Coordinate Gene Expression Research Articles

Spatial clustering and common regulatory elements correlate with coordinated gene expression.

Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression. In eukaryotic cells, transcriptional activity of a gene is affected by not only transcription factors but also the epigenetic modifications and three-dimensional chromosome structure of the gene. To examine how local gene environment and transcription factor regulation are coupled, we performed a combined analysis of time-course RNA-seq data of TGF-β treated MCF10A cells and related epigenomic and Hi-C data. Using Dynamic Regulatory Events Miner (DREM), we clustered differentially expressed genes based on gene expression profiles and associated transcription factors. Genes in each class have similar temporal gene expression patterns and share common transcription factors. Next, we defined a set of linear and radial distribution functions, as used in statistical physics, to measure the distributions of genes within a class both spatially and linearly along the genomic sequence. Remarkably, genes within the same class despite sometimes being separated by tens of million bases (Mb) along genomic sequence show a significantly higher tendency to be spatially close despite sometimes being separated by tens of Mb along the genomic sequence than those belonging to different classes do. Analyses extended to the process of mouse nervous system development arrived at similar conclusions. Future studies will be able to test whether this spatial organization of chromosomes contributes to concerted gene expression.

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

The aberrant activities of transcription factors such as the androgen receptor (AR) underpin prostate cancer development. While the AR cis-regulation has been extensively studied in prostate cancer, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited. In this paper, we propose a novel framework to profile long-range chromatin interactions associated with AR and its collaborative transcription factor, erythroblast transformation-specific related gene (ERG), using chromatin interaction analysis by paired-end tag (ChIA-PET). We identified ERG-associated long-range chromatin interactions as a cooperative component in the AR-associated chromatin interactome, acting in concert to achieve coordinated regulation of a subset of AR target genes. Through multifaceted functional data analysis, we found that AR-ERG interaction hub regions are characterized by distinct functional signatures, including bidirectional transcription and cotranscription factor binding. In addition, cancer-associated long noncoding RNAs were found to be connected near protein-coding genes through AR-ERG looping. Finally, we found strong enrichment of prostate cancer genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) at AR-ERG co-binding sites participating in chromatin interactions and gene regulation, suggesting GWAS target genes identified from chromatin looping data provide more biologically relevant findings than using the nearest gene approach. Taken together, our results revealed an AR-ERG-centric higher-order chromatin structure that drives coordinated gene expression in prostate cancer progression and the identification of potential target genes for therapeutic intervention.

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type-specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment for genes that regulate neuronal connectivity and chromatin remodeling, and evidence for coordinated transcriptional regulation and proteomic interaction of the participating genes. Developmentally regulated chromosomal conformation changes at schizophrenia-relevant sequences disproportionally occurred in neurons, highlighting the existence of cell type-specific disease risk vulnerabilities in spatial genome organization.

Isolation and Characterization of Different Mesenchymal Stem Cell Populations from Rat Femur.

Purified mesenchymal stem cells (MSCs) may be used for a multitude of applications, from the study of biological processes such as cell division and coordinated gene expression to tissue engineering and regenerative medicine. However, although highly similar, MSCs isolated and purified from different tissues may be biologically different in the ability of the cells to respond to environmental cues that instigate and propagate changes in cell fate such as differentiation, proliferation, apoptosis, and senescence. Selecting which MSC subtype to study may therefore profoundly influence the outcome of the investigation. Here we outline the isolation, purification, and differentiation of three different MSC subtypes derived from various depots within rat bone. These include MSCs from bone marrow, compact bone, and the proximal femur. Osteoblastic and adipogenic differentiation exemplify differences between these cells.

Reciprocal Reprogramming of Cancer Cells and Associated Mesenchymal Stem Cells in Gastric Cancer.

The interactions of cancer stem cells (CSCs) within the tumor microenvironment (TME), contribute to the overall phenomenon of intratumoral heterogeneity, which also involve CSC interactions with noncancer stromal cells. Comprehensive understanding of the tumorigenesis process requires elucidating the coordinated gene expression between cancer and tumor stromal cells for each tumor. We show that human gastric cancer cells (GSC1) subvert gene expression and cytokine production by mesenchymal stem cells (GSC‐MSC), thus promoting tumor progression. Using mixed composition of human tumor xenografts, organotypic culture, and in vitro assays, we demonstrate GSC1‐mediated specific reprogramming of “naïve” MSC into specialized tumor associated MSC equipped with a tumor‐promoting phenotype. Although paracrine effect of GSC‐MSC or primed‐MSC is sufficient to enable 2D growth of GSC1, cell–cell interaction with GSC‐MSC is necessary for 3D growth and in vivo tumor formation. At both the transcriptional and at the protein level, RNA‐Seq and proteome analyses, respectively, revealed increased R‐spondin expression in primed‐MSC, and paracrine and juxtacrine mediated elevation of Lgr5 expression in GSC1, suggesting GSC‐MSC‐mediated support of cancer stemness in GSC1. CSC properties are sustained in vivo through the interplay between GSC1 and GSC‐MSC, activating the R‐spondin/Lgr5 axis and WNT/β‐catenin signaling pathway. β‐Catenin+ cell clusters show β‐catenin nuclear localization, indicating the activation of the WNT/β‐catenin signaling pathway in these cells. The β‐catenin+ cluster of cells overlap the Lgr5+ cells, however, not all Lgr5+ cells express β‐catenin. A predominant means to sustain the CSC contribution to tumor progression appears to be subversion of MSC in the TME by cancer cells. Stem Cells 2018 Stem Cells 2019;37:176–189

Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit

BackgroundPseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cultivars of Actinidia chinensis var. chinensis. To gain information about the expression of genes involved in pathogenicity we have carried out transcriptome analysis of Psa during the early stages of kiwifruit infection.ResultsGene expression in Psa was investigated during the first five days after infection of kiwifruit plantlets, using RNA-seq. Principal component and heatmap analyses showed distinct phases of gene expression during the time course of infection. The first phase was an immediate transient peak of induction around three hours post inoculation (HPI) that included genes that code for a Type VI Secretion System and nutrient acquisition (particularly phosphate). This was followed by a significant commitment, between 3 and 24 HPI, to the induction of genes encoding the Type III Secretion System (T3SS) and Type III Secreted Effectors (T3SE). Expression of these genes collectively accounted for 6.3% of the bacterial transcriptome at this stage. There was considerable variation in the expression levels of individual T3SEs but all followed the same temporal expression pattern, with the exception of hopAS1, which peaked later in expression at 48 HPI. As infection progressed over the time course of five days, there was an increase in the expression of genes with roles in sugar, amino acid and sulfur transport and the production of alginate and colanic acid. These are both polymers that are major constituents of extracellular polysaccharide substances (EPS) and are involved in biofilm production. Reverse transcription-quantitative PCR (RT-qPCR) on an independent infection time course experiment showed that the expression profile of selected bacterial genes at each infection phase correlated well with the RNA-seq data.ConclusionsThe results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the immediate contact with the host, those involved in the initiation of infection, and finally those responsible for nutrient acquisition.

Microbial Biofilm and Quorum Sensing Inhibition: Endowment of Medicinal Plants to Combat Multidrug-Resistant Bacteria.

Continued emergence and spread of multidrug-resistant bacteria behooved the development of alternative treatment strategies, including antimicrobial drugs. A hopeful approach is to target cellto- cell communications, commonly known as quorum-sensing (QS) and microbial biofilm formation. Quorum Sensing is a method used on bacteria to determine their physiological behavior and coordinate gene expression based on the cell to cell signaling. Many physiological functions of bacteria are controlled by quorum sensings such as virulence, motility, sporulation, luminescence, and biofilm formation. Microbial biofilms are organized aggregations of cells attached to a substratum and surrounded by a self-produced extrapolymeric substance (EPS) matrix. Currently, biofilm formation and quorum sensing are considered as a prospective novel target for antimicrobial therapy to control multidrug- resistant infections. Plant-based natural products have been comprehensively studied in this context. In this review, a comprehensive overview of various research papers published in the last decade on plant-derived molecules that are capable of inhibiting quorum sensing or microbial biofilm formation is reviewed, mentioning the biosynthetic classes of active compounds and their biological activity in the performed assays.

BASI74, a Virulence-Related sRNA in Brucella abortus

Brucella spp. are intracellular pathogens that infect a wide variety of mammals including humans, posing threats to the livestock industry and human health in developing countries. A number of genes associated with the intracellular trafficking and multiplication have so far been identified in Brucella spp. However, the sophisticated post-transcriptional regulation and coordination of gene expression that enable Brucella spp. to adapt to changes in environment and to evade host cell defenses are not fully understood. Bacteria small RNAs (sRNAs) play a significant role in post-transcriptional regulation, which has already been confirmed in a number of bacteria but the role of sRNAs in Brucella remains elusive. In this study, we identified several different sRNAs in Brucella spp., and found that over-expression of a sRNA, tentatively termed BASI74, led to alternation in virulence of Brucella in macrophage infection model. The expression level of BASI74 increased while Brucella abortus 2308 was grown in acidic media. In addition, BASI74 affected the growth ratio of the Brucella cells in minimal media and iron limiting medium. Using a two-plasmid reporter system, we identified four genes as the target of BASI74. One target gene, BABI1154, was predicted to encode a cytosine-N4-specific DNA methyltransferase, which protects cellular DNA from the restriction endonuclease in Brucella. These results show that BASI74 plays an important role in Brucella survival in macrophage infection model, speculatively by its connection with stress response or impact on restriction-modification system. Our study promotes the understanding of Brucella sRNAs, as well as the mechanism by which sRNAs use to influence Brucella physiology and pathogenesis.

Abstract A07: Alterations in G2/M phase associated transcriptional networks highlight lung cancer predisposition in COPD patients

Abstract Background: Patients with chronic obstructive pulmonary disease (COPD) are at increased risk of developing lung cancer. COPD, clinically defined by reduced lung function measurements, is characterized by chronic airway inflammation, remodeling and loss as well as destruction of alveoli (emphysema). While this disease is an important lung cancer risk factor independent of smoking, the molecular progression from COPD to lung cancer tumourigenesis is relatively understudied. Method: We first analyzed small-airway epithelial gene expression profiles obtained from bronchial brushings from 127 COPD and 140 non-COPD ever-smoker patients. We performed weighted gene correlation network analysis (WGCNA) on these gene expression profiles to discover deregulated gene modules (“metagenes”) associated with reduced lung function (Forced Expiratory Volume at 1 second, FEV-1)—a clinical measure of COPD severity most robustly negatively correlated with lung cancer risk. We then assessed the preservation of these modules in two non-small cell lung cancer (NSCLC) tumor/normal data sets (lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), n= 887 tumors total) to examine the molecular overlap between COPD and lung cancer. Airway and tumor patient cohorts were matched for age, gender, tumor stage, and smoking status. Result: We discovered 10 distinct small-airway gene expression modules, two of which were significantly negatively correlated (p < 0.05) with patient FEV-1. One of these FEV-1 modules was the top overall module preserved in both NSCLC subtypes. This lung cancer-FEV-1 module contained 31 genes solely enriched for two related mitotic functions—G2/M phase transition (BH-p = 0.02) and mitotic roles of polo-like kinase (BH-p = 0.001, n=31). Of these, 28 genes were significantly overexpressed in both LUAD and LUSC, and mapped to a highly clustered sub-network of 23 proteins with 465 known and in silico-predicted protein-protein interactions. When tumors enriched for this lung cancer-FEV-1 gene signature were further examined, we observed a significant co-occurrence of DNA-level alterations in DNA damage-associated checkpoints, specifically mutated TP53. Conclusion: Coordinated gene expression changes associated with COPD severity measures in small airways and preserved in NSCLC tumors are enriched for G2/M phase transition genes. These genes are further disrupted in tumors, where co-occurring mutations to gatekeeper genes are present. Progression of mitosis during abnormal aneuploidy in lung tissues of COPD patients may confer increased risk of oncogenic transformation in this population, and may underlie the molecular progression from COPD to lung cancer. Citation Format: Erin A. Marshall, Emily A. Vucic, Victor D. Martinez, Raymond T. Ng, Wan L. Lam. Alterations in G2/M phase associated transcriptional networks highlight lung cancer predisposition in COPD patients [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A07.

Periodic and coordinated gene expression between a diazotroph and its diatom host.

In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom-diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day-night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont-host physiological ecology is strongly interconnected in the NPSG.

Multiple Posttranscriptional Strategies To Regulate the Herpes Simplex Virus 1 vhs Endoribonuclease.

The herpes simplex virus 1 (HSV-1) virion host shutoff (vhs) protein is an endoribonuclease that binds to the cellular translation initiation machinery and degrades associated mRNAs, resulting in the shutoff of host protein synthesis. Hence, its unrestrained activity is considered lethal, and it has been proposed that vhs is regulated by two other virus proteins, VP22 and VP16. We have found that during infection, translation of vhs requires VP22 but not the VP22-VP16 complex. Moreover, in the absence of VP22, vhs is not overactive against cellular or viral transcripts. In transfected cells, vhs was also poorly translated, correlating with the aberrant localization of its mRNA. Counterintuitively, vhs mRNA was predominantly nuclear in cells where vhs protein was detected. Likewise, transcripts from cotransfected plasmids were also retained in the same nuclei where vhs mRNA was located, while poly(A) binding protein (PABP) was relocalized to the nucleus in a vhs-dependent manner, implying a general block to mRNA export. Coexpression of VP16 and VP22 rescued the cytoplasmic localization of vhs mRNA but failed to rescue vhs translation. We identified a 230-nucleotide sequence in the 5' region of vhs that blocked its translation and, when transferred to a heterologous green fluorescent protein transcript, reduced translation without altering mRNA levels or localization. We propose that expression of vhs is tightly regulated by a combination of inherent untranslatability and autoinduced nuclear retention of its mRNA that results in a negative feedback loop, with nuclear retention but not translation of vhs mRNA being the target of rescue by the vhs-VP16-VP22 complex.IMPORTANCE A myriad of gene expression strategies has been discovered through studies carried out on viruses. This report concerns the regulation of the HSV-1 vhs endoribonuclease, a virus factor that is important for counteracting host antiviral responses by degrading their mRNAs but that must be regulated during infection to ensure that it does not act against and inhibit the virus itself. We show that regulation of vhs involves multifaceted posttranscriptional cellular and viral processes, including aberrant mRNA localization and a novel, autoregulated negative feedback loop to target its own and coexpressed mRNAs for nuclear retention, an activity that is relieved by coexpression of two other virus proteins, VP22 and VP16. These studies reveal the interplay of strategies by which multiple virus-encoded factors coordinate gene expression at the time that they are needed. These findings are broadly relevant to both virus and cellular gene expression.

Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process

Genes are transcribed in irregular pulses of activity termed transcriptional bursts. Cellular differentiation requires coordinated gene expression; however, it is unknown whether the burst fraction (i.e. the number of active phases of transcription) or size/intensity (the number of RNA molecules produced within a burst) changes during cell differentiation. In the ocular lens, the positions of lens fiber cells correlate precisely with their differentiation status, and the most advanced cells degrade their nuclei. Here, we examined the transcriptional parameters of the β-actin and lens differentiation-specific α-, β-, and γ-crystallin genes by RNA fluorescent in situ hybridization (FISH) in the lenses of embryonic day (E) E12.5, E14.5, and E16.5 mouse embryos and newborns. We found that cellular differentiation dramatically alters the burst fraction in synchronized waves across the lens fiber cell compartment with less dramatic changes in burst intensity. Surprisingly, we observed nascent transcription of multiple genes in nuclei just before nuclear destruction. Nuclear condensation was accompanied by transfer of nuclear proteins, including histone and nonhistone proteins, to the cytoplasm. Although lens-specific deletion of the chromatin remodeler SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (Smarca5/Snf2h) interfered with denucleation, persisting nuclei remained transcriptionally competent and exhibited changes in both burst intensity and fraction depending on the gene examined. Our results uncover the mechanisms of nascent transcriptional control during differentiation and chromatin remodeling, confirm the burst fraction as the major factor adjusting gene expression levels, and reveal transcriptional competence of fiber cell nuclei even as they approach disintegration.

Discovery of a Nitric Oxide Responsive Quorum Sensing Circuit in Vibrio cholerae.

Group behavior of the human pathogen Vibrio cholerae, including biofilm formation and virulence factor secretion, is mediated by a process known as quorum sensing. Quorum sensing is a way by which bacteria coordinate gene expression in response to population density through the production, secretion, and detection of small molecules called autoinducers. Four autoinducer-mediated receptor histidine kinases have been implicated in quorum sensing through the phosphotransfer protein LuxU: CqsS, LuxP/Q, CqsR, and VpsS (Vc1445). Of these receptor kinases, VpsS is predicted to be cytosolic, and its cognate autoinducer is currently unknown. In this study, we demonstrate that the nitric oxide-bound complex of a member of the recently discovered family of nitric oxide-responsive hemoproteins called NosP (VcNosP is encoded by Vc1444; this gene product is also known as VpsV) inhibits the autophosphorylation activity of VpsS and thus phosphate flow to LuxU. Therefore, we propose that VpsS contributes to the regulation of quorum sensing in a nitric-oxide-dependent manner through its interaction with NosP.

The plastid genome as a chassis for synthetic biology-enabled metabolic engineering: players in gene expression.

Owing to its small size, prokaryotic-like molecular genetics, and potential for very high transgene expression, the plastid genome (plastome) is an attractive plant synthetic biology chassis for metabolic engineering. The plastome exists as a homogenous, compact, multicopy genome within multiple-specialized differentiated plastid compartments. Because of this multiplicity, transgenes can be highly expressed. For coordinated gene expression, it is the prokaryotic molecular genetics that is an especially attractive feature. Multiple genes in a metabolic pathway can be expressed in a series of operons, which are regulated at the transcriptional and translational levels with cross talk from the plant's nuclear genome. Key features of each regulatory level are reviewed, as well as some examples of plastome-enabled metabolic engineering. We also speculate about the transformative future of plastid-based synthetic biology to enable metabolic engineering in plants as well as the problems that must be solved before routine plastome-enabled synthetic circuits can be installed.

Abstract SY43-01: Coordinated gene expression mediated by RNA modifications

Abstract Gene transcription and mRNA translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. We identified that the rate of transcription regulates the efficacy of translation. We show that RNA modification, in the form of N6-adenosine methylation (m6A), is co-transcriptional and depends on the dynamics of RNA transcription. Altogether, our study uncovered a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs. We postulate that this mechanism will play a role in cancer-related processes. Citation Format: Reuven Agami. Coordinated gene expression mediated by RNA modifications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr SY43-01.

Covariate-dependent negative binomial factor analysis of RNA sequencing data.

MotivationHigh-throughput sequencing technologies, in particular RNA sequencing (RNA-seq), have become the basic practice for genomic studies in biomedical research. In addition to studying genes individually, for example, through differential expression analysis, investigating co-ordinated expression variations of genes may help reveal the underlying cellular mechanisms to derive better understanding and more effective prognosis and intervention strategies. Although there exists a variety of co-expression network based methods to analyze microarray data for this purpose, instead of blindly extending these methods for microarray data that may introduce unnecessary bias, it is crucial to develop methods well adapted to RNA-seq data to identify the functional modules of genes with similar expression patterns.ResultsWe have developed a fully Bayesian covariate-dependent negative binomial factor analysis (dNBFA) method—dNBFA—for RNA-seq count data, to capture coordinated gene expression changes, while considering effects from covariates reflecting different influencing factors. Unlike existing co-expression network based methods, our proposed model does not require multiple ad-hoc choices on data processing, transformation, as well as co-expression measures and can be directly applied to RNA-seq data. Furthermore, being capable of incorporating covariate information, the proposed method can tackle setups with complex confounding factors in different experiment designs. Finally, the natural model parameterization removes the need for a normalization preprocessing step, as commonly adopted to compensate for the effect of sequencing-depth variations. Efficient Bayesian inference of model parameters is derived by exploiting conditional conjugacy via novel data augmentation techniques. Experimental results on several real-world RNA-seq datasets on complex diseases suggest dNBFA as a powerful tool for discovering the gene modules with significant differential expression and meaningful biological insight.Availability and implementationdNBFA is implemented in R language and is available at https://github.com/siamakz/dNBFA.

Blimp-1 Mediates Tracheal Lumen Maturation in Drosophila melanogaster.

The specification of tissue identity during embryonic development requires precise spatio-temporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here, we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extracellular matrix organization.

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

Splicing efficiency varies among transcripts, and tight control of splicing kinetics is crucial for coordinated gene expression. N-6-methyladenosine (m6A) is the most abundant RNA modification and is involved in regulation of RNA biogenesis and function. The impact of m6A on regulation of RNA splicing kinetics is unknown. Here, we provide a time-resolved high-resolution assessment of m6A on nascent RNA transcripts and unveil its importance for the control of RNA splicing kinetics. We find that early co-transcriptional m6A deposition near splice junctions promotes fast splicing, while m6A modifications in introns are associated with long, slowly processed introns and alternative splicing events. In conclusion, we show that early m6A deposition specifies the fate of transcripts regarding splicing kinetics and alternative splicing.

Quorum sensing signals and related virulence inhibition of Pseudomonas aeruginosa by a potential probiotic strain's organic acid

Studies conducted in recent years show that pathogen bacteria are not asocial assets and they use the cell to cell communication mechanism called quorum sensing that depends on population density to adapt changing environmental conditions. This mechanism is coordinate gene expression of various bacterial factors like bioluminescence, antibiotic biosynthesis, plasmid conjugation and virulence. Bacteria communicate with each other by producing signal molecules and regulate the production of virulence factors that have importance in the pathogenity formation. Virulence mechanisms of Pseudomonas aeruginosa, which causes various types of infections in humans, are also regulated by quorum sensing. Nowadays, biotechnological researches are focused on the development of homoserine lactone antagonists. The use of these type of molecules are considered to be a new treatment approach for blocking communication between bacteria and reducing virulence, therefore improving infection control. In this study, lactic acid of a potential probiotic Pediococcus acidilactici M7 strain isolated from newborn faeces was used to evaluate the inhibitory effect on quorum sensing signal molecules and some virulence factors of clinical Pseudomonas aeruginosa isolates. Results showed that lactic acid has an inhibitory effect on short-chain HSL production and swarming-swimming-twitching motility, elastase, protease, pyocyanin, and biofilm production of Pseudomonas aeruginosa isolates in certain quantities that are regulated by the quorum sensing system.

Enhancer Logic and Mechanics in Development and Disease.

Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health. Advances in DNA sequencing and genome-editing technologies have dramatically expanded our ability to identify enhancers and investigate their properties in vivo, revealing an extraordinary level of interconnectivity underlying cis-regulatory networks. We discuss here these recently developed methodologies, as well as emerging trends and remaining questions in the field of enhancer biology, and how perturbation of enhancer activities/functions results in enhanceropathies.