Development, validation, and application of the ribosome separation and reconstitution system for protein translation in vitro

Mrna Translation ◽

Protein Translation ◽

Transcription Control ◽

Vitro Assay ◽

Translational Machinery ◽

The conventional view regarding regulation of gene expression is based on transcription control. However, a growing number of recent studies has revealed the important additional impact of translational regulation. Eukaryotic translational machinery appears to be capable of reprogramming mRNA translation to generate proteins required to maintain a healthy cellular proteostasis under particular physiological conditions or to adapt to stress. Although the mechanisms of such remarkable regulation are beginning to emerge, recent studies have identified the ribosome as one of the major constituents of translation-dependent control of gene expression that is especially important during stress. Built of RNA and proteins, ribosomes are susceptible to environmental and intracellular stresses. How stress-modified ribosomes regulate translation and whether they play a role in stress-induced gene expression remain largely elusive. This knowledge gap is likely due to the lack of an appropriate experimental system. Canonical approaches based on exposing cells or cell-free extracts to stressors provide inconclusive results due to off-target effects of modifying agents. Here we describe a robust and simple in vitro assay that allows separation of yeast ribosomes from other translational machinery constituents, followed by reconstitution of the translation reaction. This ribosome separation and reconstitution assay (RSR) is highly advantageous, as it allows modification of ribosomes without compromising other key translational components, followed by supplementing the ribosomes back into translation reactions containing undamaged, translationally-competent yeast lysate. Besides addressing the impact of ribosome-derived stress on translation, RSR can also be used to characterize mutated ribosomes and ribosomes devoid of associated factors.

Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0900028106 ◽

2009 ◽

Vol 106 (17) ◽

pp. 7028-7033 ◽

Cited By ~ 356

Author(s):

Zhe Ji ◽

Ju Youn Lee ◽

Zhenhua Pan ◽

Bingjun Jiang ◽

Bin Tian

Keyword(s):

Gene Expression ◽

Embryonic Development ◽

Posttranscriptional Regulation ◽

Alternative Polyadenylation ◽

Untranslated Regions ◽

C2c12 Myoblast ◽

Differentiation And Proliferation

The 3′ untranslated regions (3′ UTRs) of mRNAs containcis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3′ UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3′ UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3′ UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3′ UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.

Characterization of five purine riboswitches in cellular and cell-free expression systems

10.1101/2021.04.14.439898 ◽

2021 ◽

Author(s):

Milca Rachel da Costa Ribeiro Lins ◽

Graciely Gomes Correa ◽

Laura Araujo da Silva Amorim ◽

Rafael Augusto Lopes Franco ◽

Nathan Vinicius Ribeiro ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

In Vitro Transcription ◽

Vitro Assay ◽

Transcription Terminator ◽

Variable Expression ◽

Expression Platform

Bacillus subtilis employs five purine riboswitches for the control of purine de novo synthesis and transport at the transcription level. All of them are formed by a structurally conserved aptamer, and a variable expression platform harboring a rho-independent transcription terminator. In this study, we characterized all five purine riboswitches under the context of active gene expression processes both in vitro and in vivo. We identified transcription pause sites located in the expression platform upstream of the terminator of each riboswitch. Moreover, we defined a correlation between in vitro transcription readthrough and in vivo gene expression. Our in vitro assay demonstrated that the riboswitches operate in the micromolar range of concentration for the cognate metabolite. Our in vivo assay showed the dynamics of control of gene expression by each riboswitch. This study deepens the knowledge of the regulatory mechanism of purine riboswitches.

Identification of Nrl1 Domains Responsible for Interactions with RNA-Processing Factors and Regulation of Nrl1 Function by Phosphorylation

International Journal of Molecular Sciences ◽

10.3390/ijms22137011 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7011

Author(s):

Barbora Mikolaskova ◽

Matus Jurcik ◽

Ingrid Cipakova ◽

Tomas Selicky ◽

Jan Jurcik ◽

...

Keyword(s):

Gene Expression ◽

Rna Processing ◽

Affinity Purification ◽

Terminal Region ◽

Mass Spectrometry Analysis ◽

Post Translational Modification ◽

Vitro Assay ◽

Spectrometry Analysis

Pre-mRNA splicing is a key process in the regulation of gene expression. In the fission yeast Schizosaccharomyces pombe, Nrl1 regulates splicing and expression of several genes and non-coding RNAs, and also suppresses the accumulation of R-loops. Here, we report analysis of interactions between Nrl1 and selected RNA-processing proteins and regulation of Nrl1 function by phosphorylation. Bacterial two-hybrid system (BACTH) assays revealed that the N-terminal region of Nrl1 is important for the interaction with ATP-dependent RNA helicase Mtl1 while the C-terminal region of Nrl1 is important for interactions with spliceosome components Ctr1, Ntr2, and Syf3. Consistent with this result, tandem affinity purification showed that Mtl1, but not Ctr1, Ntr2, or Syf3, co-purifies with the N-terminal region of Nrl1. Interestingly, mass-spectrometry analysis revealed that in addition to previously identified phosphorylation sites, Nrl1 is also phosphorylated on serines 86 and 112, and that Nrl1-TAP co-purifies with Cka1, the catalytic subunit of casein kinase 2. In vitro assay showed that Cka1 can phosphorylate bacterially expressed Nrl1 fragments. An analysis of non-phosphorylatable nrl1 mutants revealed defects in gene expression and splicing consistent with the notion that phosphorylation is an important regulator of Nrl1 function. Taken together, our results provide insights into two mechanisms that are involved in the regulation of the spliceosome-associated factor Nrl1, namely domain-specific interactions between Nrl1 and RNA-processing proteins and post-translational modification of Nrl1 by phosphorylation.

Precise tuning of gene expression output levels in mammalian cells

10.1101/352377 ◽

2018 ◽

Cited By ~ 1

Author(s):

Yale S. Michaels ◽

Mike B. Barnkob ◽

Hector Barbosa ◽

Toni A. Baeumler ◽

Mary K. Thompson ◽

...

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

High Throughput Sequencing ◽

Antigen Expression ◽

Precise Control ◽

Mouse Melanoma Model

ABSTRACTPrecise, analogue regulation of gene expression is critical for development, homeostasis and regeneration in mammals. In contrast, widely employed experimental and therapeutic approaches such as knock-in/out strategies are more suitable for binary control of gene activity, while RNA interference (RNAi) can lead to pervasive off-target effects and unpredictable levels of repression. Here we report on a method for the precise control of gene expression levels in mammalian cells based on engineered, synthetic microRNA response elements (MREs). To develop this system, we established a high-throughput sequencing approach for measuring the efficacy of thousands of miR-17 MRE variants. This allowed us to create a library of microRNA silencing-mediated fine-tuners (miSFITs) of varying strength that can be employed to control the expression of user specified genes. To demonstrate the value of this technology, we used a panel of miSFITs to tune the expression of a peptide antigen in a mouse melanoma model. This analysis revealed that antigen expression level is a key determinant of the anti-tumour immune response in vitro and in vivo. miSFITs are a powerful tool for modulating gene expression output levels with applications in research and cellular engineering.

Development of Flexible Polycation-Based mRNA Delivery Systems for In Vivo Applications

Materials Proceedings ◽

10.3390/iocn2020-07988 ◽

2020 ◽

Vol 4 (1) ◽

pp. 5

Author(s):

Takuya Miyazaki ◽

Satoshi Uchida ◽

Yuji Miyahara ◽

Akira Matsumoto ◽

Horacio Cabral

Keyword(s):

Gene Expression ◽

Protein Translation ◽

Delivery Systems ◽

Systemic Injection ◽

Broad Application ◽

Effective Delivery ◽

The Impact ◽

Delivery Efficiency

mRNA is a promising therapeutic nucleic acid, although effective delivery systems are required for its broad application. Polyion complex (PIC) micelles loading mRNA via polyion complexation with block catiomers are emerging as promising carriers for mRNA delivery, but the PIC stability has been limited so far. Controlling the binding of polycations to mRNA could affect the micelle stability. Nevertheless, the impact of binding affinity between polycations and mRNA on the function of mRNA-loaded PIC micelles (mRNA/m) remains unknown. Herein, we review our recent orthogonal approaches controlling the stiffness and the valency of polycations to improve the performance of mRNA/m toward enhancing stability and delivery efficiency. Thus, block catiomers with contrasting flexibility were developed to prepare mRNA/m. The flexible catiomer stabilized mRNA/m against enzymatic attack and polyanion exchange compared to the rigid catiomer, promoting protein translation in vitro and in vivo, and prolonged mRNA bioavailability in blood after systemic injection. Based on these observations, we also developed flexible catiomers with different valencies. The guanidinated catiomer stabilized mRNA/m compared to the aminated catiomers, facilitating intracellular delivery and eventual gene expression. Our findings indicate the importance of controlling the polymer binding to mRNA for developing flexible polycation-based systems directed to in vivo applications.

Regulation of mRNA translation by a photoriboswitch

eLife ◽

10.7554/elife.51737 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Kelly A Rotstan ◽

Michael M Abdelsayed ◽

Luiz FM Passalacqua ◽

Fabio Chizzolini ◽

Kasireddy Sudarshan ◽

...

Keyword(s):

Gene Expression ◽

Protein Expression ◽

In Vitro Selection ◽

Mrna Translation ◽

Spatiotemporal Analysis ◽

Reading Frame ◽

Controlled Systems

Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)–a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.

Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice

Epigenetics & Chromatin ◽

10.1186/s13072-020-00373-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Federico Tinarelli ◽

Elena Ivanova ◽

Ilaria Colombi ◽

Erica Barini ◽

Edoardo Balzani ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Neuronal Networks ◽

Molecular Mechanisms ◽

Ex Vivo ◽

Neuronal Cultures ◽

Functional Impairments ◽

After Hours ◽

Abstract Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.

Effects of Vitrification on the Blastocyst Gene Expression Profile in a Porcine Model

International Journal of Molecular Sciences ◽

10.3390/ijms22031222 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1222

Author(s):

Cristina Cuello ◽

Cristina A. Martinez ◽

Josep M. Cambra ◽

Inmaculada Parrilla ◽

Heriberto Rodriguez-Martinez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Analysis ◽

Survival Rates ◽

Control Group ◽

P Value ◽

Transcriptome Profile ◽

Embryo Viability ◽

This study was designed to investigate the impact of vitrification on the transcriptome profile of blastocysts using a porcine (Sus scrofa) model and a microarray approach. Blastocysts were collected from weaned sows (n = 13). A total of 60 blastocysts were vitrified (treatment group). After warming, vitrified embryos were cultured in vitro for 24 h. Non-vitrified blastocysts (n = 40) were used as controls. After the in vitro culture period, the embryo viability was morphologically assessed. A total of 30 viable embryos per group (three pools of 10 from 4 different donors each) were subjected to gene expression analysis. A fold change cut-off of ±1.5 and a restrictive threshold at p-value < 0.05 were used to distinguish differentially expressed genes (DEGs). The survival rates of vitrified/warmed blastocysts were similar to those of the control (nearly 100%, n.s.). A total of 205 (112 upregulated and 93 downregulated) were identified in the vitrified blastocysts compared to the control group. The vitrification/warming impact was moderate, and it was mainly related to the pathways of cell cycle, cellular senescence, gap junction, and signaling for TFGβ, p53, Fox, and MAPK. In conclusion, vitrification modified the transcriptome of in vivo-derived porcine blastocysts, resulting in minor gene expression changes.

Speciation and changes in male gene expression in Drosophila

Genome ◽

10.1139/gen-2020-0025 ◽

2020 ◽

pp. 1-11

Author(s):

Bahar Patlar ◽

Alberto Civetta

Keyword(s):

Gene Expression ◽

Reproductive Isolation ◽

Potential Role ◽

Drosophila Model ◽

Depth Analysis ◽

The Impact ◽

Plastic Responses ◽

Male Gene

It has long been acknowledged that changes in the regulation of gene expression may account for major organismal differences. However, we still do not fully understand how changes in gene expression evolve and how do such changes influence organisms’ differences. We are even less aware of the impact such changes might have in restricting gene flow between species. Here, we focus on studies of gene expression and speciation in the Drosophila model. We review studies that have identified gene interactions in post-mating reproductive isolation and speciation, particularly those that modulate male gene expression. We also address studies that have experimentally manipulated changes in gene expression to test their effect in post-mating reproductive isolation. We highlight the need for a more in-depth analysis of the role of selection causing disrupted gene expression of such candidate genes in sterile/inviable hybrids. Moreover, we discuss the relevance to incorporate more routinely assays that simultaneously evaluate the potential effects of environmental factors and genetic background in modulating plastic responses in male genes and their potential role in speciation.

Impact of the acidic environment on gene expression and functional parameters of tumors in vitro and in vivo

Journal of Experimental & Clinical Cancer Research ◽

10.1186/s13046-020-01815-4 ◽

2021 ◽

Vol 40 (1) ◽

Author(s):

Mandy Rauschner ◽

Luisa Lange ◽

Thea Hüsing ◽

Sarah Reime ◽

Alexander Nolze ◽

...

Keyword(s):

Gene Expression ◽

Cell Death ◽

Western Blot ◽

Tumor Cell ◽

Low Ph ◽

Strong Increase ◽

Acidic Ph ◽

Abstract Background The low extracellular pH (pHe) of tumors resulting from glycolytic metabolism is a stress factor for the cells independent from concomitant hypoxia. The aim of the study was to analyze the impact of acidic pHe on gene expression on mRNA and protein level in two experimental tumor lines in vitro and in vivo and were compared to hypoxic conditions as well as combined acidosis+hypoxia. Methods Gene expression was analyzed in AT1 prostate and Walker-256 mammary carcinoma of the rat by Next Generation Sequencing (NGS), qPCR and Western blot. In addition, the impact of acidosis on tumor cell migration, adhesion, proliferation, cell death and mitochondrial activity was analyzed. Results NGS analyses revealed that 147 genes were uniformly regulated in both cell lines (in vitro) and 79 genes in both experimental tumors after 24 h at low pH. A subset of 25 genes was re-evaluated by qPCR and Western blot. Low pH consistently upregulated Aox1, Gls2, Gstp1, Ikbke, Per3, Pink1, Tlr5, Txnip, Ypel3 or downregulated Acat2, Brip1, Clspn, Dnajc25, Ercc6l, Mmd, Rif1, Zmpste24 whereas hypoxia alone led to a downregulation of most of the genes. Direct incubation at low pH reduced tumor cell adhesion whereas acidic pre-incubation increased the adhesive potential. In both tumor lines acidosis induced a G1-arrest (in vivo) of the cell cycle and a strong increase in necrotic cell death (but not in apoptosis). The mitochondrial O2 consumption increased gradually with decreasing pH. Conclusions These data show that acidic pHe in tumors plays an important role for gene expression independently from hypoxia. In parallel, acidosis modulates functional properties of tumors relevant for their malignant potential and which might be the result of pH-dependent gene expression.