scholarly journals Transcription bursting and epigenetic plasticity: an updated view

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
William F. Beckman ◽  
Miguel Ángel Lermo Jiménez ◽  
Pernette J. Verschure
Keyword(s):  
Molecular Mechanisms ◽  
Regulation Of Transcription ◽  
Epigenetic Factors ◽  
Dynamic Interactions ◽  
Eukaryotic Transcription ◽  
State Process ◽  
Genome Wide ◽  
Transcriptional Bursting ◽  
The Impact ◽  
Epigenetic Plasticity

AbstractThe vast majority of eukaryotic transcription occurs in bursts during discrete periods of promoter activity, separated by periods of deep repression and inactivity. Elucidating the factors responsible for triggering transitions between these two states has been extremely challenging, partly due to the difficulties in measuring transcriptional bursting genome-wide, but also due to the vast array of candidate transcriptional and epigenetic factors and their complex and dynamic interactions. Additionally, this long-held view of transcriptional bursting as a two-state process has become increasingly challenged, and a resulting lack in consensus on terminology of the involved events has further complicated our understanding of the molecular mechanisms involved. Here, we review the impact of epigenetics on dynamic gene expression, with a focus on transcription bursting. We summarise current understanding of the epigenetic regulation of transcription bursting and propose new terminology for the interpretation of future results measuring transcription dynamics.

scholarly journals Developmental cannabidiol exposure increases anxiety and modifies genome-wide brain DNA methylation in adult female mice

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Nicole M. Wanner ◽  
Mathia Colwell ◽  
Chelsea Drown ◽  
Christopher Faulk
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Coat Color ◽  
Brain Regions ◽  
Functional Enrichment ◽  
Positive Effects ◽  
Genome Wide ◽  
Nulliparous Female ◽  
The Impact ◽  
The Brain

Abstract Background Use of cannabidiol (CBD), the primary non-psychoactive compound found in cannabis, has recently risen dramatically, while relatively little is known about the underlying molecular mechanisms of its effects. Previous work indicates that direct CBD exposure strongly impacts the brain, with anxiolytic, antidepressant, antipsychotic, and other effects being observed in animal and human studies. The epigenome, particularly DNA methylation, is responsive to environmental input and can direct persistent patterns of gene regulation impacting phenotype. Epigenetic perturbation is particularly impactful during embryogenesis, when exogenous exposures can disrupt critical resetting of epigenetic marks and impart phenotypic effects lasting into adulthood. The impact of prenatal CBD exposure has not been evaluated; however, studies using the psychomimetic cannabinoid Δ9-tetrahydrocannabinol (THC) have identified detrimental effects on psychological outcomes in developmentally exposed adult offspring. We hypothesized that developmental CBD exposure would have similar negative effects on behavior mediated in part by the epigenome. Nulliparous female wild-type Agouti viable yellow (Avy) mice were exposed to 20 mg/kg CBD or vehicle daily from two weeks prior to mating through gestation and lactation. Coat color shifts, a readout of DNA methylation at the Agouti locus in this strain, were measured in F1 Avy/a offspring. Young adult F1 a/a offspring were then subjected to tests of working spatial memory and anxiety/compulsive behavior. Reduced-representation bisulfite sequencing was performed on both F0 and F1 cerebral cortex and F1 hippocampus to identify genome-wide changes in DNA methylation for direct and developmental exposure, respectively. Results F1 offspring exposed to CBD during development exhibited increased anxiety and improved memory behavior in a sex-specific manner. Further, while no significant coat color shift was observed in Avy/a offspring, thousands of differentially methylated loci (DMLs) were identified in both brain regions with functional enrichment for neurogenesis, substance use phenotypes, and other psychologically relevant terms. Conclusions These findings demonstrate for the first time that despite positive effects of direct exposure, developmental CBD is associated with mixed behavioral outcomes and perturbation of the brain epigenome.

scholarly journals Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Abinaya Manivannan ◽  
Jin-Hee Kim ◽  
Eun-Young Yang ◽  
Yul-Kyun Ahn ◽  
Eun-Su Lee ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Disease Resistance ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
The Impact ◽  
Generation Sequencing

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

scholarly journals Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

2019 ◽  
Author(s):  
Hiroshi Ochiai ◽  
Tetsutaro Hayashi ◽  
Mana Umeda ◽  
Mika Yoshimura ◽  
Akihito Harada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Transcription Elongation ◽  
Mapk Signaling ◽  
Kinetic Properties ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Transcriptional Bursting

AbstractTranscriptional bursting is stochastic activation and inactivation of promoters, leading to discontinuous production of mRNA, and is considered to be a contributing factor to cell-to-cell heterogeneity in gene expression. However, it remains elusive how the kinetic properties of transcriptional bursting (e.g., burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing. We found that the kinetics of transcriptional bursting was determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. Furthermore, large-scale CRISPR-Cas9-based screening and functional analysis revealed that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncover key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

scholarly journals Mechanochemical Model of Transcriptional Bursting

2019 ◽  
Author(s):  
A. Klindziuk ◽  
B. Meadowcroft ◽  
A. B. Kolomeisky
Keyword(s):  
Rna Synthesis ◽  
Molecular Mechanisms ◽  
Dynamic Properties ◽  
Dna Supercoiling ◽  
Chemical Processes ◽  
Energetic Cost ◽  
Regulation Of Transcription ◽  
Large Variability ◽  
Rna Molecules ◽  
Transcriptional Bursting

ABSTRACTPopulations of genetically identical cells generally show a large variability in cell phenotypes, which is typically associated with the stochastic nature of gene expression processes. It is widely believed that a significant source of such randomness is the transcriptional bursting, which is when periods of active production of RNA molecules alternate with periods of RNA degradation. However, the molecular mechanisms of such strong fluctuations remain unclear. Recent studies suggest that DNA supercoiling, which happens during transcription, might be directly related to the bursting behavior. Stimulated by these observations, we developed a stochastic mechano-chemical model of supercoiling-induced transcriptional bursting where the RNA synthesis leads to the buildup of torsion in DNA. This slows down the RNA production until binding of an enzyme gyrase to DNA, which releases the stress and allows for the RNA synthesis to restart with the original rate. Using a thermodynamically consistent coupling between mechanical and chemical processes, dynamic properties of transcription are explicitly evaluated. In addition, a first-passage method to evaluate the dynamics of transcription is developed. Theoretical analysis shows that the transcriptional bursting is observed when both the supercoiling and the mechanical stress-release due to gyrase are present in the system. It is also found that the overall RNA production rate is not constant and depends on the number of previously synthesized RNA molecules. A comparison with experimental data on bacteria allows us to evaluate the energetic cost of supercoiling during transcription. It is argued that the relatively weak mechanochemical coupling allows transcription to be regulated most effectively.SIGNIFICANCETranscriptional bursting has been cited as one of the probable causes of phenotypic differences in cells with identical genomes. However, the microscopic origin of noisy dynamics in RNA production remains unclear. We developed a thermodynamically-consistent mechano-chemical stochastic model, which, via explicit calculations of dynamic properties, provides a consistent physical-chemical description of how the supercoiling of DNA together with enzymatic activity of gyrases produce transcriptional bursting. It also allows us to explain that the coupling between mechanical and chemical processes might be the reason for efficient regulation of transcription.

scholarly journals A cross-disorder dosage sensitivity map of the human genome

2021 ◽  
Author(s):  
Ryan L. Collins ◽  
Joseph T. Glessner ◽  
Eleonora Porcu ◽  
Lisa-Marie Niestroj ◽  
Jacob Ulirsch ◽  
...  
Keyword(s):  
Human Genome ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Association Studies ◽  
Disease Genes ◽  
Driver Genes ◽  
Genome Wide ◽  
A Genome ◽  
The Impact ◽  
Dosage Sensitivity

SUMMARYRare deletions and duplications of genomic segments, collectively known as rare copy number variants (rCNVs), contribute to a broad spectrum of human diseases. To date, most disease-association studies of rCNVs have focused on recognized genomic disorders or on the impact of haploinsufficiency caused by deletions. By comparison, our understanding of duplications in disease remains rudimentary as very few individual genes are known to be triplosensitive (i.e., duplication intolerant). In this study, we meta-analyzed rCNVs from 753,994 individuals across 30 primarily neurological disease phenotypes to create a genome-wide catalog of rCNV association statistics across disorders. We discovered 114 rCNV-disease associations at 52 distinct loci surpassing genome-wide significance (P=3.72×10−6), 42% of which involve duplications. Using Bayesian fine-mapping methods, we further prioritized 38 novel triplosensitive disease genes (e.g., GMEB2 in brain abnormalities), including three known haploinsufficient genes that we now reveal as bidirectionally dosage sensitive (e.g., ANKRD11 in growth abnormalities). By integrating our results with prior literature, we found that disease-associated rCNV segments were enriched for genes constrained against damaging coding variation and identified likely dominant driver genes for about one-third (32%) of rCNV segments based on de novo mutations from exome sequencing studies of developmental disorders. However, while the presence of constrained driver genes was a common feature of many pathogenic large rCNVs across disorders, most of the rCNVs showing genome-wide significant association were incompletely penetrant (mean odds ratio=11.6) and we also identified two examples of noncoding disease-associated rCNVs (e.g., intronic CADM2 deletions in behavioral disorders). Finally, we developed a statistical model to predict dosage sensitivity for all genes, which defined 3,006 haploinsufficient and 295 triplosensitive genes where the effect sizes of rCNVs were comparable to deletions of genes constrained against truncating mutations. These dosage sensitivity scores classified disease genes across molecular mechanisms, prioritized pathogenic de novo rCNVs in children with autism, and revealed features that distinguished haploinsufficient and triplosensitive genes, such as insulation from other genes and local cis-regulatory complexity. Collectively, the cross-disorder rCNV maps and metrics derived in this study provide the most comprehensive assessment of dosage sensitive genomic segments and genes in disease to date and set the foundation for future studies of dosage sensitivity throughout the human genome.

scholarly journals Impact of the X chromosome and sex on regulatory variation

2015 ◽  
Author(s):  
Kimberly R Kukurba ◽  
Princy Parsana ◽  
Kevin S Smith ◽  
Zachary Zappala ◽  
David A Knowles ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Specific Gene ◽  
Specific Expression ◽  
Regulatory Variation ◽  
Regulatory Variants ◽  
Genome Wide ◽  
The Impact

The X chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. We have conducted an analysis of the impact of both sex and the X chromosome on patterns of gene expression identified through transcriptome sequencing of whole blood from 922 individuals. We identified that genes on the X chromosome are more likely to have sex-specific expression compared to the autosomal genes. Furthermore, we identified a depletion of regulatory variants on the X chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X chromosome. To resolve the molecular mechanisms underlying such effects, we generated and connected sex-specific chromatin accessibility to sex-specific expression and regulatory variation. As sex-specific regulatory variants can inform sex differences in genetic disease prevalence, we have integrated our data with genome-wide association study data for multiple immune traits and to identify traits with significant sex biases. Together, our study provides genome-wide insight into how the X chromosome and sex shape human gene regulation and disease.

Long-Lasting Dysregulation of the Hematopoietic Stem Cell Compartment in Obesity

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 245-245
Author(s):  
Jung-Mi Lee ◽  
Bryan Goddard ◽  
Ashwini S. Hinge ◽  
Bruce J. Aronow ◽  
Nathan Salomonis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
Molecular Mechanisms ◽  
Interferon Response ◽  
Compensatory Mechanisms ◽  
Hematopoietic Stem ◽  
Genome Wide ◽  
A Genome ◽  
The Impact

Abstract Obesity is a complex pathological state defined by the excessive accumulation of adipose tissue and an array of hormonal, immunological and metabolic dysregulations. As such, obesity is a systemic stress that directly affects numerous organs and tissues. Notably, obesity and its sequelae modulate the immune system and the hematopoietic activity in the bone marrow (BM). Not surprisingly, obesity is also a well-established risk factor for leukemia associated with increased incidence and poor prognosis. However, despite their clinical relevance, mechanisms by which obesity affects the hematopoietic system remain elusive. Particularly, the impact of obesity on the hematopoietic stem cell (HSC) compartment has not been described. Using genetic and dietary mouse models of obesity, we conducted a "HSC-centered study" to determine how obesity affects HSCs and how these cells develop specific compensatory mechanisms to respond to this environment. Although HSCs in an obese environment displayed limited phenotypic and functional perturbations at steady state, they showed an aberrant response to hematopoietic stresses. In serial competitive transplantation assays, obesity-primed HSCs (defined as Lin- Sca-1+ c-Kit+ CD48- CD150+) showed a higher level of engraftment than controls in primary recipient mice (control, 20.8% +/-6.2 vs obese, 45.5% +/-14.6, p=0.022) but a dramatically reduced level of engraftment in secondary recipient mice (control: 25.8% +/-14.0 vs obese: 5.4% +/-3.9, p=0.033). Interestingly, BM analysis of secondary recipients showed reduced chimerism in all hematopoietic compartments but not in the HSC compartment. Altogether these results uncovered a biphasic behavior of the obesity-primed HSCs, characterized by an excessive differentiation response followed by a functional decline in which HSCs self-renew but fail to produce downstream progenitors. To unveil the molecular mechanisms involved in this aberrant activity, we performed a genome-wide gene expression analysis on HSCs isolated from normal and obese mice. Although the phenotype observed upon serial transplantation partially mimics HSC aging, obesity-primed HSCs did not share the molecular signature of old HSCs. Furthermore, down-regulation of interferon response-related genes (e.g Irak4, Irf7, Ifi27) and stress response-related genes (e.g. Stip1, Cgrrf1) showed that, unlike what has been described for committed progenitors, HSCs do not elicit a dramatic response to the inflammatory environment associated with obesity. In contrast obesity leads to the activation of specific molecular programs in HSCs. Firstly, obesity-primed HSCs showed up-regulation of multiples genes involved in the phosphatidylinositol signaling pathway (e.g. Pi4ka, Pi4k2b, Pi3kap1, Pi3kip1). Phosphoflow cytometry analysis indicated that this gene expression pattern was associated with the constitutive activation of the protein kinase AKT. While AKT activation is linked to functional HSC exhaustion, obesity-primed HSCs appeared refractory to this signal, suggesting the existence of compensatory mechanisms that protect the integrity of the HSCs in an obese environment. In parallel, we found that the aberrant activity of the obesity-primed HSCs was correlated with an elevated expression of Gfi1, a transcription factor critical for HSC quiescence and differentiation. Interestingly, the 2-fold increase in Gfi1 expression (p<10-5) observed in obesity-primed HSCs was maintained after serial transplantations in normal recipient mice indicating that the obese environment was able to promote the selection of a stable molecular program in the HSC compartment. Consistent with this idea, single-cell genome-wide analyses suggested a significant clonal shift within the obesity-primed HSC compartment. Finally, consistent with epidemiological data, we found that disruption of HSC homeostasis by obesity promotes the development of spontaneous hematopoietic pathologies resembling to myeloproliferative diseases. Altogether, our results establish the long lasting impact of obesity on the HSC compartment and uncover potential molecular mechanisms linking obesity to hematological diseases. Notably our results support the intriguing possibility that obesity, by directly acting on the HSC compartment, contributes to the development of a clonal hematopoiesis and favors the emergence of aberrant HSC clones. Disclosures No relevant conflicts of interest to declare.

High resolution mapping of nucleic acid containing complexes in vitro and in situ

1996 ◽  
Vol 54 ◽  
pp. 48-49
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Regulation Of Transcription ◽  
High Exposure ◽  
Resolution Mapping ◽  
Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

The Impact of Ultraviolet Radiation on Barrier Function in Human Skin: Molecular Mechanisms and Topical Therapeutics

2019 ◽  
Vol 25 (40) ◽  
pp. 5503-5511 ◽  
Author(s):  
Abdulaziz Alhasaniah ◽  
Michael J. Sherratt ◽  
Catherine A. O'Neill
Keyword(s):  
Ultraviolet Radiation ◽  
Barrier Function ◽  
Molecular Mechanisms ◽  
Transepidermal Water Loss ◽  
Protective Effects ◽  
Barrier Dysfunction ◽  
Epidermal Barrier ◽  
Positive Effects ◽  
Terrestrial Mammals ◽  
The Impact

A competent epidermal barrier is crucial for terrestrial mammals. This barrier must keep in water and prevent entry of noxious stimuli. Most importantly, the epidermis must also be a barrier to ultraviolet radiation (UVR) from the sunlight. Currently, the effects of ultraviolet radiation on epidermal barrier function are poorly understood. However, studies in mice and more limited work in humans suggest that the epidermal barrier becomes more permeable, as measured by increased transepidermal water loss, in response UVR, at doses sufficiently high to induce erythema. The mechanisms may include disturbance in the organisation of lipids in the stratum corneum (the outermost layer of the epidermis) and reduction in tight junction function in the granular layer (the first living layer of the skin). By contrast, suberythemal doses of UVR appear to have positive effects on epidermal barrier function. Topical sunscreens have direct and indirect protective effects on the barrier through their ability to block UV and also due to their moisturising or occlusive effects, which trap water in the skin, respectively. Some topical agents such as specific botanical extracts have been shown to prevent the loss of water associated with high doses of UVR. In this review, we discuss the current literature and suggest that the biology of UVR-induced barrier dysfunction, and the use of topical products to protect the barrier, are areas worthy of further investigation.

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