Differentiation Dependent Dynamics of Histone Modifications during Myelopoiesis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2716-2716
Author(s):  
Robert G. Harris ◽  
Diane Krause
Keyword(s):  
Gene Expression ◽  
Gene Transcription ◽  
Histone Modifications ◽  
Transcriptional Activation ◽  
Gene Activation ◽  
Chromatin Modification ◽  
Gene Expression Pattern ◽  
Chromatin Accessibility ◽  
Induced Differentiation ◽  
Control Of Gene Expression

Abstract Covalent modifications on histones are epigenetic changes that play critical roles in control of gene expression. Most studies correlating specific histone modifications with transcriptional activity have been performed in yeast, and little is known about their dynamics during hematopoietic differentiation. We examined the dynamics of histone modifications and chromatin accessibility during all-trans retinoic acid (ATRA) induced differentiation of promyelocytes down the neutrophil lineage. As a model system, we used the human promyelocytic NB4 cell line, which undergoes neutrophil differentiation in response to ATRA. Using chromatin immunoprecipitation (ChIP) and quantitative PCR, we measured changes in dimethyl K4 (2MeH3K4), trimethyl K4 (3MeH3K4) and acetyl lysine 9 (Ac9H3K9) of histone H3 in the promoters of 3 genes that undergo transcriptional activation (Defensin-a, C/EBP-b and RAR-b), 1 gene that undergoes transcriptional downregulation (Myeloperoxidase), one gene that is constitutively active (GAPDH) and 1 gene that is silent (Albumin) during ATRA-induced differentiation. We correlated the changes in histone modifications with the gene expression pattern of these genes. AcH3K9 levels correlated with active gene transcription. At time 0, levels of AcH3K9 were enriched 50-fold and 100-fold over input in the MPO and GAPDH promoters, respectively, but only 5-fold on the C/EBP-b, Def-a and RAR-b promoters. Consistent with this finding, levels of AcH3K9 increased to 40-fold over input within 24h of differentiation in the Def-a and C/EBP-b promoters. On the silent albumin promoter, AcH3K9 levels never increased over input after ATRA. For the methylation patterns on H3K4, however, the findings were quite revealing. As expected, on the active MPO promoter, 2MeH3K4 was enriched 60-fold. However, 2MeH3K4was also present at high levels (15-30-fold) on the promoters of unexpressed Def-a, C/EBP-b and RAR-b suggesting that silent genes that are “primed” for activation are enriched for 2MeH3K4, consistent with previous data in yeast. After differentiation with ATRA, 2MeH3K4 went up only 3-fold for Def-a and C/EBP-b. The most surprising changes were found in 3MeH3K4 levels and in chromatin modification at the RAR-b promoter. Consistent with previous data showing that 3MeH3K4 is associated with gene activation, time 0 levels of 3MeH3K4 were enriched 80-fold and 150-fold over input in the MPO and GAPDH promoters, respectively, and were at background levels in the C/EBP-b, Def-a, and RAR-b promoters. After differentiation, however, although there was a significant increase in 3MeH3K4 levels within 12 hours in the Def-a promoter, 3MeH3K4 never was present on the C/EBP-b promoter, despite a huge increase in gene transcription, as well as significant and rapid increases in AcH3K9 and 2MeH3K4. Perhaps the most significant findings, however, were at the promoter of the RAR-b gene. RAR-b is unique amongst the genes studies in that it is directly bound by the PML-RAR-a fusion protein. This promoter was not detectable by PCR in ChIP assays after ATRA addition. To test the hypothesis that histones were lost on the RAR-b promoter during ATRA-induced differentiation, we used MNase digestion of chromatin. Nucleosome loss was confirmed by a decrease in precipitated RAR-b promoter DNA within 24 hours of ATRA addition. In contrast, exon1 of RAR-b was modified in a manner similar to Def-a and C/EBP-b. These findings indicate that despite the seemingly coordinately regulated increase in transcription of multiple genes upon myeloid differentiation, the chromatin modifications on the promoters of these genes are regulated quite differently.

scholarly journals Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

2016 ◽  
Author(s):  
Alexis Vandenbon ◽  
Yutaro Kumagai ◽  
Yutaka Suzuki ◽  
Kenta Nakai
Keyword(s):  
Gene Expression ◽  
Dendritic Cells ◽  
Histone Modifications ◽  
Transcriptional Activation ◽  
Control Of Gene Expression ◽  
Time Series Dataset ◽  
Binding Data ◽  
A Genome ◽  
Extracellular Stimuli ◽  
Wide Scale

AbstractBackgroundThe importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyzed the ordering of these events on a genome-wide scale in dendritic cells (DCs) in response to lipopolysaccharide (LPS) stimulation.ResultsUsing a ChIP-seq time series dataset, we found that the LPS-induced accumulation of different histone modifications follow clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data revealed potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 were associated with binding by STAT1/2, and were severely impaired inStat1-/-cells.ConclusionsWhile the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs, and their interactions with chromatin modifiers.

scholarly journals A copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana.

2021 ◽  
Author(s):  
Elena Garcia-Perez ◽  
Borja Diego-Martin ◽  
Alfredo Quijano-Rubio ◽  
Elena Moreno Gimenez ◽  
Diego Orzaez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Nicotiana Benthamiana ◽  
Gene Networks ◽  
Rna Binding ◽  
Gene Activation ◽  
Dependent Manner ◽  
Copper Binding ◽  
Control Of Gene Expression ◽  
Guide Rna

CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations in place, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold for the endogenous N. benthamiana DFR gene, with negligible expression in the absence of the trigger. The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

scholarly journals HOS15 is a transcriptional corepressor of NPR1-mediated gene activation of plant immunity

2020 ◽  
Vol 117 (48) ◽  
pp. 30805-30815
Author(s):  
Mingzhe Shen ◽  
Chae Jin Lim ◽  
Junghoon Park ◽  
Jeong Eun Kim ◽  
Dongwon Baek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ubiquitin Ligase ◽  
Transcriptional Activation ◽  
Plant Immunity ◽  
Gene Activation ◽  
Transcriptional Corepressor ◽  
Defense Gene Expression ◽  
Dynamic Regulation ◽  
Defense Gene ◽  
Transcriptional Corepressors

Transcriptional regulation is a complex and pivotal process in living cells. HOS15 is a transcriptional corepressor. Although transcriptional repressors generally have been associated with inactive genes, increasing evidence indicates that, through poorly understood mechanisms, transcriptional corepressors also associate with actively transcribed genes. Here, we show that HOS15 is the substrate receptor for an SCF/CUL1 E3 ubiquitin ligase complex (SCFHOS15) that negatively regulates plant immunity by destabilizing transcriptional activation complexes containing NPR1 and associated transcriptional activators. In unchallenged conditions, HOS15 continuously eliminates NPR1 to prevent inappropriate defense gene expression. Upon defense activation, HOS15 preferentially associates with phosphorylated NPR1 to stimulate rapid degradation of transcriptionally active NPR1 and thus limit the extent of defense gene expression. Our findings indicate that HOS15-mediated ubiquitination and elimination of NPR1 produce effects contrary to those of CUL3-containing ubiquitin ligase that coactivate defense gene expression. Thus, HOS15 plays a key role in the dynamic regulation of pre- and postactivation host defense.

scholarly journals Gene activation precedes DNA demethylation in response to infection in human dendritic cells

2019 ◽  
Vol 116 (14) ◽  
pp. 6938-6943 ◽  
Author(s):  
Alain Pacis ◽  
Florence Mailhot-Léonard ◽  
Ludovic Tailleux ◽  
Haley E. Randolph ◽  
Vania Yotova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dendritic Cells ◽  
Transcriptional Activation ◽  
Time Course ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Epigenetic Mark ◽  
Distal Enhancer ◽  
Human Dendritic Cells

DNA methylation is considered to be a relatively stable epigenetic mark. However, a growing body of evidence indicates that DNA methylation levels can change rapidly; for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells withMycobacterium tuberculosis. We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements. However, virtually all changes in gene expression in response to infection occur before detectable changes in DNA methylation, indicating that the observed losses in methylation are a downstream consequence of transcriptional activation. Footprinting analysis revealed that immune-related transcription factors (TFs), such as NF-κB/Rel, are recruited to enhancer elements before the observed losses in methylation, suggesting that DNA demethylation is mediated by TF binding to cis-acting elements. Collectively, our results show that DNA demethylation plays a limited role to the establishment of the core regulatory program engaged upon infection.

scholarly journals Purification and characterization of the stage-specific embryonic enhancer-binding protein SSAP-1.

1993 ◽  
Vol 13 (3) ◽  
pp. 1746-1758 ◽  
Author(s):  
D J DeAngelo ◽  
J DeFalco ◽  
G Childs
Keyword(s):  
Gene Expression ◽  
Molecular Weight ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Gene Activation ◽  
Upstream Sequence ◽  
Blastula Stage ◽  
Sequence Element ◽  
Enhancer Element ◽  
Beta Gene

We have demonstrated that a highly conserved segment of DNA between positions -288 and -317 (upstream sequence element IV [USE IV]) is largely responsible for the transcriptional activation of the sea urchin H1-beta histone gene during the blastula stage of embryogenesis. This sequence is capable of acting as an embryonic enhancer element, activating target genes in a stage-specific manner. Nuclear extracts prepared from developmentally-staged organisms before and after the gene is activated all contain a factor which specifically binds to the enhancer. We have purified a 43-kDa polypeptide which binds to and footprints the USE IV enhancer element. We refer to this protein as stage-specific activator protein 1 (SSAP-1). Early in development before the enhancer is active, SSAP appears as a 43-kDa monomer, but it undergoes a change in its molecular weight beginning at about 12 h postfertilization (early blastula) which precisely parallels the increase in H1-beta gene expression. Modified SSAP has an apparent molecular mass of approximately 90 to 100 kDa and contains at least one 43-kDa SSAP polypeptide. Thus, it is the disappearance of the 43-kDa species and the appearance of the 90- to 100-kDa species which coincide with the H1-beta gene activation. The correlation between the change in molecular weight of SSAP and the stage-specific activation of H1-beta gene expression strongly suggests that this higher-molecular-weight form of SSAP is directly responsible for the blastula stage-specific transcriptional activation of the late H1 gene.

scholarly journals Phosphorylated forms of GAL4 are correlated with ability to activate transcription.

1990 ◽  
Vol 10 (9) ◽  
pp. 4623-4629 ◽  
Author(s):  
L M Mylin ◽  
M Johnston ◽  
J E Hopper
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Polyacrylamide Gel Electrophoresis ◽  
Gene Activation ◽  
Sodium Dodecyl ◽  
Immunoblot Analysis ◽  
Transcriptional Activator Protein ◽  
Mel Gene ◽  
High Level

GAL4I, GAL4II, and GAL4III are three forms of the yeast transcriptional activator protein that are readily distinguished on the basis of electrophoretic mobility during sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Phosphorylation accounts for the reduced mobility of the slowest-migrating form, GAL4III, which is found to be closely associated with high-level GAL/MEL gene expression (L. Mylin, P. Bhat, and J. Hopper, Genes Dev. 3:1157-1165, 1989). Here we show that GAL4II, like GAL4III, can be converted to GAL4I by phosphatase treatment, suggesting that in vivo GAL4II is derived from GAL4I by phosphorylation. We found that cells which overproduced GAL4 under conditions in which it drove moderate to low levels of GAL/MEL gene expression showed only forms GAL4I and GAL4II. To distinguish which forms of GAL4 (GAL4I, GAL4II, or both) might be responsible for transcription activation in the absence of GAL4III, we performed immunoblot analysis on UASgal-binding-competent GAL4 proteins from four gal4 missense mutants selected for their inability to activate transcription (M. Johnston and J. Dover, Proc. Natl. Acad. Sci. USA 84:2401-2405, 1987; Genetics 120;63-74, 1988). The three mutants with no detectable GAL1 expression did not appear to form GAL4II or GAL4III, but revertants in which GAL4-dependent transcription was restored did display GAL4II- or GAL4III-like electrophoretic species. Detection of GAL4II in a UASgal-binding mutant suggests that neither UASgal binding nor GAL/MEL gene activation is required for the formation of GAL4II. Overall, our results imply that GAL4I may be inactive in transcriptional activation, whereas GAL4II appears to be active. In light of this work, we hypothesize that phosphorylation of GAL4I makes it competent to activate transcription.

scholarly journals Retrotransposon expression as a defining event of genome reprograming in fertilized and cloned bovine embryos

Reproduction ◽  
2009 ◽  
Vol 138 (2) ◽  
pp. 289-299 ◽  
Author(s):  
L C Bui ◽  
A V Evsikov ◽  
D R Khan ◽  
C Archilla ◽  
N Peynot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Ribosomal Proteins ◽  
Gene Expression Pattern ◽  
Cdna Array ◽  
Ltr Retrotransposons ◽  
Bovine Embryos ◽  
Genes Encoding ◽  
Low Efficiency ◽  
Cloned Bovine

Genome reprograming is the ability of a nucleus to modify its epigenetic characteristics and gene expression pattern when placed in a new environment. Low efficiency of mammalian cloning is attributed to the incomplete and aberrant nature of genome reprograming after somatic cell nuclear transfer (SCNT) in oocytes. To date, the aspects of genome reprograming critical for full-term development after SCNT remain poorly understood. To identify the key elements of this process, changes in gene expression during maternal-to-embryonic transition in normal bovine embryos and changes in gene expression between donor cells and SCNT embryos were compared using a new cDNA array dedicated to embryonic genome transcriptional activation in the bovine. Three groups of transcripts were mostly affected during somatic reprograming: endogenous terminal repeat (LTR) retrotransposons and mitochondrial transcripts were up-regulated, while genes encoding ribosomal proteins were downregulated. These unexpected data demonstrate specific categories of transcripts most sensitive to somatic reprograming and likely affecting viability of SCNT embryos. Importantly, massive transcriptional activation of LTR retrotransposons resulted in similar levels of their transcripts in SCNT and fertilized embryos. Taken together, these results open a new avenue in the quest to understand nuclear reprograming driven by oocyte cytoplasm.

scholarly journals Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis

2020 ◽  
Author(s):  
Beatrice Borsari ◽  
Pablo Villegas-Mirón ◽  
Hafid Laayouni ◽  
Alba Segarra-Casas ◽  
Jaume Bertranpetit ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryonic Stem ◽  
Gene Expression Pattern ◽  
Specific Gene ◽  
Control Of Gene Expression ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression ◽  
Expression Of Genes ◽  
Genomic Location

AbstractTissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic location of enhancers and their role in tissue-specific gene expression. We found that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, while housekeeping genes are more often controlled by intergenic enhancers. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, while the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic location of active enhancers is key for the tissue-specific control of gene expression.

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