Thanks to their expertise in single-molecule imaging of RNAs, researchers from the group of Jeff Chao at the FMI helped to reveal the biological mechanism of a small molecule that restricts Ewings sarcoma cell growth. The study - published in Nature Chemical Biology - is further evidence that each step of the gene expression pathway may be druggable, and a great example of a Novartis-FMI collaboration.
The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers.
Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We propose that such splice sites represent a ...
We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G0), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G0 TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G0-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
Introduction: Lung cancer is the number one cancer killer in the United States accounting for nearly 30% of all cancer deaths. Survival rates continue to be abysmal with 5-year survival only 15% despite contemporary therapies, making it clear that novel therapeutic agents need to be discovered. The translation of mRNA into protein, a central control point in the gene expression pathway, has been increasingly implicated as a critical checkpoint in tumor genesis and progression. This checkpoint serves as a traffic signal at the intersection of cell pathways controlling cell division and survival. The cell machinery controlling the first step in protein synthesis, a hetero-trimer designated eIF4F, is stuck in the "on" position in many human cancers. When this happens cells evade restraints on proliferation and survival. The activation state of eIF4F is controlled at multiple levels with the primary mechanism being negative regulation by the 4E binding proteins (4E-BPs). 4E-BPs are inactivated when ...
... :Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA p
Translational contributions to tissue specificity in rhythmic and constitutive gene expression. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases provides an extremely dynamic environment for research into the aging process and its diseases.
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isnt always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. Thats how identical cells can have different levels of gene expression, and how people and horses and dogs with identical ...
You need to be familiar with all of the different ways and levels at which cells can control gene expression, including gene expression, Chromatin packing, DNA methylation, Histone acetylation, control elements and transcription factors, alternative RNA splicing, mRNA degredation, translational control by regulatory proteins, proteasomic protein degradation, etc. (Damn, that s a lot of control ...
Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were
RBF1 and E2F2 are components of the Drosophila, Rb, E2F, and Myb‐associated protein (dREAM) complex, a transcriptional silencing complex that represses many E2F target genes (Korenjak et al, 2004). To determine whether components of the Pum complex are targets for dREAM‐mediated repression, we analyzed datasets of published genome‐wide dREAM ChIP experiments from Drosophila Kc cells (Georlette et al, 2007) and found a strong ChIP enrichment for all of the dREAM components (E2F2, Myb, Mip120, Mip130, and Lin‐52) on the pumilio, nanos, and brat genes (Supplementary Fig S1B). To establish the functional significance of E2F2/RBF1 binding to these promoters, we assayed gene expression levels from Drosophila S2 cells and flies containing dsRNA or RNAi sequences targeting E2F/RBF family members. Depletion of RBF1 or E2F2 (but not E2F1) strongly induced the expression of nanos and modestly elevated the levels of pum and brat (Fig 1C, Supplementary Figs S1C and S2A and B). To further assess the ...
Systems biology aims to understand the behavior of and interaction between various components of the living cell, such as genes, proteins, and metabolites. A large number of components are involved in these complex systems and the diversity of relationships between the components can be overwhelming, and there is therefore a need for analysis methods incorporating data integration. We here present a method for exploring gene regulatory mechanisms which integrates various types of data to assist the identification of important components in gene regulation mechanisms. By first analyzing gene expression data, a set of differentially expressed genes is selected. These genes are then further investigated by combining various types of biological information, such as clustering results, promoter sequences, binding sites, transcription factors and other previously published information regarding the selected genes. Inspired by Information Fusion research, we also mapped functions of the proposed method ...
Nashun B, Hill PW, Hajkova P, 2015, Reprogramming of cell fate: epigenetic memory and the erasure of memories past., EMBO Journal, Vol: 34, Pages: 1296-1308, ISSN: 0261-4189 Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and ...
Mammalian genomic imprinting is an epigenetic gene regulatory mechanism that results in parental‐specific gene expression of a small number of genes in diploid somatic cells (Beechey et al., 2001; Reik and Walter, 2001; Li, 2002; Sleutels and Barlow, 2002). Several features of the imprinting mechanism have been identified; however, it is not yet clear whether imprinting is regulated by a unique process or whether it is part of the general epigenetic apparatus used to regulate mammalian gene expression. Clustering and coordinate regulation is one feature imprinted genes share with non‐imprinted genes (Engemann et al., 2000; Onyango et al., 2000), and it is now clear that many imprinted genes are functionally grouped such that imprinted expression of several genes is regulated by one long‐range imprint control element (Thorvaldsen et al., 1998; Horike et al., 2000; Zwart et al., 2001; Fitzpatrick et al., 2002). The frequent occurrence of an imprinted non‐coding RNA within an imprinted gene ...
Over several decades, the therapeutic use of glucocorticoids have established these molecules as potent inflammation suppressors. The description of transcriptional repression of pro-inflammatory genes as a nuclear receptor mediated mechanism represents a more recent topic of glucocorticoid signaling. However, new evidences suggest that steroidal regulation of inflammation is more complex, including epigenetic and receptor-independent pathways. It is also likely that sets of genes behaves in contradictory ways, making gene repression not a rule, but rather one of the possible modulatory modes. A similar level of complexity might apply to other steroidal hormones, such as those involved in sexually dimorphic immune responses. In fact, some autoimmune diseases are much more prevalent in one gender compared to the other. In addition to well-known steroid hormones, including aldosterone and vitamin D, this review topic intends to cover also non-canonical steroid signaling, including oxysteroids and
99 Tumorigenesis is often attributed to aberrant gene expression control leading to altered cell cycle control, resistance to apoptosis, abnormal differentiation, decreased genomic stability and inefficient DNA repair. The activity of chromatin remodeling complexes is vital to maintaining proper control of gene expression. The SWI/SNF complex is conserved from yeast to man and is responsible for remodeling up to 6% of the human genome, with many of those genes known to be associated with cell cycle control. Therefore, impaired or defective activity of SWI/SNF chromatin remodeling complex, involved in regulation of gene transcription, could encourage tumor development. The complex is composed of 10 or more members but requires only three core members to do the basic task of remodeling nucleosomes: BRG1/BRM, SNF5, and BAF155. BRG1 and SNF5 both lead to tumor development in haploinsufficient mice and embryonic lethality in null mice, and are mutated or inactivated in human tumors. The third and ...
Cancer can be understood as a disease of dysfunctional gene expression control. Research in Chris Vakocs lab investigates how transcription factors and chromatin regulators cooperate to control gene expression and maintain the cancer cell state. This work makes extensive use of genetic screens to reveal cancer-specific functions for transcriptional regulators, as well as genomic and biochemical approaches to identify molecular mechanisms. One theme that has emerged from their efforts is that blood cancers are often vulnerable to targeting transcriptional coactivators, such as BRD4 and the SWI/SNF chromatin remodeling complex. Vakocs team demonstrated that chemical inhibition of BRD4 exhibits therapeutic effects in mouse models of leukemia, a finding that has motivated ongoing clinical trials in human leukemia patients. The Vakoc lab has also developed a CRISPR-Cas9 screening approach that can reveal individual protein domains that sustain cancer cells. Their lab is now deploying this ...
The present study describes a novel cell type-specific mechanism of transcriptional regulation of TSP-1 in vascular cells in response to glucose. We report here that unlike our recently identified short promoter region (−280/+66) responsible for the increased THBS1 transcription in ECs, a longer promoter fragment (−1270/+66) is required for THBS1 regulation in HASMCs, as was described for specialized pericytes and mesangial cells.27 Interestingly, glucose responsiveness in ECs was in fact inhibited by the distal fragment of the promoter,10 suggesting the presence of an inhibitory element in this region, which is not active in either VSMCs or mesangial cells.27 The longer promoter region, −1270/+66, responsible for the increased THBS1 transcription in HASMCs contained distinctly different binding elements, as identified by MatInspector, located in the distal end of the promoter. These binding elements had no similarity to those in the EC-specific THBS1 promoter fragment, −280/+66, ...
Abstract: Interleukin-2 (IL-2) gene regulation was investigated in primary cultures of highly purified human peripheral blood CD28+T cells. Two discrete mechanisms for induction of T-cell proliferation could be distinguished by examining cell cycle progression and the expression of the IL-2 gene. Stimulation of cells by CD3 MoAb induced only transiently expressed, small amounts of IL-2 mRNA that was completely suppressed by cyclosporine. Costimulation of T cells with CD3 MoAb and either CD28 MoAb or PMA, but not calcium ionophore, induced a 50-100-fold increased in IL-2 gene expression and secretion. High levels of IL-2 gene expression could also be achieved by stimulation with calcium ionophore and PMA or CD28 MoAb and PMA, but not by CD28 MoAb plus calcium ionophore. IL-2 gene expression and T-cell proliferation induced by CD3 MoAb plus PMA or calcium ionophore plus PMA were completely suppressible by cyclosporine. In contrast, IL-2 gene expression and T-cell proliferation induced by CD28 MoAb ...
Buffo, A., Carulli, D., Rossi, F. and Strata, P. (2003), Extrinsic regulation of injury/growth-related gene expression in the inferior olive of the adult rat. European Journal of Neuroscience, 18: 2146-2158. doi: 10.1046/j.1460-9568.2003.02940.x ...
Kusakabe T., Yoshida, R., Ikeda, Y., Tsuda, M. (2004). "Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona." Dev Biol 276:563-580. (PUBMED ...
Antibodies for proteins involved in negative regulation of gene expression pathways, according to their Panther/Gene Ontology Classification
Ca(2+)-dependent gene expression is critical for cell growth, proliferation, plasticity, and adaptation [1-3]. Because a common mechanism in vertebrates linking cytoplasmic Ca(2+) signals with activation of protein synthesis involves the nuclear factor of activated T cells (NFAT) family of transcription factors [4, 5], we have quantified protein expression in single cells following physiological Ca(2+) signals by using NFAT-driven expression of a genetically encoded fluorescent protein. We find that gene expression following CRAC channel activation is an all-or-nothing event over a range of stimulus intensities. Increasing agonist concentration recruits more cells but each responding cell does so in an essentially digital manner. Furthermore, Ca(2+)-dependent gene expression shows both short-term memory and strong synergy, where two pulses of agonist, which are ineffectual individually, robustly activate gene expression provided that the time interval between them is short. Such temporal filtering
Is there a gene or genes that are activated at age 1 that signal to the other genes to perform gene expression appropriate for a one year old? Futhermore, is there a gene or genes that are activated at age 20 that signal to the other genes to perform gene expression appropriate for a twenty year old? Lastly, if there were a gene or genes that signals for twenty year old gene expression regulation, then if that gene were activated in an 80 year old, would the body of the 80 year old begin to exhibit the physiology of a 20 year old, thus increasing lifespan and healthspan? DE. ...
The discovery of the obese gene in the mouse and its conserved homologue in humans has led to important discoveries in energy metabolism. One of the chief findings was the fact that the expression of the leptin gene was regulated and that it, in turn, could regulate metabolism and behavior. Much of the literature has focused on the physiological role of leptin in driving processes as diverse as reproduction, starvation defence, feeding behavior or body weight, all dependent on expression levels of the ob gene. Here, we will describe our work, in which we have begun to elucidate the regulatory processes controlling obese gene expression.. Keywords: Gene Expression Regulation ; Obesity. ...
Summary Basic biological processes require gene expression. Tightly regulated molecules known as transcription factors mediate the expression of genes in development and disease. Signal transduction pathways, which respond to environmental cues or stressors are major regulators of the transcription factors. Use of macromolecular synthesis inhibitors in models of normal neurodevelopment and neurodegenerative cell death has led to the discovery that gene expression is required for these processes to occur (Martin et. al.,(1988), J Cell Biol 106 p829). To date, however, the identities of very few of the genes required in these events have been revealed. Hence, the activation or requirement of specific signaling pathways leading to the expression of known apoptotic genes is not well established. Utilizing the neurothrophic factor deprivation and neurotoxin models of programmed cell death we address these gaps in our understanding of the molecular mechanism of apoptosis as it occurs in neuronal cell death.
Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems.
Sreenivas was awarded PhD in Biotechnology in 2009 by University of Pune, India for his research work on understanding the genetic determinants of human diseases, undertaken at CSIR-Institute of Genomics and Integrative Biology, India. Subsequently, he undertook postdoctoral studies investigating the role of gene expression regulation in human diseases at the University of Gothenburg, Sweden.. He came to Cambridge in November 2010 as Career Development Fellow to MRC Laboratory of Molecular Biology and has subsequently become an EMBO long-Term fellow. He currently investigates the role of genetic variation on the gene expression regulation and different observable traits in diverse organisms from yeast to humans. He aims to extend the general principles derived by such comprehensive studies to understand the molecular determinants of human diseases.. ...
This study provides a genome-wide screen of neuronal activity-driven gene expression in response to different chemical stimuli and downstream of four important PRTFs (CREB, SRF, EGR1, and FOS). The use of a common approach to manipulate the activity of different PRTFs, making their transactivation activity independent of the upstream signaling cascades that normally would regulate it, provides an alternative and innovative way to explore the neuronal gene programs downstream of these TFs under highly comparable conditions. Furthermore, the integration of PRTF- and stimulation-dependent patterns through meta-analysis has allowed us to gain novel insight into the transcriptional networks underlying neuronal activity-dependent gene expression, which is usually disregarded in single-molecule reductionist approaches.. Our screen identified hundreds of novel stimulus-specific activity-regulated transcripts, including novel stimulus-associated miRNAs and candidate genes that may be differentially ...
This study has confirmed the long-held view that integration of Ca2+ and kinase signaling is needed for efficient activation of inducible gene expression in T cells. We found that for many immune response genes, both signals are needed to open up the chromatin and activate transcription. However, the immune system encompasses other genes that are induced in a range of cell types, by a wide variety of other receptors linked to kinase but not Ca2+ signaling pathways. These include proinflammatory receptors, such as Toll family receptors, and receptors that respond to cytokines such as IL-1 and TNF, which also lead to induction of the TFs AP-1 and NF-κB. For these reasons it makes sense that we find a subset of genes that are induced by PMA via PKC-dependent pathways, in the absence of Ca2+ signaling. Significantly, we found that two-thirds of all of the genes induced 5-fold by TNF were also induced 5-fold by PMA (Table I). In contrast, there appear to be fewer gene-inducing signaling pathways ...
Background Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological...
Effect of the stem-loop element on gene expression in different gene contexts. (A) Cell lines were generated which expressed luciferase under the control of a
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins. [from MeSH] ...
Buy or Rent Interaction of Translational and Transcriptional controls in the regulation of gene Expression as an eTextbook and get instant access.
Transcription factor that is involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in…
IKKα-targeting miRNAs affects noncanonical and canonical NF-κ.B gene expression(a) Real time PCR analysis of ELC mRNA in monocytes and macrophages, normalized
J:99346 Lee CS, Friedman JR, Fulmer JT, Kaestner KH, The initiation of liver development is dependent on Foxa transcription factors. Nature. 2005 Jun 16;435(7044):944-7 ...
J:112202 Krizhanovsky V, Soreq L, Kliminski V, Ben-Arie N, Math1 target genes are enriched with evolutionarily conserved clustered E-box binding sites. J Mol Neurosci. 2006;28(2):211-29 ...
21:47, 20 November 2012 (diff , hist) . . (+4,409)‎ . . N Structural Biochemistry/Modulation of Translation ‎ (Created page with ==Introduction== An effective way gene expression can be controlled is by regulating the translation of RNA. By controlling RNA (primarily mRNA) certain genes can be expresse...) ...
Scientists have made a medical breakthrough which may help bring new insights on how genes are activated. Roughly 3 metres of DNA is tightly folded into the nucleus of every cell in our body. This folding allows some genes to be expressed, or activated, while excluding others.
Gene expression is controlled by transcription factors that regulate the rates at which genes are expressed either by recruiting or inhibiting protein complexes that bind to the promoters or enhancers of target genes. Molecules that can specifically modulate these protein-DNA interfaces show promise as tools for understanding gene regulation pathways and may have application in human medicine. Hairpin pyrrole-imidazole polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells, disrupt protein-DNA interactions, and downregulate endogenous gene expression. This thesis describes the use of polyamides to modulate gene expression in order to probe gene regulation mechanisms of several different biologically relevant systems. A polyamide is designed to target the glucocorticoid receptor transcription factor ...
A great many aspects of the anatomy and physiology of large animals are constrained by the need to match oxygen supply to cellular metabolism and appear likely to involve the regulation of gene expression by oxygen. Some insight into possible underlying mechanisms has been provided by studies of erythropoietin, a haemopoietic growth factor which stimulates red cell production in response to hypoxia. Studies of hypoxia-inducible cis-acting sequences from the erythropoietin gene have led to the recognition of a widespread transcriptional response to hypoxia based on the activation of a DNA-binding complex termed hypoxia-inducible factor-1 (HIF-1). Perturbation of the transcriptional response by particular transition metal ions, iron chelators and certain redox-active agents have suggested a specific oxygen sensing mechanism, perhaps involving a haem protein in a flavoprotein/cytochrome system. In addition to erythropoietin, HIF-1-responsive genes include examples with functions in cellular energy
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome. The term "intergenic" refers to the identification of these transcripts from regions of the genome that do not contain protein-encoding genes. These regions coincide with what was once labeled as the "junk DNA" portions of our genomes, which, upon careful examination by whole genome RNA sequencing experiments, clearly encode RNA transcripts. LincRNAs also contain promoter- or enhancer-associated RNAs that are gene proximal and ...
Our present study has provided, for the first time to our knowledge, a systematic analysis of the inflammation-relevant gene expression in ECs and SMCs in their coculture under static condition and in response to shear stress. We demonstrated that SMCs cause an upregulation of proinflammatory gene expression in ECs located in close proximity and that shear stress acts as a negative regulator for these proinflammatory gene expression in ECs cocultured with SMCs. Under static coculture condition, DNA microarray technology identified 23 inflammation-relevant genes that exhibit significant changes (18 increases and 5 decreases) in their expression in ECs cocultured with SMCs, as compared with the control monocultured ECs. All 18 genes upregulated in ECs by the coculture encode products that serve proinflammatory and thrombogenic functions. These functions include: (1) mediation of leukocyte-EC interaction and signal transduction (ICAM-1, VCAM-1, CD44, and NK-4); (2) promotion of chemotaxis and ...
Abstract: In this work, I focus on the development and testing of tools to explore differential gene expression as a molecular mechanism underlying the predisposition to complex disease. By definition, complex diseases (e.g. hypertension, diabetes, asthma) demonstrate both environmental and genetic factors in disease susceptibility, implicating genes that show both environmental response and genetic variability in predisposing disease. Differential gene expression is one important cellular response that reflects both of these factors in complex disease. Given their combined genetic and environmental influences, complex diseases are studied using a variety of analytical approaches. Consequently, the integration of data from diverse sources is a significant and important challenge in modern biomedical science. I demonstrate a statistical approach to integrating differential gene expression and genetic linkage data from multiple sources to reveal candidate genes, metabolic pathways, and DNA ...
Studies spanning the past three decades have revealed that differential gene expression is one of the most widely used modes of cellular regulation in both normal physiological processes such as development and differentiation and aberrant processes such as cancer. The Gene Regulation, Epigenomics and Transcriptomics Home Areas mission is to train students in the principles and concepts of contemporary gene regulation research with an emphasis on developing skills in cellular, proteomic and genome-wide analyses in order to study mechanisms of differential gene expression during cell signaling, differentiation, development and disease. Our program consists of a specialized curriculum focused on generating a comprehensive understanding of current concepts and mechanisms of gene regulation at the fundamental level and in relation to specific biological pathways. Our groups studies range from basic biochemical analysis of chromatin transcription to detailed analysis of RNA-based pathways involved ...
Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels. Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental ...
Email: [email protected] Translation of messenger RNAs into polypeptides represents the interface between the genome and the proteome. Not surprisingly, this step in the gene expression pathway is frequently used for the regulation of biological responses. I will discuss principles by which structural features of mRNAs, regulatory RNA elements and RNA- binding proteins regulate protein synthesis. This will include findings that imply a new role of the poly(A) tail in the translation of messenger RNAs via IRESes (internal ribosome entry sequences), the understanding of an important switch in Drosophila development, and results from whole genome microarray analyses in yeast which suggest that signal-induced changes in the transcriptome are amplified at the translational level. These latter results unveil a novel, higher level of coordinated gene regulation, which we refer to as potentiation .. ...
In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed (housekeeping) genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues. We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher connectivity and shorter paths between the proteins than the global network. Ontology enrichment scoring
Regulation of gene expression is a multi-layered process - from transcription to translation, including regulatory pathways such as epigenetics, chromatin remodeling and splicing, to name a few. A long-standing question in cellular and molecular neuroscience is the establishment of causality between gene expression and neurophysiology. One way to understand causality is to visualize the dynamic behavior of mRNAs and proteins in their native context and in response to neuronal activity. While transcriptomic and proteomic approaches have been the methods of choice to study genome-wide changes in neuronal gene expression, the
Life: The Science of Biology 11th Edition answers to Chapter 16 - Regulation of Gene Expression - 16.2 - Eukaryotic Gene Expression Is Regulated by Transcription Factors - 16.2 Recap - Learning Outcomes - Page 345 2 including work step by step written by community members like you. Textbook Authors: Sadava, David E.; Hillis, David M.; Heller, H. Craig; Hacker, Sally D. , ISBN-10: 1-31901-016-4, ISBN-13: 978-1-31901-016-4, Publisher: W. H. Freeman
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA), and is informally termed gene regulation. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein.. Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Histone, DNA modifying enzymes and chromatin remodelling factors are major area to concentrate.. Relevant Conferences: Nucleic Acids Conferences , Biochemistry Conferences. 2ndInternational Conference on Transcriptomics, September 12-14, 2016 Philadelphia ...
What is meant by gene expression? Gene expression refers to genes being turned on and producing a product. The product could be an enzyme, a structural protein, or a control molecule. Studies of gene expression typically measure the production of mRNA. Most mechanisms that control gene expression do so by controlling transcription, the synthesis of mRNA. However there are other mechanisms for controlling the rate of protein synthesis that occur downstream (between transcription and translation). Several of these are described in this animation. View the animation below, then complete the quiz to test your knowledge of the concept.. ...
Control of gene expression is a highly complex process involving the coordinated activity of multiple and heterogeneous biological factors. An underlying and intriguing general phenomenon is that biological molecules may act in a variety of different combinations to modulate cellular activities and to specifically react to changes in the biological milieu. To provide coordinated and multiple complex responses, several mechanisms are known to integrate a number of molecules in a combinatorial way.. Combinatorial post-translational modifications, such as methylation, acetylation, phosphorylation, and/or variations in regulatory trans-factors amounts, can influence the global regulation of gene expression at different levels. For example, the combinatorial epigenetic tagging of DNA and histones may enforce or reverse chromatin remodeling, thus playing a fundamental role in a variety of physiological and diseased cellular states [1, 2]. Such combinatorial patterns of epigenomic modifications were ...
Changes on chromatin accessibility take an important part in the regulation of gene expression. ATAC-seq is proven to be useful in studying chromatin accessibility, and many pipelines have been used in sequencing read analysis. By combining our short read aligner and read quantifier, the Homer peak caller and the Limma/edgeR packages, our pipeline provides a fast yet systematic view to the changes on chromatin accessibility between sample, therefore helping biologists to understand the roles of the key transcription factors in gene expression regulation. In this talk, I will briefly introduce the ATAC-seq technologies and its use in analyses, then present our pipeline for studying the functions of key transcription factors in two real cases ...
View Notes - Control of Gene Expression from BSC BSC1005 at Broward College. mRNA and translational mechanisms control the synthesis of protein after mRNA has been produced. Operons Operons are
Differential cardiac gene expression during cardiopulmonary bypass: ischemia-independent upregulation of proinflammatory genes.s profile, publications, research topics, and co-authors
The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during development. Recently, high-resolution sampling approaches, such as RNA tomography or single-cell RNA-seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images. This article will examine the basic principle of modern in situ and single-cell genetic methods, hurdles in quantifying intrinsic and extrinsic forces that influence cell decision-making, and technological requirements for making a visual map of gene regulation, form, and function. Successfully addressing these challenges will be essential for investigating the functional evolution of regulatory sequences during growth, development, and cancer ...
Control transcription activation of target genes. Previously available from ARIAD as the ARGENT Regulated Transcription Plasmid Kit & AP21967.
Control transcription activation of target genes. Previously available from ARIAD as the ARGENT Regulated Transcription Plasmid Kit & AP21967.
As you learned in BIO101, the cell nucleus is the storage area for all genetic material and constantly full of activity. The nucleus in fact contains not only DNA, but RNA and protein as well. This unit will take a detailed look at chromosomes, the cell nucleus, gene expression, and expression regulation. When we refer to "expression regulation," we are talking about the fact that not all genes are expressed in the cell at the same time. After all, though a liver cell and a nerve cell have the same genome (and thus the same DNA), they look and act completely differently. How does this happen? The answer is regulated gene expression!. ...
The absence of Ser389 phosphorization in p53 affects the basal gene expression level of many p53-dependent genes and alters the biphasic response to UV exposure in mouse embryonic ...
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Filtering by: Department Dept. of Cell and Developmental Biology Remove constraint Department: Dept. of Cell and Developmental Biology Keyword gene expression regulation Remove constraint Keyword: gene expression regulation Collection Scholars Archive Remove constraint Collection: Scholars Archive Rights http://rightsstatements.org/vocab/InC/1.0/ Remove constraint Rights: http://rightsstatements.org/vocab/InC/1.0/ School School of Medicine Remove constraint School: School of Medicine ...
Filtering by: Date 2007 Remove constraint Date: 2007 Department Dept. of Cell and Developmental Biology Remove constraint Department: Dept. of Cell and Developmental Biology Keyword gene expression regulation Remove constraint Keyword: gene expression regulation Resource type thesis Remove constraint Resource type: thesis ...
... emphasizes signal transduction and gene regulation in the hypothalamic-pituitary-gonadal axis. Lectures cover physiologic to molecular actions of peptide, protein and steroid hormones and the intracellular signaling as well as the transcriptional gene regulatory mechanisms that drive reproductive biology. Section 1 laboratories teach methods key to studying hormone action and cell biology. Techniques include quantification of second messengers and transcriptional activity; cell culture and transient transfection; western blot analysis; ELISAs; quantitative RT-PCR; gene silencing; chromatin immunoprecipitation; immunofluorescence and in situ hybridization; mutagenesis; tissue dissection. Principles of microscopy and imaging methods are also discussed and applied.. The schedule for Section 1 of FIR2018 can be downloaded here. ...
Study Regulation of Eukaryotic Gene Expression (Biochem Ch 5) flashcards from dheeraj chintapalli's garranps class online, or in Brainscape's iPhone or Android app. ✓ Learn faster with spaced repetition.
Genomes contain all the genetic information needed by an organism, regardless of the circumstance or environment. Generally, however, even single-cell organisms use only a fraction of their genome at any time; that is, cells generally express only a fraction of their genome at any given time. This is especially true among the individual cells that make up multicellular organisms, where cell specialization (differentiation) dictates that only certain genes be expressed in certain cells, and only at particular times during the organisms life span.. ...
Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Often transcription is activated when a molecule binds to a protein. What happens next is that bound protein undergoes a change that eventually results in the activation of transcription. The molecule that binds is called a ligand, and the protein that binds the protein is called the receptor protein. Ligands can be small molecules such as protein that pass through the cell membrane and activate transcription, or they can be protein molecules that can not move through the cell membrane and must find a receptor protein that resides in the cell membrane. We will discuss each of these models for gene expression.. Copyright © 1997. Phillip McClean. ...
One common method for profiling the state of a cell is to measure levels of gene expression, the process by which the information within our genes is used to make a gene product. Cells control expression of genes as a way to adapt to their environment. Researchers at the LINCS Transcriptomics Center have released an updated version of the Connectivity Map (CMap) which now contains over 1.3 million gene expression profiles from treating numerous types of human cells with over 42,000 agents that disrupt cellular function (perturbagens). This extremely large set of data is based on the L1000 assay which allows for inexpensive and large-scale analysis of gene expression. CMap is a freely available public resource that any research scientist can use and already has more than 18,000 registered users. For example, researchers can gain insight regarding how a small-molecule drug works in a cell by determining the changes in gene expression it produces. Alternatively, they can find a molecule from all ...
Gene Expression Macro Version 1.1 Instructions Rev B 1 Bio-Rad Gene Expression Macro Users Guide 2004 Bio-Rad Laboratories Table of Contents: Introduction Opening
Mouse polyclonal antibody raised against a full-length human CEBPB protein. CEBPB (AAH21931.1, 1 a.a. ~ 345 a.a) full-length human protein. (H00001051-B01P) - Products - Abnova
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NFAT1 (NFATc2), 0.1 ml. Nuclear factor of activated T cells (NFAT) is a family of transcription factors implicated in multiple biological processes including cytokine gene expression, cardiac hypertrophy and adipocyte differentiation.
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Chapter 18 Regulation of Gene Expression Gene Regulation Is Necessary By switching genes off when they are not needed, cells can prevent resources from being wasted. There should be natural selection
Lyubetsky V., Gorbunov K., Pirogov S., Rubanov L., Seliverstov A., An algorithm and search results for a model of gene expression regulation with RNA secondary structures in bacteria Information Processes, 2005, V. 5, No 5, pp. 337 366. [in Russian] http://www.jip.ru/2005/337-366.pdf ...
In this study we describe the spatial regulation of RNA interference (RNAi) using an RNA-carrier protein labeled with a fluorescent dye and a light source to trigger the RNAi. We demonstrate photo-dependent gene silencing using several dyes with diff
I am fascinated by a fundamental question in biology; How is regulation of gene expression as a response to external stimulus achieved? My laboratory
Akhilesh Bajpai, Sravanthi Davuluri and Acharya KK* (*Correspondence: [email protected]), A comparative account of gene expression resources, feature-validations and application-based categorizations; In: Startbioinfo; 12 Oct 2011, http://www.startbioinfo.com/gene-expression/" ...
Im just not quite sure the answer to this. When we talk about epigenetics and gene expression, does it not matter if we have snps or not? For...
Genotyping & gene expression full services from Eurofins Genomics . Wide range of platforms and assays available ** Call +49 8092 8289-0
An expression system refers to the factors that work together to yield a particular gene product such as a protein, ribozyme or RNA particle.
The need to analyze rare cells is based on the nature of tissue differentiation and regeneration, the initiation and propagation of disease processes in multicellular organisms, and the functional diversity of individual cells
People who want to take free transcription training online can take courses offered by Meditec, Online-medical-transcription-course.com and the eLearn Medical Transcription course. Although these...
This category lists sites for medical transcription associations that inform, and enable the support and advancement of the medical transcription industry. <
C57BL/6 mice were injected with 400 mg of anti-CD4 (clone GK one.five BioXcell, NH, Usa) or anti-CD8 (clone 53,.seventy two BioXcell, NH, United states of
I dont have a TV because it seems such a time sink. Nevertheless, over the past few years Ive felt the creep of media convergence. Now I found this site, not quite as bad as channel surfing...but its getting there ...
ON-TARGETplus and siGENOME SMARTpool siRNA reagent and at least 3 of 4 individual siRNAs will silence target gene expression by at least 75% at the mRNA level when used under optimal delivery conditions.. ...
Sources tell TMZ the network has told the cast if they dont accept MTVs deal by the end of business Monday, they will be replaced. And, MTV has told them it does not have to be a package deal -- the cast members who accept the offer will stay ... those who do not can have a nice life ...
The Workshop on Evolutionary Tinkering in Gene Expression which was held at the end of August 1988. was planned to celebrate 20 successful Advanced Study Institutes (A. S. I.) in Molecular and Cell
MicroRNA, also known as miRNA, is a class of non-coding ribonucleic acid (RNA) which plays a vital role in the regulation of gene expression. It founds in
Find info concerning Fairmont State medical transcription. Qualifications for nursing programs vary widely. Learn about the various medical specializations available within technical training programs.
The generation of transgenic mice by DNA microinjection is a powerful tool to investigate the molecular regulation of gene expression, development, and disease
Expression. At very early time-points (,53 hrs following exposure) insufficient numbers of peripheral cells are undergoing the conserved stimulation required to