA's target prediction databases were used for predicting the miRNA binding sites. Results: We identified 125 SNPs with MAF>0.05 located in the binding site of the miRNA of 35 genes among 59 inflammatory genes related to MS. Bioinformatics analysis predicted 62 MRE-modulating SNPs and 59 MRE-creating SNPs in the 3'UTR of MSimplicated inflammatory genes. These candidate SNPs within miRNA binding sites of inflammatory genes can alter the miRNAs binding, and consequently lead to the mRNA gene regulation. Conclusion: Therefore, these miRNA and MRE-SNPs may play important roles in personalized medicine of MS, and hence, they would be valuable for further functional verification investigations.


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