Messenger RNA Production Research Articles

Deciphering the Impact of miR-92a-3p on Controlling BCL11A Gene Expression and Its Implication in Easing Thalassemia Symptoms

Deciphering the Impact of miR-92a-3p on Controlling BCL11A Gene Expression and Its Implication in Easing Thalassemia Symptoms

Quality by design approach to improve quality and decrease cost of in vitro transcription of mRNA using design of experiments.

In vitro transcription (IVT) reaction is an RNA polymerase-catalyzed production of messenger RNA (mRNA) from DNA template, and the unit operation with highest cost of goods in the mRNA drug substance production process. To decrease the cost of mRNA production, reagents should be optimally utilized. Due to the catalytic, multicomponent nature of the IVT reaction, optimization is a multi-factorial problem, ideally suited to design-of-experiment approach for optimization and identification of design space. We derived a data-driven model of the IVT reaction and explored factors that drive process yield (in g/L), including impact of nucleoside triphosphate (NTP) concentration and Mg:NTP ratio on reaction yield and how to optimize the main cost drivers RNA polymerase and DNA template, while minimizing dsRNA formation, a critical quality attribute in mRNA products. We report a methodological approach to derive an optimum reaction design, with which cost efficiency of the reaction was improved by 44%. We demonstrate the validity of the model on mRNA construct of different lengths. Finally, we maximized the yield of the IVT reaction to 24.9 ± 1.5 g/L in batch, thus doubling the highest ever reported IVT yield.

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9.

RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial promoter directionality. After transcription begins, the opposing functions of the endonucleolytic subunit of Integrator, INTS11, and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9

RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial promoter directionality. After transcription begins, the opposing functions of the endonucleolytic subunit of Integrator, INTS11, and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.

Salacia reticulata: An Integrative Review of its Antioxidant, Lipid-Lowering, and Glucose-Regulating Properties in Diabetes and Obesity

: Across the globe, approximately half of the population diagnosed with diabetes use complementary medicines for the treatment of diabetes. Salacia reticulata (family Hypocrataceae), is an indigenous woody climber flowering plant commonly employed within the Ayurvedic healthcare framework for addressing diabetes and obesity. It is also known as Kothala himbutu and grows in the dry zone forests of India and Sri Lanka. It is documented to exhibit antioxidant, lipid-lowering, hypertrophy- reducing, and fibrosis-inhibiting properties and hepatoprotective activity. We critically analyze the available in-vitro, animal, and clinical research supporting the utilization of Salacia reticulata in managing type 2 diabetes and obesity. Compounds that have been recognized for their ability to counteract diabetes include salacinol, kotalanol, ponkoranol, and salaprinol. Various invitro research depicted salacia's capacity to impede intestinal alpha-glucosidase function. Furthermore, it enhances the breakdown of stored fat (lipolysis) and reduces insulin resistance by increasing the production of messenger RNA for hormone-sensitive lipase (HSL) as well as adiponectin, respectively, in the mouse mesenteric fat. Salacia reticulata treatment up-regulates the lipolysis factors while downregulating the 3T3-L1 adipocytes lipogenesis factors. Both animal studies and clinical research consistently showed significant improvement in levels of glucose when fasting compared to being exposed to sucrose and maltose. Furthermore, 6 weeks to 3 months of treatment showed a substantial reduction in the HbA1c and plasma Insulin. Salacia reticulata efficiently decreases obesity and insulin resistance while enhancing glucose metabolism therefore, more substantial evidence derived from meticulously designed research is necessary to confirm its effectiveness and safety. Moreover, the research aimed at improving the growth of callus, increasing polyphenolic content, promoting mangiferin synthesis, and assessing the biological properties of the salaciagenus suggests its potential as a valuable source for the industrial production of important industrial secondary compounds. At the same time, data indicate cumulative knowledge, highlighting its strong antioxidant effect and unveiling its capabilities without impacting natural reserves.

PACAP Controls Endocrine and Behavioral Stress Responses via Separate Brain Circuits

BackgroundThe neuropeptide PACAP (pituitary adenylate cyclase-activating polypeptide) is a master regulator of central and peripheral stress responses, yet it is not clear how PACAP projections throughout the brain execute endocrine and behavioral stress responses. MethodsWe used AAV (adeno-associated virus) neuronal tracing, an acute restraint stress (ARS) paradigm, and intersectional genetics, in C57BL/6 mice, to identify PACAP-containing circuits controlling stress-induced behavior and endocrine activation. ResultsPACAP deletion from forebrain excitatory neurons, including a projection directly from medial prefrontal cortex to hypothalamus, impairs c-fos activation and corticotropin-releasing hormone (CRH) messenger RNA elevation in the paraventricular nucleus after 2 hours of restraint, without affecting ARS-induced hypophagia, or c-fos elevation in nonhypothalamic brain. Elimination of PACAP within projections from lateral parabrachial nucleus to extended amygdala, on the other hand, attenuates ARS-induced hypophagia, along with extended amygdala fos induction, without affecting ARS-induced CRH messenger RNA elevation in the paraventricular nucleus. PACAP projections to extended amygdala terminate at protein kinase C delta type (PKCδ) neurons in both the central amygdala and the oval bed nucleus of the stria terminalis. Silencing of PKCδ neurons in the central amygdala, but not in the oval bed nucleus of the stria terminalis, attenuates ARS-induced hypophagia. Experiments were carried out in mice of both sexes with n ≥ 3 per group. ConclusionsA frontocortical descending PACAP projection controls paraventricular nucleus CRH messenger RNA production to maintain hypothalamic-pituitary-adrenal axis activation and regulate the endocrine response to stress. An ascending PACAPergic projection from the external lateral parabrachial nucleus to PKCδ neurons in the central amygdala regulates behavioral responses to stress. Defining two separate limbs of the acute stress response provides broader insight into the specific brain circuitry engaged by the psychogenic stress response.

DNA-binding, multivalent interactions and phase separation in transcriptional activation

Transcription is an essential process in biology whereby gene-specific transcription factors target sites on DNA to recruit the basal transcription machinery that will produce messenger RNA (mRNA). It is a highly regulated multi-step process that involves many proteins and protein complexes. Transcription factors, the proteins that mark genes for activation, and other transcriptional regulators are highly enriched in low-complexity disordered regions, which are strongly linked to multivalent binding and phase separation. These disordered regions can form multivalent dynamic complexes that are essential for many aspects of transcription. Many of these proteins can phase separate in vitro and show evidence of phase separation in vivo. Whether these interactions represent biologically relevant phase separation in vivo is controversial. However, what these events do demonstrate is that many transcriptional proteins co-cluster with other factors in vivo, forming multivalent dynamic clusters that contribute to transcriptional events. We review some of these recently investigated events and consider how they contribute to our understanding of transcription.

Cap-binding complex assists RNA polymerase II transcription in plant salt stress response.

Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in messenger RNA (mRNA) production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 coregulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.

Recipharm acquires 2 biologics firms

Recipharm, a Swedish pharmaceutical services firm, has acquired Arranta Bio, a contract development and manufacturing organization (CDMO) specializing in microbiome therapeutics and messenger RNA production. It also bought Vibalogics, a virotherapy CDMO with expertise in making oncolytic viruses, viral vaccines, and gene therapies. Both firms are based in Massachusetts. Meanwhile, Recipharm plans to expand its sterile fill-and-finish capabilities at its facility in Monts, France, by adding a high-speed filling line.

A Novel Soft Clustering Approach for Gene Expression Data

Gene expression data represents a condition matrix where each row represents the gene and the column shows the condition. Micro array used to detect gene expression in lab for thousands of gene at a time. Genes encode proteins which in turn will dictate the cell function. The production of messenger RNA along with processing the same are the two main stages involved in the process of gene expression. The biological networks complexity added with the volume of data containing imprecision and outliers increases the challenges in dealing with them. Clustering methods are hence essential to identify the patterns present in massive gene data. Many techniques involve hierarchical, partitioning, grid based, density based, model based and soft clustering approaches for dealing with the gene expression data. Understanding the gene regulation and other useful information from this data can be possible only through effective clustering algorithms. Though many methods are discussed in the literature, we concentrate on providing a soft clustering approach for analyzing the gene expression data. The population elements are grouped based on the fuzziness principle and a degree of membership is assigned to all the elements. An improved Fuzzy clustering by Local Approximation of Memberships (FLAME) is proposed in this work which overcomes the limitations of the other approaches while dealing with the non-linear relationships and provide better segregation of biological functions.

Coexistence of Hopf-born rotation and heteroclinic cycling in a time-delayed three-gene auto-regulated and mutually-repressed core genetic regulation network

In this work, we study the behavior of a time-delayed mutually repressive auto-activating three-gene system. Delays are introduced to account for the location difference between DNA transcription that leads to production of messenger RNA and its translation that result in protein synthesis. We study the dynamics of the system using numerical simulations, computational bifurcation analysis and mathematical analysis. We find Hopf bifurcations leading to stable and unstable rotation in the system, and we study the rotational behavior as a function of cyclic mutual repression parameter asymmetry between each gene pair in the network. We focus on how rotation co-exists with a stable heteroclinic flow linking the three saddles in the system. We find that this coexistence allows for a transition between two markedly different types of rotation leading to strikingly different phenotypes. One type of rotation belongs to Hopf-induced rotation while the other type, belongs to heteroclinic cycling between three saddle nodes in the system. We discuss the evolutionary and biological implications of our findings.

The Regulation of Staphylococcus aureus-Induced Inflammatory Responses in Bovine Mammary Epithelial Cells.

Mastitis, an inflammatory disease, causes severe economic loss in the dairy industry, which is mainly infected by bacteria. Staphylococcus aureus (S. aureus), the major pathogenic microorganism, derived from lipoteichoic acid (LTA) has been identified to activate inflammatory responses, but the cellular or intercellular regulatory mechanism is unclear. This study mainly focused on the effects of LTA in bovine mammary epithelial cells (Mac-T) and elaborated the regulation of microRNAs (miRNAs). The results showed that LTA enhanced the messenger RNA (mRNA) expression and production of tumor necrosis factor α (TNF-α) and interleukin (IL)-6. Furthermore, LTA could activate Toll-like receptor (TLR)2/MyD88-mediated phosphoinositide 3-kinase (PI3K)/AKT pathway, and TLR2 plays a pivotal role in LTA-induced inflammatory responses. The results of qRT-PCR showed that miRNA levels increased and reached the highest at 3 h and then gradually decreased over time in Mac-T cells. In exosomes, the levels of 11 and three miRNAs were upregulated and downregulated at 24 h, respectively. In addition, miR-23a showed the highest increase in Mac-T cells treated with LTA and targeted PI3K to regulate inflammatory responses. Furthermore, Mac-T cell-derived exosomes were identified to play a cell–cell communication by promoting M1 polarization of bovine macrophages. In summary, our study demonstrated that LTA could activate inflammatory responses via TLR2/MyD88/PI3K/AKT signaling pathway, and miR-23a inhibited it by targeting PI3K. Furthermore, we found that Mac-T cell-derived exosomes might be associated with inflammatory responses by promoting M1 polarization of bovine macrophages.

High- and low-molecular-weight chitosan act as adjuvants during single-dose influenza A virus protein vaccination through distinct mechanisms.

The investigation of new adjuvants is essential for the development of efficacious vaccines. Chitosan (CS), a derivative of chitin, has been shown to act as an adjuvant, improving vaccine‐induced immune responses. However, the effect of CS molecular weight (MW) on this adjuvanticity has not been investigated, despite MW having been shown to impact CS biological properties. Here, two MW variants of CS were investigated for their ability to enhance vaccine‐elicited immune responses in vitro and in vivo, using a single‐dose influenza A virus (IAV) protein vaccine model. Both low‐molecular‐weight (LMW) and high‐molecular‐weight (HMW) CS‐induced interferon regulatory factor pathway signaling, antigen‐presenting cell activation, and cytokine messenger RNA (mRNA) production, with LMW inducing higher mRNA levels at 24 h and HMW elevating mRNA responses at 48 h. LMW and HMW CS also induced adaptive immune responses after vaccination, indicated by enhanced immunoglobulin G production in mice receiving LMW CS and increased CD4 interleukin 4 (IL‐4) and IL‐2 production in mice receiving HMW CS. Importantly, both LMW and HMW CS adjuvantation reduced morbidity following homologous IAV challenge. Taken together, these results support that LMW and HMW CS can act as adjuvants, although this protection may be mediated through distinct mechanisms based on CS MW.

A Stochastic Model of Gene Expression with Polymerase Recruitment and Pause Release

Transcriptional bursting is a major source of noise in gene expression. The telegraph model of gene expression, whereby transcription switches between on and off states, is the dominant model for bursting. Recently, it was shown that the telegraph model cannot explain a number of experimental observations from perturbation data. Here, we study an alternative model that is consistent with the data and which explicitly describes RNA polymerase recruitment and polymerase pause release, two steps necessary for messenger RNA (mRNA) production. We derive the exact steady-state distribution of mRNA numbers and an approximate steady-state distribution of protein numbers, which are given by generalized hypergeometric functions. The theory is used to calculate the relative sensitivity of the coefficient of variation of mRNA fluctuations for thousands of genes in mouse fibroblasts. This indicates that the size of fluctuations is mostly sensitive to the rate of burst initiation and the mRNA degradation rate. Furthermore, we show that 1) the time-dependent distribution of mRNA numbers is accurately approximated by a modified telegraph model with a Michaelis-Menten like dependence of the effective transcription rate on RNA polymerase abundance, and 2) the model predicts that if the polymerase recruitment rate is comparable or less than the pause release rate, then upon gene replication, the mean number of RNA per cell remains approximately constant. This gene dosage compensation property has been experimentally observed and cannot be explained by the telegraph model with constant rates.

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.

Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

CFIm25 in Solid Tumors: Current Research Progress.

Cleavage factor I m25 is a newly discovered solid tumor-related gene, however, its precise role in cancer pathogenesis has not yet been characterized. Alternative polyadenylation is an RNA-processing mechanism that generates distinct 3′-termini on messenger RNAs, producing messenger RNA isoforms. Different factors influence the initiation and development of this process. As a key factor in alternative polyadenylation, cleavage factor I m25 plays an important role in messenger RNA maturation and cell signal transduction. Moreover, by regulating the process of alternative polyadenylation, it can inhibit the proliferation, invasion, and metastasis of a variety of tumors. Cleavage factor I m25 also acts as an oncogene in select tumors. The present review focuses on the role of cleavage factor I m25 in solid tumors and treatment. Due to the lack of current knowledge regarding the mechanisms of action and regulation of cleavage factor I m25 and alternative polyadenylation, it is necessary to further examine their role in cancer as well as in other diseases.

Nascent RNA and the Coordination of Splicing with Transcription.

At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.

Quantifying the noise in bursty gene expression under regulation by small RNAs

Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of messenger RNA (mRNA), sRNA and protein make the exact solution for this stochastic process intractable. This is particularly the case when quantifying the protein noise level, which has great impact on multiple cellular processes. Here, we propose an approximate yet reasonably accurate solution for the gene expression noise with infrequent burst and strong regulation by sRNAs. This analytical solution allows us to better analyze the noise and stochastic deviation of protein level. We find that the regulation amplifies the noise, reduces the protein level. The stochasticity in the regulation generates more proteins than what if the stochasticity is removed from the system. The sRNA level is most important to the relationship between the noise and stochastic deviation. The results provide analytical tools for more general studies of gene expression and strengthen our quantitative understandings of post-transcriptional regulation in controlling gene expression processes.

The myeloid lineage‐determining transcription factor PU.1 induces enhancer‐promoter looping that promotes IL‐1β enhancer and messenger RNA production in non‐myeloid melanoma cells

The DNA‐binding protein purine rich (PU.1) is a lineage determining transcription factor required for development of myeloid cells such as monocytes/macrophages. PU.1 is regarded as a pioneering transcription factor for macrophage differentiation due to its ability to bind “closed” genomic sites and initiate/maintain “open” chromatin state in macrophage‐restricted response genes. To date, however, precise mechanism of PU.1 in remodeling chromatin is yet to be elucidated. The non‐myeloid melanoma B16.BL6 cells response to the bacterial cell wall component lipopolysaccharide (LPS) and activate the transcription factor NF‐κB, but do not produce cytokines. Ectopic expression of PU.1 rendered these cells express the cytokine interleukin 1‐β (IL1b) in response to LPS. PU.1 induced chromatin remodeling that caused interaction between the IL1b promoter and enhancer (located ~10 kb upstream of the IL1b transcription start site) in non‐activated cells; upon activation, PU.1 recruited NF‐κB to these genomic regions. The N‐terminal domain (1–30) of PU.1 was important for both promoter‐enhancer looping and IL1b eRNA/mRNA production; whereas, the acidic and glutamine rich domains (33–100) were required for eRNA/mRNA production but dispensable for the DNA looping. eRNA production and histone acetylation were required for NF‐κB recruitment and IL1b mRNA expression, but not for the DNA looping. Altogether, this study indicates that PU.1 induces enhancer‐promoter looping that sequentially allows activation‐dependent histone acetylation, recruitment of NF‐κB and production of enhancer RNAs, all of which are required for an optimal IL1b production.Support or Funding InformationThe Natural Sciences and Engineering Research Council of Canada ‐ Discovery Grant (RGPIN‐2018‐05514)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Decoupling of recombinant protein production from Escherichia coli cell growth enhances functional expression of plant Leloir glycosyltransferases.

Sugar nucleotide‐dependent (Leloir) glycosyltransferases from plants are important catalysts for the glycosylation of small molecules and natural products. Limitations on their applicability for biocatalytic synthesis arise because of low protein expression (≤10 mg/L culture) in standard microbial hosts. Here, we showed two representative glycosyltransferases: sucrose synthase from soybean and UGT71A15 from apple. A synthetic biology‐based strategy of decoupling the enzyme expression from the Escherichia coli BL21(DE3) cell growth was effective in enhancing their individual (approximately fivefold) or combined (approximately twofold) production as correctly folded, biologically active proteins. The approach entails a synthetic host cell, which is able to shut down the production of host messenger RNA by inhibition of the E. coli RNA polymerase. Overexpression of the enzyme(s) of interest is induced by the orthogonal T7 RNA polymerase. Shutting down of the host RNA polymerase is achieved by l‐arabinose‐inducible expression of the T7 phage‐derived Gp2 protein from a genome‐integrated site. The glycosyltransferase genes are encoded on conventional pET‐based expression plasmids that allow T7 RNA polymerase‐driven inducible expression by isopropyl‐β‐ d‐galactoside. Laboratory batch and scaled‐up (20 L) fed‐batch bioreactor cultivations demonstrated improvements in an overall yield of active enzyme by up to 12‐fold as a result of production under growth‐decoupled conditions. In batch culture, sucrose synthase and UGT71A15 were obtained, respectively, at 115 and 2.30 U/g cell dry weight, corresponding to ∼5 and ∼1% of total intracellular protein. Fed‐batch production gave sucrose synthase in a yield of 2,300 U/L of culture (830 mg protein/L). Analyzing the isolated glycosyltransferase, we showed that the improvement in the enzyme production was due to the enhancement of both yield (5.3‐fold) and quality (2.3‐fold) of the soluble sucrose synthase. Enzyme preparation from the decoupled production comprised an increased portion (61% compared with 26%) of the active sucrose synthase homotetramer. In summary, therefore, we showed that the expression in growth‐arrested E. coli is promising for recombinant production of plant Leloir glycosyltransferases.