Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli.

PubWeight™: 1.13‹?› | Rank: Top 10%

🔗 View Article (PMC 3202801)

Published in Mol Syst Biol on September 13, 2011

Authors

Amit Zeisel1, Wolfgang J Köstler, Natali Molotski, Jonathan M Tsai, Rita Krauthgamer, Jasmine Jacob-Hirsch, Gideon Rechavi, Yoav Soen, Steffen Jung, Yosef Yarden, Eytan Domany

Author Affiliations

1: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.

Articles citing this

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol (2015) 1.62

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS Comput Biol (2015) 1.44

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell (2014) 1.13

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc Natl Acad Sci U S A (2013) 1.01

MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale. Elife (2014) 0.94

IL-1 receptor 2 (IL-1R2) and its role in immune regulation. Brain Behav Immun (2012) 0.93

Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets. Nucleic Acids Res (2012) 0.92

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample. PLoS One (2014) 0.90

Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol (2013) 0.90

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol (2016) 0.89

Deep sequencing of HIV-infected cells: insights into nascent transcription and host-directed therapy. J Virol (2014) 0.89

Beta-catenin/HuR post-transcriptional machinery governs cancer stem cell features in response to hypoxia. PLoS One (2013) 0.84

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. Proc Natl Acad Sci U S A (2015) 0.84

Reactivation of epigenetically silenced miR-512 and miR-373 sensitizes lung cancer cells to cisplatin and restricts tumor growth. Cell Death Differ (2015) 0.81

A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nat Commun (2015) 0.81

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol (2014) 0.81

Epidermal growth-factor-induced transcript isoform variation drives mammary cell migration. PLoS One (2013) 0.80

UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells. PLoS Genet (2014) 0.78

Perfect timing: splicing and transcription rates in living cells. Wiley Interdiscip Rev RNA (2016) 0.77

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression. BMC Genomics (2016) 0.77

Defining a role for acid sphingomyelinase in the p38/interleukin-6 pathway. J Biol Chem (2014) 0.76

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proc Natl Acad Sci U S A (2016) 0.75

Interferon-Induced Transmembrane Protein 3 Inhibits Hantaan Virus Infection, and Its Single Nucleotide Polymorphism rs12252 Influences the Severity of Hemorrhagic Fever with Renal Syndrome. Front Immunol (2017) 0.75

Measures of RNA metabolism rates: Toward a definition at the level of single bonds. Transcription (2016) 0.75

Steering tumor progression through the transcriptional response to growth factors and stroma. FEBS Lett (2014) 0.75

Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Res (2014) 0.75

Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol (2011) 0.75

An immediate-late gene expression module decodes ERK signal duration. Mol Syst Biol (2017) 0.75

Articles cited by this

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99

Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93

Global quantification of mammalian gene expression control. Nature (2011) 22.36

The transcriptional program in the response of human fibroblasts to serum. Science (1999) 19.19

Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A (2003) 12.50

Integrating mRNA processing with transcription. Cell (2002) 9.74

Molecular cloning of gene sequences regulated by platelet-derived growth factor. Cell (1983) 9.03

Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69

Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science (1998) 8.55

The highways and byways of mRNA decay. Nat Rev Mol Cell Biol (2007) 8.42

Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet (2004) 8.30

A unified theory of gene expression. Cell (2002) 7.61

Expression of a set of growth-related immediate early genes in BALB/c 3T3 cells: coordinate regulation with c-fos or c-myc. Proc Natl Acad Sci U S A (1987) 7.38

Control of inducible gene expression by signal-dependent transcriptional elongation. Cell (2009) 6.57

Negative autoregulation speeds the response times of transcription networks. J Mol Biol (2002) 6.32

A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell (2009) 6.26

In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol (2007) 6.10

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07

Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58

Primary response genes induced by growth factors and tumor promoters. Annu Rev Biochem (1991) 5.48

Transcriptional control of the inflammatory response. Nat Rev Immunol (2009) 5.20

The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol (2003) 5.20

RNA polymerase II is an essential mRNA polyadenylation factor. Nature (1998) 4.87

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell (2011) 4.42

Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell (2000) 4.38

A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35

Transcription dynamics. Mol Cell (2009) 4.15

Transcriptional autoregulation of the proto-oncogene fos. Nature (1988) 4.10

Mammalian genes are transcribed with widely different bursting kinetics. Science (2011) 4.08

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules. Nat Immunol (2009) 3.85

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81

Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc Natl Acad Sci U S A (2002) 3.71

Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science (2011) 3.67

Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol (2009) 3.39

The potential for the formation of a biosynthetic enzyme in Escherichia coli. Biochim Biophys Acta (1957) 3.19

A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration. Nat Cell Biol (2007) 2.85

Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature (2010) 2.74

RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science (2009) 2.63

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell (2010) 2.43

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol (2008) 2.27

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26

A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18

EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16

The splicing of U12-type introns can be a rate-limiting step in gene expression. EMBO J (2002) 1.84

Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics (2010) 1.46

Immediate-early and delayed primary response genes are distinct in function and genomic architecture. J Biol Chem (2007) 1.37

Digital NFATc2 activation per cell transforms graded T cell receptor activation into an all-or-none IL-2 expression. PLoS One (2007) 1.35

Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes. Proc Natl Acad Sci U S A (2009) 1.31

Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. BMC Bioinformatics (2010) 1.09

Dissection of a complex transcriptional response using genome-wide transcriptional modelling. Mol Syst Biol (2009) 1.01

The abundance of the spliceosomal snRNPs is not limiting the splicing of U12-type introns. RNA (2006) 1.01

Articles by these authors

Blood monocytes consist of two principal subsets with distinct migratory properties. Immunity (2003) 21.56

Development of monocytes, macrophages, and dendritic cells. Science (2010) 12.86

ATP mediates rapid microglial response to local brain injury in vivo. Nat Neurosci (2005) 11.55

EGF-ERBB signalling: towards the systems level. Nat Rev Mol Cell Biol (2006) 10.39

VEGF-induced adult neovascularization: recruitment, retention, and role of accessory cells. Cell (2006) 9.32

CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science (2005) 8.97

Control of microglial neurotoxicity by the fractalkine receptor. Nat Neurosci (2006) 8.25

Outcome signature genes in breast cancer: is there a unique set? Bioinformatics (2004) 7.96

Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol (2004) 7.61

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00

Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol (2008) 6.41

Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A (2006) 6.26

Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity (2012) 6.18

A clonogenic bone marrow progenitor specific for macrophages and dendritic cells. Science (2005) 5.88

A Cre-inducible diphtheria toxin receptor mediates cell lineage ablation after toxin administration. Nat Methods (2005) 5.59

Donor-derived brain tumor following neural stem cell transplantation in an ataxia telangiectasia patient. PLoS Med (2009) 5.50

Intestinal lamina propria dendritic cell subsets have different origin and functions. Immunity (2009) 5.43

Alum adjuvant boosts adaptive immunity by inducing uric acid and activating inflammatory dendritic cells. J Exp Med (2008) 5.42

Monocytes give rise to mucosal, but not splenic, conventional dendritic cells. J Exp Med (2006) 4.91

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science (2014) 4.91

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics (2004) 4.88

A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35

In vivo depletion of lung CD11c+ dendritic cells during allergen challenge abrogates the characteristic features of asthma. J Exp Med (2005) 4.34

Derailed endocytosis: an emerging feature of cancer. Nat Rev Cancer (2008) 4.25

Circulating activated platelets exacerbate atherosclerosis in mice deficient in apolipoprotein E. Nat Med (2002) 4.02

Inducible ablation of mouse Langerhans cells diminishes but fails to abrogate contact hypersensitivity. J Cell Biol (2005) 3.75

Infiltrating blood-derived macrophages are vital cells playing an anti-inflammatory role in recovery from spinal cord injury in mice. PLoS Med (2009) 3.68

Feedback regulation of EGFR signalling: decision making by early and delayed loops. Nat Rev Mol Cell Biol (2011) 3.52

Diagnostic assay based on hsa-miR-205 expression distinguishes squamous from nonsquamous non-small-cell lung carcinoma. J Clin Oncol (2009) 3.47

Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res (2006) 3.32

Role of protein ubiquitylation in regulating endocytosis of receptor tyrosine kinases. Oncogene (2004) 3.27

The deaf and the dumb: the biology of ErbB-2 and ErbB-3. Exp Cell Res (2003) 3.18

Ly6C hi monocytes in the inflamed colon give rise to proinflammatory effector cells and migratory antigen-presenting cells. Immunity (2012) 3.18

Distinct differentiation potential of blood monocyte subsets in the lung. J Immunol (2007) 3.16

Directed differentiation of human embryonic stem cells into functional retinal pigment epithelium cells. Cell Stem Cell (2009) 3.09

A distinctive DNA damage response in human hematopoietic stem cells reveals an apoptosis-independent role for p53 in self-renewal. Cell Stem Cell (2010) 2.95

GeneNote: whole genome expression profiles in normal human tissues. C R Biol (2004) 2.92

A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration. Nat Cell Biol (2007) 2.85

Endocytosis of receptor tyrosine kinases is driven by monoubiquitylation, not polyubiquitylation. J Biol Chem (2003) 2.77

The EGF receptor family: spearheading a merger of signaling and therapeutics. Curr Opin Cell Biol (2007) 2.74

STIM1 mutation associated with a syndrome of immunodeficiency and autoimmunity. N Engl J Med (2009) 2.72

Role of CCR8 and other chemokine pathways in the migration of monocyte-derived dendritic cells to lymph nodes. J Exp Med (2004) 2.68

PML, YAP, and p73 are components of a proapoptotic autoregulatory feedback loop. Mol Cell (2008) 2.66

Notch2 receptor signaling controls functional differentiation of dendritic cells in the spleen and intestine. Immunity (2011) 2.61

Lung macrophages serve as obligatory intermediate between blood monocytes and alveolar macrophages. J Immunol (2007) 2.55

CX3CR1 is required for monocyte homeostasis and atherogenesis by promoting cell survival. Blood (2008) 2.52

Ineffective erythropoiesis in beta-thalassemia is characterized by increased iron absorption mediated by down-regulation of hepcidin and up-regulation of ferroportin. Blood (2007) 2.52

Mutant p53 oncogenic functions are sustained by Plk2 kinase through an autoregulatory feedback loop. Cell Cycle (2011) 2.46

Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group. Blood (2009) 2.44

A mutant EGF-receptor defective in ubiquitylation and endocytosis unveils a role for Grb2 in negative signaling. EMBO J (2002) 2.42

Signal transduction and oncogenesis by ErbB/HER receptors. Int J Radiat Oncol Biol Phys (2004) 2.41

Altered adenosine-to-inosine RNA editing in human cancer. Genome Res (2007) 2.38

Perivascular clusters of dendritic cells provide critical survival signals to B cells in bone marrow niches. Nat Immunol (2008) 2.33

Is abundant A-to-I RNA editing primate-specific? Trends Genet (2005) 2.32

Epigenetic ontogeny of the Igk locus during B cell development. Nat Immunol (2004) 2.25

p38 MAP kinase mediates stress-induced internalization of EGFR: implications for cancer chemotherapy. EMBO J (2006) 2.23

LRIG1 restricts growth factor signaling by enhancing receptor ubiquitylation and degradation. EMBO J (2004) 2.20

Drug-induced ubiquitylation and degradation of ErbB receptor tyrosine kinases: implications for cancer therapy. EMBO J (2002) 2.17

EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16

Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res (2003) 2.15

Alveolar type II epithelial cells present antigen to CD4(+) T cells and induce Foxp3(+) regulatory T cells. Am J Respir Crit Care Med (2008) 2.15

Hsp90 recognizes a common surface on client kinases. J Biol Chem (2006) 2.12

Recruitment of beneficial M2 macrophages to injured spinal cord is orchestrated by remote brain choroid plexus. Immunity (2013) 2.08

CD8alpha+ dendritic cells are required for efficient entry of Listeria monocytogenes into the spleen. Immunity (2006) 2.06

Concordance between epidermal growth factor receptor status in primary non-small-cell lung cancer and metastases: a post-mortem study. Eur J Cardiothorac Surg (2010) 2.06

Lack of conventional dendritic cells is compatible with normal development and T cell homeostasis, but causes myeloid proliferative syndrome. Immunity (2008) 2.04

The neuronal chemokine CX3CL1/fractalkine selectively recruits NK cells that modify experimental autoimmune encephalomyelitis within the central nervous system. FASEB J (2006) 2.04

A new type of microglia gene targeting shows TAK1 to be pivotal in CNS autoimmune inflammation. Nat Neurosci (2013) 2.03

Association between common Toll-like receptor 4 mutations and severe respiratory syncytial virus disease. J Infect Dis (2004) 2.03

Securing the immune tightrope: mononuclear phagocytes in the intestinal lamina propria. Nat Rev Immunol (2010) 2.02

Isolation of primitive endoderm, mesoderm, vascular endothelial and trophoblast progenitors from human pluripotent stem cells. Nat Biotechnol (2012) 2.00

Synergistic down-regulation of receptor tyrosine kinases by combinations of mAbs: implications for cancer immunotherapy. Proc Natl Acad Sci U S A (2005) 2.00

Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs. Am J Hum Genet (2006) 1.97

Regulation of MAPKs by growth factors and receptor tyrosine kinases. Biochim Biophys Acta (2007) 1.97

Evolutionarily conserved human targets of adenosine to inosine RNA editing. Nucleic Acids Res (2005) 1.96

A coding VKORC1 Asp36Tyr polymorphism predisposes to warfarin resistance. Blood (2006) 1.94

CX3CR1+ CD8alpha+ dendritic cells are a steady-state population related to plasmacytoid dendritic cells. Proc Natl Acad Sci U S A (2010) 1.94

Microbe sampling by mucosal dendritic cells is a discrete, MyD88-independent step in DeltainvG S. Typhimurium colitis. J Exp Med (2008) 1.92

Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc (2013) 1.91

Runx3 regulates mouse TGF-beta-mediated dendritic cell function and its absence results in airway inflammation. EMBO J (2004) 1.90

Two phases of mitogenic signaling unveil roles for p53 and EGR1 in elimination of inconsistent growth signals. Mol Cell (2011) 1.89

Transepithelial pathogen uptake into the small intestinal lamina propria. J Immunol (2006) 1.88

Transcriptional programs following genetic alterations in p53, INK4A, and H-Ras genes along defined stages of malignant transformation. Cancer Res (2005) 1.86

MIR-451 and Imatinib mesylate inhibit tumor growth of Glioblastoma stem cells. Biochem Biophys Res Commun (2008) 1.85