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Transcriptional outcomes and kinetic patterning of gene

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Transcriptional outcomes and kinetic patterning of gene

Sep 10,2018 Transcriptional outcomes and kinetic patterning of gene#0183;Transcriptional outcomes and kinetic patterning of gene expression in response to NF-B activation.Zhao M(1),Joy J(1),Zhou W(2),De S(3),Wood WH 3rd(3),Becker KG(3),Ji H(2),Sen R(1).Author information (1)Gene Regulation Section,Laboratory of Molecular Biology and Immunology,National Institute on Aging,Baltimore,Maryland,United Transcriptional outcomes and kinetic patterning of gene Sep 10,2018 Transcriptional outcomes and kinetic patterning of gene#0183;Citation Zhao M,Joy J,Zhou W,De S,Wood WH III,Becker KG,et al.(2018) Transcriptional outcomes and kinetic patterning of gene expression in response to NF-B activation.PLoS Biol 16(9) e2006347.Transcription an overview of DNA transcription (article In transcription,the DNA sequence of a gene is transcribed (copied out) to make an RNA molecule. Post-transcriptional regulation.Eukaryotic gene transcription Going from DNA to mRNA.Overview of transcription.This is the currently selected item.Eukaryotic pre-mRNA processing.

Some results are removed in response to a notice of local law requirement.For more information,please see here.Previous123456NextDevelopmental Pattern Formation Insights from Physics and

Oct 12,2012 Transcriptional outcomes and kinetic patterning of gene#0183;Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns.Together,this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular,cellular,and tissue scales.Some results are removed in response to a notice of local law requirement.For more information,please see here.12345NextMicroarray analysis reveals differential gene expression Microarray analysis reveals differential gene expression patterns and regulation of single target genes contributing to the opposing phenotype of TrkA- and TrkB-expressing neuroblastomasSome results are removed in response to a notice of local law requirement.For more information,please see here.

Single-cell mapping of gene expression landscapes and

As embryos develop,numerous cell types with distinct functions and morphologies arise from pluripotent cells.Three research groups have used single-cell RNA sequencing to analyze the transcriptional changes accompanying development of vertebrate embryos (see the Perspective by Harland).Wagner et al.sequenced the transcriptomes of more than 90,000 cells throughout zebrafish development to Role of the NF-B system in context-specific tuning of the The canonical NF-B pathway instructs the expression of inflammatory genes by the RelA:p50 transcription factor in response to diverse cell-activatingRole of the NF-B system in context-specific tuning of the The canonical NF-B pathway instructs the expression of inflammatory genes by the RelA:p50 transcription factor in response to diverse cell-activating

Rhythms and synchronization patterns in gene expression in

A large number of transcriptional studies have been made in the species and these usually report transcript quantities observed at a certain age or stage of development.However,circadian oscillation is an important characteristic of gene expression in many animals and plants,modulating both their physiology and behavior.Rhythms and synchronization patterns in gene expression in A large number of transcriptional studies have been made in the species and these usually report transcript quantities observed at a certain age or stage of development.However,circadian oscillation is an important characteristic of gene expression in many animals and plants,modulating both their physiology and behavior.Response to Nodal morphogen gradient is determined byApr 14,2015 Transcriptional outcomes and kinetic patterning of gene#0183;Smad2 activation has been used as a read-out for Nodal signaling,but it has been unclear whether this transcriptional regulator is the main transducer of Nodal signaling in zebrafish (Dick et al.,2000; Jia et al.,2008).To test the role of Smad2 in Nodal signal transduction,we used TILLING (Wienholds et al.,2003) to recover a non-sense mutation in smad2 and generated embryos lacking

Reciprocal occupancy of BCL6 and STAT5 on Growth

Expression of the Growth Hormone (GH)-stimulated gene Socs2 (Suppressor of Cytokine Signaling 2) is mediated by the transcription activator STAT5 (Signal Transducer and Activator of Transcription 5) and the transcription repressor BCL6 (B-Cell Lymphoma 6).ChIP-Sequencing identified Cish (Cytokine-IProkaryotic Gene Regulation Biology for Majors IA repressor is a transcription factor that suppresses transcription of a gene in response to an external stimulus by binding to a DNA sequence within the regulatory region called the operator,which is located between the RNA polymerase binding site of the promoter and the transcriptional start site of the first structural gene.Repressor Organismal benefits of transcription speed control atArticle Organismal benefits of transcription speed control at gene boundaries Xueyuan Leng1,Maxim Ivanov1,Peter Kindgren1,Indranil Malik2,,Axel Thieffry3,4,Peter Brodersen4,Albin Sandelin3,4,Craig D Kaplan2,5 Sebastian Marquardt1,* Abstract RNA polymerase II (RNAPII) transcription is crucial for gene

Multimodal transcriptional control of pattern formation in

Dec 26,2019 Transcriptional outcomes and kinetic patterning of gene#0183;Binary Control of the Transcriptional Time Window Is the Primary Driver of Stripe Formation.To test the simple model of pattern formation put forward in Eq.2,we quantified transcription of stripe 2 of eve in the fruit fly.We imaged the transcription of an eve stripe 2 reporter,using the MS2 system (18,27,28).Transcripts of a reporter gene driven by the eve stripe 2 enhancer and the eve Multimodal transcriptional control of pattern formation in Dec 26,2019 Transcriptional outcomes and kinetic patterning of gene#0183;Binary Control of the Transcriptional Time Window Is the Primary Driver of Stripe Formation.To test the simple model of pattern formation put forward in Eq.2,we quantified transcription of stripe 2 of eve in the fruit fly.We imaged the transcription of an eve stripe 2 reporter,using the MS2 system (18,27,28).Transcripts of a reporter gene driven by the eve stripe 2 enhancer and the eve Kinetic sculpting of the seven stripes of the Drosophila Aug 20,2020 Transcriptional outcomes and kinetic patterning of gene#0183;Abstract.We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms,and developed tools to characterize and visualize how transcriptional bursting varies over time and space.We find that despite being created by the independent activity of

Gene regulation Biological Principles

Aug 12,2014 Transcriptional outcomes and kinetic patterning of gene#0183;When a gene is subject to negative transcriptional control,the binding of a specific transcription factor to a regulator elements represses transcription.A single gene can be subject to both positive and negative transcriptional control by differentGene regulation Biological PrinciplesAug 12,2014 Transcriptional outcomes and kinetic patterning of gene#0183;When a gene is subject to negative transcriptional control,the binding of a specific transcription factor to a regulator elements represses transcription.A single gene can be subject to both positive and negative transcriptional control by differentDiverse Spatial Expression Patterns Emerge from Unified Theory Diverse Spatial Expression Patterns Emerge from Unied Kinetics of Transcriptional Bursting Benjamin Zoller,1,5 Shawn C.Little,2,3,5 and Thomas Gregor1,4,6,* 1Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics,Princeton University,Princeton,NJ 08544,USA 2Department of Molecular Biology and Howard Hughes Medical Institute,Princeton

Diverse Spatial Expression Patterns Emerge from Unified

Theory Diverse Spatial Expression Patterns Emerge from Unied Kinetics of Transcriptional Bursting Benjamin Zoller,1,5 Shawn C.Little,2,3,5 and Thomas Gregor1,4,6,* 1Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics,Princeton University,Princeton,NJ 08544,USA 2Department of Molecular Biology and Howard Hughes Medical Institute,Princeton Diverse Spatial Expression Patterns Emerge from Unified Oct 18,2018 Transcriptional outcomes and kinetic patterning of gene#0183;Single-Parameter Distribution of Transcriptional Activity across All Expression Boundaries.The expression patterns of the gap genes are determined by multiple enhancer elements at varying distances from their promoters (Kvon et al.,2014,Perry et al.,2011).Each enhancer contains a variable number of binding sites for multiple patterning input factors with cross-regulatory interactions Developmental Regulation of an Adhesin Gene during Candida albicans expresses specific virulence traits that promote disease establishment and progression.These traits include morphological transitions between yeast and hyphal growth forms that are thought to contribute to dissemination and invasion and cell surface adhesins that promote attachment to the host.Here,we describe the regulation of the adhesin gene ALS3 ,which is expressed

Developmental Regulation of an Adhesin Gene during

Candida albicans expresses specific virulence traits that promote disease establishment and progression.These traits include morphological transitions between yeast and hyphal growth forms that are thought to contribute to dissemination and invasion and cell surface adhesins that promote attachment to the host.Here,we describe the regulation of the adhesin gene ALS3 ,which is expressed Developmental Pattern Formation Insights from Physics and Oct 12,2012 Transcriptional outcomes and kinetic patterning of gene#0183;Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns.Together,this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular,cellular,and tissue scales.Computational and Functional Analysis of Growth Hormone The changes in expression of most of the genes in this cluster,including the dramatic decrease in Bcl6 expression,were confirmed by quantitative real-time PCR of RNA from GH-treated 3T3-F442A adipocytes ().The overall changes in mRNA for each gene correspond with microarray findings at 4 or 48 h Expression of SOCS2 and CISH mRNA was the most highly stimulated by GH (50- to 60-fold).

Combinatorial Gene Regulation through Kinetic Control of

Scholes et al.present a quantitative model of combinatorial control of transcription that captures kinetic control of the transcription cycle.They show that,by independently regulating different slow steps in transcription,transcription factors can generate the same analog and digital computations as have previously been ascribed to cooperative physical interactions.Cited by 11Publish Year 2018Author Mingming Zhao,Jaimy Joy,Weiqiang Zhou,Supriyo De,William H.Wood,Kevin G.Becker,Hong Kai Ji,Transcriptional outcomes and kinetic patterning of gene Sep 10,2018 Transcriptional outcomes and kinetic patterning of gene#0183;Transcriptional outcomes and kinetic patterning of gene expression in response to NF-B activation. Kinetic patterns of gene induction of direct (304) and indirect (502) RELA target genes in activated BJAB cells.Cells were activated with P+I for the indicated times,followed by RNA-Seq.Mean normalized reads for direct and indirect target Cited by 11Publish Year 2018Author Mingming Zhao,Jaimy Joy,Weiqiang Zhou,Supriyo De,William H.Wood,Kevin G.Becker,Hong Kai Ji,Transcriptional outcomes and kinetic patterning of gene Consequently,time dependency of transcriptional responses is a unique signature of the initiating stimulus.Here we probed mechanisms that generate kinetic patterns of NF-B-dependent gene expression in B lymphoma cells responding to a transient NF-B-activating stimulus.

Cited by 11Publish Year 2018Author Mingming Zhao,Jaimy Joy,Weiqiang Zhou,Supriyo De,William H.Wood,Kevin G.Becker,Hong Kai Ji,Kinetic sculpting of the seven stripes of the Drosophila

Aug 20,2020 Transcriptional outcomes and kinetic patterning of gene#0183;Abstract.We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms,and developed tools to characterize and visualize how transcriptional bursting varies over time and space.We find that despite being created by the independent activity ofCarD contributes to diverse gene expression outcomes Jul 02,2019 Transcriptional outcomes and kinetic patterning of gene#0183;Our comparison of gene expression patterns shows that CarD mutants with similar effects on RP o stability possess similar transcriptional profiles,indicating that the stabilization of RP o by CarD is responsible for gene expression outcomes,which can be diverse and depend on the promoter.Our studies broaden our understanding of how CarD An evolutionarily biased distribution of miRNA sites miRNAs are a major class of regulators of gene expression in metazoans.By targeting cognate mRNAs,miRNAs are involved in regulating most,if not all,biological processes in different cell and tissue types.To better understand how this regulatory potential is allocated among different target gene sets,we carried out a detailed and systematic analysis of miRNA target sites distribution in

An evolutionarily biased distribution of miRNA sites

miRNAs are a major class of regulators of gene expression in metazoans.By targeting cognate mRNAs,miRNAs are involved in regulating most,if not all,biological processes in different cell and tissue types.To better understand how this regulatory potential is allocated among different target gene sets,we carried out a detailed and systematic analysis of miRNA target sites distribution in ARACNe-based inference,using curated microarray data,of Uncovering the complex transcriptional regulatory networks (TRNs) that underlie plant and animal development remains a challenge.However,a vast amount of data from public microarray experiments is available,which can be subject to inference algorithms in order to recover reliable TRN architectures.In this study we present a simple bioinformatics methodology that uses public,carefully

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