scholarly journals Evidence for a Bigenic Chromatin Subdomain in Regulation of the Fetal-to-Adult Hemoglobin Switch

2008 ◽  
Vol 29 (6) ◽  
pp. 1635-1648 ◽  
Author(s):  
Hugues Beauchemin ◽  
Marie Trudel
Keyword(s):  
Transcriptional Activation ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Open Chromatin ◽  
Chromosome Conformation ◽  
Hemoglobin Switching ◽  
Switching Patterns ◽  
Adult Hemoglobin ◽  
Globin Promoter

ABSTRACT During development, human β-globin locus regulation undergoes two critical switches, the embryonic-to-fetal and fetal-to-adult hemoglobin switches. To define the role of the fetal Aγ-globin promoter in switching, human β-globin-YAC transgenic mice were produced with the Aγ-globin promoter replaced by the erythroid porphobilinogen deaminase (PBGD) promoter (PBGDAγ-YAC). Activation of the stage-independent PBGDAγ-globin strikingly stimulated native Gγ-globin expression at the fetal and adult stages, identifying a fetal gene pair or bigenic cooperative mechanism. This impaired fetal silencing severely suppressed both δ- and β-globin expression in PBGDAγ-YAC mice from fetal to neonatal stages and altered kinetics and delayed switching of adult β-globin. This regulation evokes the two human globin switching patterns in the mouse. Both patterns of DNA demethylation and chromatin immunoprecipitation analysis correlated with gene activation and open chromatin. Locus control region (LCR) interactions detected by chromosome conformation capture revealed distinct spatial fetal and adult LCR bigenic subdomains. Since both intact fetal promoters are critical regulators of fetal silencing at the adult stage, we concluded that fetal genes are controlled as a bigenic subdomain rather than a gene-autonomous mechanism. Our study also provides evidence for LCR complex interaction with spatial fetal or adult bigenic functional subdomains as a niche for transcriptional activation and hemoglobin switching.

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 Identification of a novel enhancer of CEBPE essential for granulocytic differentiation

Blood ◽  
2019 ◽  
Vol 133 (23) ◽  
pp. 2507-2517 ◽  
Author(s):  
Pavithra Shyamsunder ◽  
Mahalakshmi Shanmugasundaram ◽  
Anand Mayakonda ◽  
Pushkar Dakle ◽  
Weoi Woon Teoh ◽  
...  
Keyword(s):  
Target Genes ◽  
Core Promoter ◽  
Transcriptional Start Site ◽  
Open Chromatin ◽  
Sequencing Data ◽  
Granulocytic Differentiation ◽  
Circular Chromosome ◽  
Chromosome Conformation ◽  
Guide Rna

Abstract CCAAT/enhancer binding protein ε (CEBPE) is an essential transcription factor for granulocytic differentiation. Mutations of CEBPE occur in individuals with neutrophil-specific granule deficiency (SGD), which is characterized by defects in neutrophil maturation. Cebpe-knockout mice also exhibit defects in terminal differentiation of granulocytes, a phenotype reminiscent of SGD. Analysis of DNase I hypersensitive sites sequencing data revealed an open chromatin region 6 kb downstream of the transcriptional start site of Cebpe in murine myeloid cells. We identified an interaction between this +6-kb region and the core promoter of Cebpe using circular chromosome conformation capture sequencing (4C-seq). To understand the role of this putative enhancer in transcriptional regulation of Cebpe, we targeted it using catalytically inactive Cas9 fused to Krüppel-associated box (KRAB) domain and observed a significant downregulation of transcript and protein levels of CEBPE in cells expressing guide RNA targeting the +6-kb region. To further investigate the role of this novel enhancer further in myelopoiesis, we generated mice with deletion of this region using CRISPR/Cas9 technology. Germline deletion of the +6-kb enhancer resulted in reduced levels of CEBPE and its target genes and caused a severe block in granulocytic differentiation. We also identified binding of CEBPA and CEBPE to the +6-kb enhancer, which suggests their role in regulating the expression of Cebpe. In summary, we have identified a novel enhancer crucial for regulating expression of Cebpe and required for normal granulocytic differentiation.

scholarly journals Histone Code Modifications on Pluripotential Nuclei of Reprogrammed Somatic Cells

2004 ◽  
Vol 24 (13) ◽  
pp. 5710-5720 ◽  
Author(s):  
Hironobu Kimura ◽  
Masako Tada ◽  
Norio Nakatsuji ◽  
Takashi Tada
Keyword(s):  
Transcriptional Activation ◽  
Es Cells ◽  
Gene Activation ◽  
Embryonic Stem ◽  
Dna Demethylation ◽  
Gene Activity ◽  
Current Evidence ◽  
Hybrid Cells ◽  
Promoter Regions ◽  
Somatic Genome

ABSTRACT Following hybridization with embryonic stem (ES) cells, somatic genomes are epigenetically reprogrammed and acquire pluripotency. This results in the transcription of somatic genome-derived tissue-specific genes upon differentiation. During nuclear reprogramming, it is expected that DNA and chromatin modifications, believed to function in cell-type-specific epigenotype memory, should be significantly modified. Indeed, current evidence indicates that acetylation and methylation of histone H3 and H4 amino termini play a major role in the regulation of gene activity through the modulation of chromatin conformation. Here, we show that the reprogrammed somatic genome of ES hybrid cells becomes hyperacetylated at H3 and H4, while lysine 4 (K4) of H3 becomes globally hyper-di- and -tri-methylated. In the Oct4 promoter region, histones H3 and H4 are acetylated and H3-K4 is highly tri-methylated on both the ES and reprogrammed somatic genomes, which correlates with gene activation and DNA demethylation. However, H3-K4 is also di- and tri-methylated in the promoter regions of Neurofilament-M (Nfm), Nfl, and Thy-1, which are all silent in both ES and hybrid cells. Thus, H3-K4 di- and tri-methylation of reprogrammed somatic genomes is independent of gene activity and represents one of the major events that occurs during somatic genome reprogramming towards a transcriptional activation-permissive state.

scholarly journals Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus

2000 ◽  
Vol 14 (8) ◽  
pp. 940-950 ◽  
Author(s):  
Dirk Schübeler ◽  
Claire Francastel ◽  
Daniel M. Cimbora ◽  
Andreas Reik ◽  
David I.K. Martin ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Transcriptional Activity ◽  
Globin Gene ◽  
Gene Activation ◽  
Histone H3 ◽  
Centromeric Heterochromatin ◽  
Open Chromatin ◽  
Globin Genes ◽  
High Level ◽  
Chromatin Opening

We have investigated the mechanism, structural correlates, andcis-acting elements involved in chromatin opening and gene activation, using the human β-globin locus as a model. Full transcriptional activity of the human β-globin locus requires the locus control region (LCR), composed of a series of nuclease hypersensitive sites located upstream of this globin gene cluster. Our previous analysis of naturally occurring and targeted LCR deletions revealed that chromatin opening and transcriptional activity in the endogenous β-globin locus are dissociable and dependent on distinctcis-acting elements. We now report that general histone H3/H4 acetylation and relocation of the locus away from centromeric heterochromatin in the interphase nucleus are correlated and do not require the LCR. In contrast, LCR-dependent promoter activation is associated with localized histone H3 hyperacetylation at the LCR and the transcribed β-globin-promoter and gene. On the basis of these results, we suggest a multistep model for gene activation; localization away from centromeric heterochromatin is required to achieve general hyperacetylation and an open chromatin structure of the locus, whereas a mechanism involving LCR/promoter histone H3 hyperacetylation is required for high-level transcription of the β-globin genes.

Analysis of the light regulatory mechanism in carotenoid production in Rhodosporidium toruloides NBRC 10032

2021 ◽  
Author(s):  
Khanh Dung Pham ◽  
Yuuki Hakozaki ◽  
Takeru Takamizawa ◽  
Atsushi Yamazaki ◽  
Harutake Yamazaki ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Oleaginous Yeast ◽  
Gene Activation ◽  
Light Response ◽  
Carotenoid Biosynthesis ◽  
Rhodosporidium Toruloides ◽  
End Joining ◽  
Carotenoid Production ◽  
Non Homologous End Joining

Abstract Light stimulates carotenoid production in an oleaginous yeast Rhodosporidium toruloides NBRC 10032 by promoting carotenoid biosynthesis genes. These genes undergo two-step of transcriptional activation. The potential light regulator, Cryptochrome DASH (CRY1), has been suggested to contribute to this mechanism. In this study, based on KU70 (a component of non-homologous end joining (NHEJ)) disrupting background, CRY1 disruptant was constructed to clarify CRY1 function. From analysis of CRY1 disruptant, it was suggested that CRY1 has the activation role of the carotenogenic gene expression. To obtain further insights into the light response, mutants varying carotenoid production were generated. Through analysis of mutants, the existence of the control two-step gene activation was proposed. In addition, our data analysis showed the strong possibility that R. toruloides NBRC 10032 is a homo-diploid strain.

Butyrate induces selective transcriptional activation of a hypomethylated embryonic globin gene in adult erythroid cells

Blood ◽  
1988 ◽  
Vol 72 (5) ◽  
pp. 1536-1542
Author(s):  
LJ Burns ◽  
JG Glauber ◽  
GD Ginder
Keyword(s):  
Sodium Butyrate ◽  
Transcriptional Activation ◽  
Globin Gene ◽  
Gene Activation ◽  
Globin Genes ◽  
Erythroid Cells ◽  
Hemoglobin Switching ◽  
High Level

An animal model of hemoglobin switching has been developed in which anemic adult chickens are treated with 5-azacytidine and sodium butyrate or alpha-aminobutyric acid, thereby resulting in activation of the embryonic rho-globin gene in adult erythroid cells. In vitro nuclear runoff transcription assays using erythroid nuclei from treated birds show that the mechanism of activation of the rho-globin gene is transcriptional whereas no transcriptional activation of the embryonic epsilon-globin gene occurs. The action of 5-azacytidine appears to be as an inhibitor of DNA methylation because other S-phase active cytotoxic drugs, when substituted for 5-azacytidine, do not cause demethylation of the embryonic globin genes, nor do they allow transcriptional activation to occur. Embryonic rho-globin gene activation in this model is not due to selection of primitive erythroid cells since a subpopulation of primitive erythroid cells is not evident either morphologically or when cells are probed for embryonic and adult globin RNA by in situ hybridization. These studies show that demethylation by 5-azacytidine is a prerequisite but not sufficient cis- regulatory event for a high level of transcriptional activation of the embryonic rho-globin gene in adult erythroid cells in vivo. The possible basis for the selective transcriptional activation by sodium butyrate in this system is discussed.

scholarly journals Promoter Specificity and Biological Activity of Tethered AP-1 Dimers

2002 ◽  
Vol 22 (13) ◽  
pp. 4952-4964 ◽  
Author(s):  
Latifa Bakiri ◽  
Koichi Matsuo ◽  
Marta Wisniewska ◽  
Erwin F. Wagner ◽  
Moshe Yaniv
Keyword(s):  
Transcriptional Activation ◽  
Gene Activation ◽  
Dominant Negative ◽  
Activator Protein 1 ◽  
Loss Of Function ◽  
Single Chain ◽  
Promoter Specificity ◽  
Cycle Regulation ◽  
Nih 3T3

ABSTRACT Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of Jun, Fos, and ATF family proteins. Both gain- and loss-of-function studies have revealed specific roles for individual AP-1 components in cell proliferation, differentiation, apoptosis, and other biological processes. However, little is known about the functions of specific AP-1 dimers. To test the importance of AP-1 composition in transcriptional activation, AP-1 monomers were joined via a flexible polypeptide tether to force specific pairing. The resultant single-chain AP-1 molecules showed DNA binding specificity and transcriptional activation potentials similar to those of untethered dimers, even in the presence of dominant-negative AP-1 monomers. c-Jun-containing dimers showed distinct promoter specificity in transient-transfection experiments, depending on the Fos, Fra, or ATF partner. When stably expressed in NIH 3T3 cells, c-Jun∼Fra2, but not c-Jun∼Fra1 and c-Jun∼cFos (the tilde indicates a tethered dimer), inhibited G0 arrest at confluency and under low-serum conditions and specifically activated cyclin A expression. These data suggest that the choice of dimerization partner defines the role of c-Jun in gene activation and cell cycle regulation and that single-chain AP-1 molecules provide a powerful tool for assessing the role of specific AP-1 dimers.

scholarly journals Butyrate induces selective transcriptional activation of a hypomethylated embryonic globin gene in adult erythroid cells

Blood ◽  
1988 ◽  
Vol 72 (5) ◽  
pp. 1536-1542 ◽  
Author(s):  
LJ Burns ◽  
JG Glauber ◽  
GD Ginder
Keyword(s):  
Sodium Butyrate ◽  
Transcriptional Activation ◽  
Globin Gene ◽  
Gene Activation ◽  
Globin Genes ◽  
Erythroid Cells ◽  
Hemoglobin Switching ◽  
High Level

Abstract An animal model of hemoglobin switching has been developed in which anemic adult chickens are treated with 5-azacytidine and sodium butyrate or alpha-aminobutyric acid, thereby resulting in activation of the embryonic rho-globin gene in adult erythroid cells. In vitro nuclear runoff transcription assays using erythroid nuclei from treated birds show that the mechanism of activation of the rho-globin gene is transcriptional whereas no transcriptional activation of the embryonic epsilon-globin gene occurs. The action of 5-azacytidine appears to be as an inhibitor of DNA methylation because other S-phase active cytotoxic drugs, when substituted for 5-azacytidine, do not cause demethylation of the embryonic globin genes, nor do they allow transcriptional activation to occur. Embryonic rho-globin gene activation in this model is not due to selection of primitive erythroid cells since a subpopulation of primitive erythroid cells is not evident either morphologically or when cells are probed for embryonic and adult globin RNA by in situ hybridization. These studies show that demethylation by 5-azacytidine is a prerequisite but not sufficient cis- regulatory event for a high level of transcriptional activation of the embryonic rho-globin gene in adult erythroid cells in vivo. The possible basis for the selective transcriptional activation by sodium butyrate in this system is discussed.

scholarly journals GR-mediated transcriptional regulation of m6A metabolic genes contributes to diet-induced fatty liver in hens

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yue Feng ◽  
Yanlin Li ◽  
Wenduo Jiang ◽  
Yun Hu ◽  
Yimin Jia ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Fatty Liver ◽  
Transcriptional Activation ◽  
Laying Hens ◽  
Gene Activation ◽  
High Energy ◽  
Lipogenic Genes ◽  
Low Protein ◽  
Metabolic Genes

Abstract Background Glucocorticoid receptor (GR) mediated corticosterone-induced fatty liver syndrome (FLS) in the chicken by transactivation of Fat mass and obesity associated gene (FTO), leading to demethylation of N6-methyladenosine (m6A) and post-transcriptional activation of lipogenic genes. Nutrition is considered the main cause of FLS in the modern poultry industry. Therefore, this study was aimed to investigate whether GR and m6A modification are involved in high-energy and low protein (HELP) diet-induced FLS in laying hens, and if true, what specific m6A sites of lipogenic genes are modified and how GR mediates m6A-dependent lipogenic gene activation in HELP diet-induced FLS in the chicken. Results Laying hens fed HELP diet exhibit excess (P < 0.05) lipid accumulation and lipogenic genes activation in the liver, which is associated with significantly increased (P < 0.05) GR expression that coincided with global m6A demethylation. Concurrently, the m6A demethylase FTO is upregulated (P < 0.05), whereas the m6A reader YTHDF2 is downregulated (P < 0.05) in the liver of FLS chickens. Further analysis identifies site-specific demethylation (P < 0.05) of m6A in the mRNA of lipogenic genes, including FASN, SREBP1 and SCD. Moreover, GR binding to the promoter of FTO gene is highly enriched (P < 0.05), while GR binding to the promoter of YTHDF2 gene is diminished (P < 0.05). Conclusions These results implicate a possible role of GR-mediated transcriptional regulation of m6A metabolic genes on m6A-depenent post-transcriptional activation of lipogenic genes and shed new light in the molecular mechanism of FLS etiology in the chicken.

scholarly journals Ligand-induced gene activation is associated with oxidative genome damage whose repair is required for transcription

2020 ◽  
Vol 117 (36) ◽  
pp. 22183-22192 ◽  
Author(s):  
Shiladitya Sengupta ◽  
Haibo Wang ◽  
Chunying Yang ◽  
Bartosz Szczesny ◽  
Muralidhar L. Hegde ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Excision Repair ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Single Strand ◽  
Gene Promoters ◽  
Single Strand Break ◽  
Strand Breaks ◽  
Genome Damage

Among several reversible epigenetic changes occurring during transcriptional activation, only demethylation of histones and cytosine-phosphate-guanines (CpGs) in gene promoters and other regulatory regions by specific demethylase(s) generates reactive oxygen species (ROS), which oxidize DNA and other cellular components. Here, we show induction of oxidized bases and single-strand breaks (SSBs), but not direct double-strand breaks (DSBs), in the genome during gene activation by ligands of the nuclear receptor superfamily. We observed that these damages were preferentially repaired in promoters via the base excision repair (BER)/single-strand break repair (SSBR) pathway. Interestingly, BER/SSBR inhibition suppressed gene activation. Constitutive association of demethylases with BER/SSBR proteins in multiprotein complexes underscores the coordination of histone/DNA demethylation and genome repair during gene activation. However, ligand-independent transcriptional activation occurring during heat shock (HS) induction is associated with the generation of DSBs, the repair of which is likewise essential for the activation of HS-responsive genes. These observations suggest that the repair of distinct damages induced during diverse transcriptional activation is a universal prerequisite for transcription initiation. Because of limited investigation of demethylation-induced genome damage during transcription, this study suggests that the extent of oxidative genome damage resulting from various cellular processes is substantially underestimated.

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