scholarly journals c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs

2013 ◽  
Vol 42 (5) ◽  
pp. 3059-3072 ◽  
Author(s):  
Montse Gustems ◽  
Anne Woellmer ◽  
Ulrich Rothbauer ◽  
Sebastian H. Eck ◽  
Thomas Wieland ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Sequence ◽  
Epigenetic Silencing ◽  
Activator Protein 1 ◽  
Sequence Motifs ◽  
Promoter Regions ◽  
Barr Virus ◽  
Dna Sequence Motifs

Abstract CpG methylation in mammalian DNA is known to interfere with gene expression by inhibiting the binding of transactivators to their cognate sequence motifs or recruiting proteins involved in gene repression. An Epstein–Barr virus-encoded transcription factor, Zta, was the first example of a sequence-specific transcription factor that preferentially recognizes and selectively binds DNA sequence motifs with methylated CpG residues, reverses epigenetic silencing and activates gene transcription. The DNA binding domain of Zta is homologous to c-Fos, a member of the cellular AP-1 (activator protein 1) transcription factor family, which regulates cell proliferation and survival, apoptosis, transformation and oncogenesis. We have identified a novel AP-1 binding site termed meAP-1, which contains a CpG dinucleotide. If methylated, meAP-1 sites are preferentially bound by the AP-1 heterodimer c-Jun/c-Fos in vitro and in cellular chromatin in vivo. In activated human primary B cells, c-Jun/c-Fos locates to these methylated elements in promoter regions of transcriptionally activated genes. Reminiscent of the viral Zta protein, c-Jun/c-Fos is the first identified cellular member of the AP-1 family of transactivators that can induce expression of genes with methylated, hence repressed promoters, reversing epigenetic silencing.

scholarly journals FOS, a Critical Downstream Mediator of PGR and EGF Signaling Necessary for Ovulatory Prostaglandins in the Human Ovary

2018 ◽  
Vol 103 (11) ◽  
pp. 4241-4252 ◽  
Author(s):  
Yohan Choi ◽  
Katherine L Rosewell ◽  
Mats Brännström ◽  
James W Akin ◽  
Thomas E Curry ◽  
...  
Keyword(s):  
Target Genes ◽  
Activator Protein 1 ◽  
Egf Receptors ◽  
Human Ovary ◽  
Promoter Regions ◽  
Vitro Fertilization ◽  
Egf Signaling ◽  
Periovulatory Follicles

Abstract Context Fos null mice failed to ovulate and form a corpus luteum (CL) even when given exogenous gonadotropins, suggesting that ovarian Fos expression is critical for successful ovulation and CL formation. However, little is known about FOS in the human ovary. Objectives To determine the expression, regulation, and function of FOS in human periovulatory follicles. Design/Participants Timed periovulatory follicles were obtained from normally cycling women. Granulosa/lutein cells were collected from in vitro fertilization patients. Main Outcome Measures The in vivo expression after human chorionic gonadotropin (hCG) administration and in vitro regulation of FOS, JUN, JUNB, and JUND was evaluated at the mRNA and protein level. Binding of progesterone receptor (PGR) and FOS to their target genes was assessed by chromatin immunoprecipitation analyses. Prostaglandin E2 (PGE2) and progesterone were measured. Results The expression of FOS, JUNB, and JUND drastically increased in ovulatory follicles after hCG administration. In human granulosa/lutein cell cultures, hCG increased the expression of FOS and JUN proteins. Inhibitors of PGR and epidermal growth factor (EGF) receptors reduced hCG-induced increases in the expression and phosphorylation of FOS. PGR bound to the FOS gene. A selective FOS inhibitor blocked hCG-induced increases in PGE2 and the expression of prostaglandin (PG) synthases and transporters (PTGES, SLCO2A1, and ABCC1). FOS bound to the promoter regions of these genes. Conclusions The increase of FOS/activator protein 1 in human periovulatory follicles after hCG administration is mediated by collaborative actions of PGR and EGF signaling and critical for the upregulated expression of key ovulatory genes required for the rise in ovulatory PG in human granulosa cells.

scholarly journals MTF1, a classic metal sensing transcription factor, promotes myogenesis in response to copper

2019 ◽  
Author(s):  
Cristina Tavera-Montañez ◽  
Sarah J. Hainer ◽  
Daniella Cangussu ◽  
Shellaina J.V. Gordon ◽  
Yao Xiao ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Metal Binding ◽  
Myoblast Differentiation ◽  
Sequence Motifs ◽  
Promoter Regions ◽  
Multiple Strategies ◽  
Primary Myoblasts ◽  
C Terminus ◽  
Dna Sequence Motifs ◽  
Toxic Concentrations

AbstractMTF1 is a conserved metal-binding transcription factor in eukaryotes that binds to conserved DNA sequence motifs, termed metal response elements (MREs). MTF1 responds to metal excess and deprivation, protects cells from oxidative and hypoxic stresses, and is required for embryonic development in vertebrates. We used multiple strategies to identify an unappreciated role for MTF1 and copper (Cu) in cell differentiation. Upon initiation of myogenesis from primary myoblasts, MTF1 expression increased, as did nuclear localization. Mtf1 knockdown impaired differentiation, while addition of non-toxic concentrations of Cu+ enhanced MTF1 expression and promoted myogenesis. Cu+ bound stoichiometrically to a C-terminus tetra-cysteine of MTF1. MTF1 bound to chromatin at the promoter regions of myogenic genes and binding was stimulated by copper. MTF1 formed a complex with MyoD at myogenic promoters, the master transcriptional regulator of the myogenic lineage. These studies establish novel mechanisms by which copper and MTF1 regulate gene expression in myoblast differentiation.

scholarly journals DNA sequence influences hexasome orientation to regulate DNA accessibility

2019 ◽  
Vol 47 (11) ◽  
pp. 5617-5633 ◽  
Author(s):  
Matthew Brehove ◽  
Elan Shatoff ◽  
Benjamin T Donovan ◽  
Caroline M Jipa ◽  
Ralf Bundschuh ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Motifs ◽  
Histone H2a ◽  
Naked Dna ◽  
Dna Accessibility ◽  
Distal Side ◽  
Fold Reduction ◽  
Functional Consequences

Abstract Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs of DNA wrapped around a histone H3–H4 tetramer and two histone H2A–H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A–H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A–H2B distal side is identical to naked DNA, while the accessibility on the H2A–H2B proximal side is reduced by 2-fold, which is due to a 2-fold reduction in hexasome unwrapping probability. We then determined that a 23 bp region of the Widom-601 NPS is responsible for forming homogeneously oriented hexasomes. Analysis of published ChIP-exo data of hexasome containing genes identified two DNA sequence motifs that correlate with hexasome orientation in vivo, while ExoIII mapping studies of these sequences revealed they generate homogeneously oriented hexasomes in vitro. These results indicate that hexasome orientation, which is influenced by the underlying DNA sequence in vivo, is important for modulating DNA accessibility to regulate transcription.

scholarly journals C-Jun NH2-Terminal Kinase and p38 Inhibition Suppresses Prostaglandin E2-Stimulated Aromatase and Estrogen Receptor Levels in Human Endometriosis

2015 ◽  
Vol 100 (11) ◽  
pp. E1404-E1414 ◽  
Author(s):  
Cheng Zeng ◽  
Jia-ning Xu ◽  
Yan Zhou ◽  
Hui-xia Yang ◽  
Ying-fang Zhou ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Transcription Factor ◽  
Prostaglandin E2 ◽  
Estrogen Metabolism ◽  
Promoter Regions ◽  
Endometrial Stromal Cells ◽  
Estrogen Production ◽  
Activating Transcription Factor

Context: Endometriosis is an estrogen-dependent disease. P38 and C-jun NH2-terminal kinase (JNK) inhibitors may have a therapeutic effect on endometriosis through regulation of prostaglandin E2 (PGE2)-induced estrogen metabolism. Objective: The objective of this study was to determine whether the activated MAPKs signaling pathway observed in human ectopic endometrial stromal cells (ESCs) from ovarian endometriomas influences levels of aromatase and estrogen receptor β (ERβ) protein regulated by PGE2. In turn, the effects of inhibiting MAPKs in the presence of PGE2 on estrogen production were investigated in vitro and in vivo. Results: Expression of aromatase and ERβ regulated by PGE2 were much higher in ESCs than eutopic ESCs from the same person. Activation of p38, JNK, ERK 1/2 and ERK 5 MAPKs by PGE2 were observed in ESCs, where PGE2-stimulated aromatase and ERβ expression mainly through p38 and JNK pathway. P38 and JNK inhibition or small interfering RNA knockdown blocked PGE2-induced aromatase and ERβ expression. PGE2 enhanced binding of downstream p38 and JNK transcription factors activating transcription factor-2 and c-Jun to aromatase and ERB promoter regions in ESCs. Moreover, treatment of endometriosis xenografts with inhibitors of p38 and JNK abrogated PGE2-amplified estradiol synthesis and xenograft growth. Conclusions: PGE2 activates p38 and JNK signaling pathways, further stimulating c-Jun and activating transcription factor-2 binding to aromatase and ERB promoter regions with elevated estradiol production. Inhibition of JNK and P38 may be a potential method of treating human endometriosis.

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution

2012 ◽  
Vol 40 (2) ◽  
pp. 377-382 ◽  
Author(s):  
Philipp Korber
Keyword(s):  
Dna Sequence ◽  
Nucleosome Occupancy ◽  
Nucleosome Positioning ◽  
Major Theme ◽  
Promoter Regions ◽  
Genome Wide ◽  
Nucleosome Formation ◽  
Dna Binders

Genome-wide nucleosome maps revealed well-positioned nucleosomes as a major theme in eukaryotic genome organization. Promoter regions often show a conserved pattern with an NDR (nucleosome-depleted region) from which regular nucleosomal arrays emanate. Three mechanistic contributions to such NDR-array-organization and nucleosome positioning in general are discussed: DNA sequence, DNA binders and DNA-templated processes. Especially, intrinsic biophysics of DNA sequence preferences for nucleosome formation was prominently suggested to explain the majority of nucleosome positions (‘genomic code for nucleosome positioning’). Nonetheless, non-histone factors that bind DNA with high or low specificity, such as transcription factors or remodelling enzymes respectively and processes such as replication, transcription and the so-called ‘statistical positioning’ may be involved too. Recently, these models were tested for yeast by genome-wide reconstitution. DNA sequence preferences as probed by SGD (salt gradient dialysis) reconstitution generated many NDRs, but only few individual nucleosomes, at their proper positions, and no arrays. Addition of a yeast extract and ATP led to dramatically more in vivo-like nucleosome positioning, including regular arrays for the first time. This improvement depended essentially on the extract and ATP but not on transcription or replication. Nucleosome occupancy and close spacing were maintained around promoters, even at lower histone density, arguing for active packing of nucleosomes against the 5′ ends of genes rather than statistical positioning. A first extract fractionation identified a direct, specific, necessary, but not sufficient role for the RSC (remodels the structure of chromatin) remodelling enzyme. Collectively, nucleosome positioning in yeast is actively determined by factors beyond intrinsic biophysics, and in steady-state rather than at equilibrium.

The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

2008 ◽  
Vol 36 (4) ◽  
pp. 637-639 ◽  
Author(s):  
Questa H. Karlsson ◽  
Celine Schelcher ◽  
Elizabeth Verrall ◽  
Carlo Petosa ◽  
Alison J. Sinclair
Keyword(s):  
Single Point ◽  
Cysteine Residue ◽  
Lytic Replication ◽  
Epigenetic Silencing ◽  
Lytic Cycle ◽  
Barr Virus ◽  
Cpg Motifs ◽  
Epstein Barr

EBV (Epstein–Barr virus) alternates between latency and lytic replication. During latency, the viral genome is largely silenced by host-driven methylation of CpG motifs and in the switch to the lytic cycle this epigenetic silencing is overturned. A key event is the activation of the viral protein Zta with three ZREs (Zta-response elements) from the BRLF1 promoter (referred to as Rp). Two of these ZREs contain CpG motifs and are methylated in the latent genome. Biochemical analyses and molecular modelling of Zta bound to methylated RpZRE3 indicate the precise contacts made between a serine and a cysteine residue of Zta with methyl cytosines. A single point mutant of Zta, C189S, is defective in binding to the methylated ZREs both in vitro and in vivo. This was used to probe the functional relevance of the interaction. ZtaC189S was not able to activate Rp in a B-cell line, demonstrating the relevance of the interaction with methylated ZREs. This demonstrates that Zta plays a role in overturning the epigenetic control of viral latency.

Metal-responsive transcription factor-1 (MTF-1) selects different types of metal response elements at low vs. high zinc concentration

2004 ◽  
Vol 385 (7) ◽  
Author(s):  
Y. Wang ◽  
I. Lorenzi ◽  
O. Georgiev ◽  
W. Schaffner
Keyword(s):  
Transcription Factor ◽  
Dna Sequence ◽  
Zinc Concentration ◽  
Sequence Motifs ◽  
Response Elements ◽  
High Zinc ◽  
Different Types ◽  
Zinc Concentrations ◽  
Dna Sequence Motifs ◽  
Transcription Factor 1

AbstractMetalresponsive transcription factor-1 (MTF-1) is a zinc finger protein with a central role in heavy metal homeostasis/ detoxification. MTF-1 binds to DNA sequence motifs known as metal response elements (MREs) with a core consensus TGCRCNC. Since MTF-1 is also involved in other stress responses, we tested whether it is able to recognize different types of DNA sequence motifs. To this end we selected MTF-1-binding oligonucleotides from a collection of random sequences. Since MTF-1 binds to known target sequences at relatively high zinc concentrations, oligonucleotide selection was performed in a mammalian cell nuclear extract both at high and low zinc concentrations. Irrespective of zinc concentration, we find a robust representation of MRE consensus sequences, however with specific features. Selection was most efficient at 100 M zinc, yielding many oligonucleotides with two MRE motifs in divergent orientation of the sequence

scholarly journals Occupancy patterns of 208 DNA-associated proteins in a single human cell type

2018 ◽  
Author(s):  
E. Christopher Partridge ◽  
Surya B. Chhetri ◽  
Jeremy W. Prokop ◽  
Ryne C. Ramaker ◽  
Camden S. Jansen ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Sequence Motifs ◽  
Cell Type ◽  
Occupancy Patterns ◽  
Genome Wide ◽  
Chromatin Regulator ◽  
Associated Proteins ◽  
Dna Sequence Motifs

SummaryGenome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes, but only a small fraction of the >1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains motifs for only a minority of the numerous associated DAPs. These analyses provide a deeper and more complete overview of the gene regulatory networks that define this cell type.

Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

2005 ◽  
Vol 83 (4) ◽  
pp. 535-547 ◽  
Author(s):  
Gareth N Corry ◽  
D Alan Underhill
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Nuclear Architecture ◽  
Subnuclear Localization ◽  
Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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