scholarly journals Distinct Functions of Dispersed GATA Factor Complexes at an Endogenous Gene Locus

2006 ◽  
Vol 26 (19) ◽  
pp. 7056-7067 ◽  
Author(s):  
Jeffrey A. Grass ◽  
Huie Jing ◽  
Shin-Il Kim ◽  
Melissa L. Martowicz ◽  
Saumen Pal ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Histone Deacetylation ◽  
Gata Factor ◽  
Enhancer Activity ◽  
Chromosome Conformation ◽  
Endogenous Gene ◽  
Chromatin Interactions ◽  
Active Locus ◽  
Genomic Microarray ◽  
Estrogen Receptor Ligand

ABSTRACT The reciprocal expression of GATA-1 and GATA-2 during hematopoiesis is an important determinant of red blood cell development. Whereas Gata2 is preferentially transcribed early in hematopoiesis, elevated GATA-1 levels result in GATA-1 occupancy at sites upstream of the Gata2 locus and transcriptional repression. GATA-2 occupies these sites in the transcriptionally active locus, suggesting that a “GATA switch” abrogates GATA-2-mediated positive autoregulation. Chromatin immunoprecipitation (ChIP) coupled with genomic microarray analysis and quantitative ChIP analysis with GATA-1-null cells expressing an estrogen receptor ligand binding domain fusion to GATA-1 revealed additional GATA switches 77 kb upstream of Gata2 and within intron 4 at +9.5 kb. Despite indistinguishable GATA-1 occupancy at −77 kb and +9.5 kb versus other GATA switch sites, GATA-1 functioned uniquely at the different regions. GATA-1 induced histone deacetylation at and near Gata2 but not at the −77 kb region. The −77 kb region, which was DNase I hypersensitive in both active and inactive states, conferred equivalent enhancer activities in GATA-1- and GATA-2-expressing cells. By contrast, the +9.5 kb region exhibited considerably stronger enhancer activity in GATA-2- than in GATA-1-expressing cells, and other GATA switch sites were active only in GATA-1- or GATA-2-expressing cells. Chromosome conformation capture analysis demonstrated higher-order interactions between the −77 kb region and Gata2 in the active and repressed states. These results indicate that dispersed GATA factor complexes function via long-range chromatin interactions and qualitatively distinct activities to regulate Gata2 transcription.

scholarly journals Friend of GATA-1–independent transcriptional repression: a novel mode of GATA-1 function

Blood ◽  
2007 ◽  
Vol 109 (12) ◽  
pp. 5230-5233 ◽  
Author(s):  
Kirby D. Johnson ◽  
Meghan E. Boyer ◽  
Jeong-Ah Kang ◽  
Amittha Wickrema ◽  
Alan B. Cantor ◽  
...  
Keyword(s):  
Cell Line ◽  
Transcriptional Activation ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Ex Vivo ◽  
Gata Factor ◽  
Null Cell ◽  
Interacting Protein ◽  
Defective Mutant ◽  
Estrogen Receptor Ligand

Abstract The GATA-1–interacting protein Friend Of GATA-1 (FOG-1) is essential for the proper transcriptional activation and repression of numerous GATA-1 target genes. Although FOG-1–independent activation by GATA-1 has been described, all known examples of GATA-1–mediated repression are FOG-1 dependent. In the GATA-1–null G1E cell line, estrogen receptor ligand binding domain (ER) chimeras of either wild-type GATA-1 or a FOG-1–binding defective mutant of GATA-1 repressed several genes similarly upon activation with β-estradiol. Repression also occurred in a FOG-1–null cell line expressing ER–GATA-1 and during ex vivo erythropoiesis. At the Lyl1 and Rgs18 loci, we found highly restricted occupancy by GATA-1 and GATA-2, indicating that these genes are direct targets of GATA factor regulation. The identification of genes repressed by GATA-1 independent of FOG-1 defines a novel mode of GATA-1–mediated transcriptional regulation.

Conserved and distinct roles of kreisler in regulation of the paralogous Hoxa3 and Hoxb3 genes

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 759-769 ◽  
Author(s):  
M. Manzanares ◽  
S. Cordes ◽  
L. Ariza-McNaughton ◽  
V. Sadl ◽  
K. Maruthainar ◽  
...  
Keyword(s):  
Binding Sites ◽  
Hox Genes ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Enhancer Activity ◽  
Anteroposterior Patterning ◽  
Endogenous Gene ◽  
Transgenic Embryos ◽  
The Individual ◽  
Segmental Expression

During anteroposterior patterning of the developing hindbrain, the anterior expression of 3′ Hox genes maps to distinct rhombomeric boundaries and, in many cases, is upregulated in specific segments. Paralogous genes frequently have similar anterior boundaries of expression but it is not known if these are controlled by common mechanisms. The expression of the paralogous Hoxa3 and Hoxb3 genes extends from the posterior spinal cord up to the rhombomere (r) 4/5 boundary and both genes are upregulated specifically in r5. However, in this study, we have found that Hoxa3 expression is also upregulated in r6, showing that there are differences in segmental expression between paralogues. We have used transgenic analysis to investigate the mechanisms underlying the pattern of segmental expression of Hoxa3. We found that the intergenic region between Hoxa3 and Hoxa4 contains several enhancers, which summed together mediate a pattern of expression closely resembling that of the endogenous Hoxa3 gene. One enhancer specifically directs expression in r5 and r6, in a manner that reflects the upregulation of the endogenous gene in these segments. Deletion analysis localized this activity to a 600 bp fragment that was found to contain a single high-affinity binding site for the Maf bZIP protein Krml1, encoded by the kreisler gene. This site is necessary for enhancer activity and when multimerized it is sufficient to direct a kreisler-like pattern in transgenic embryos. Furthermore the r5/r6 enhancer activity is dependent upon endogenous kreisler and is activated by ectopic kreisler expression. This demonstrates that Hoxa3, along with its paralog Hoxb3, is a direct target of kreisler in the mouse hindbrain. Comparisons between the Krml1-binding sites in the Hoxa3 and Hoxb3 enhancers reveal that there are differences in both the number of binding sites and way that kreisler activity is integrated and restricted by these two control regions. Analysis of the individual sites revealed that they have different requirements for mediating r5/r6 and dorsal roof plate expression. Therefore, the restriction of Hoxb3 to r5 and Hoxa3 to r5 and r6, together with expression patterns of Hoxb3 in other vertebrate species suggests that these regulatory elements have a common origin but have later diverged during vertebrate evolution.

scholarly journals The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae

2004 ◽  
Vol 24 (11) ◽  
pp. 4769-4780 ◽  
Author(s):  
Jennifer G. Aparicio ◽  
Christopher J. Viggiani ◽  
Daniel G. Gibson ◽  
Oscar M. Aparicio
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Deacetylase ◽  
Transcriptional Repression ◽  
Replication Timing ◽  
Histone Deacetylation ◽  
Origin Firing ◽  
Replication Checkpoint ◽  
Genome Transcription ◽  
Late Origin

ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.

scholarly journals ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming

2020 ◽  
Author(s):  
Fei Li ◽  
Qiuyue Yuan ◽  
Wei Di ◽  
Xinyi Xia ◽  
Zhuang Liu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cell Fate ◽  
Early Stage ◽  
Cell Lineage ◽  
Basal Cells ◽  
Distal Enhancer ◽  
Enhancer Activity ◽  
Prostate Cell ◽  
Knock Out ◽  
Chromatin Interactions

AbstractWhile cancer is commonly perceived as a disease of dedifferentiation, the hallmark of early stage prostate cancer is paradoxically the loss of more plastic basal cells and the abnormal proliferation of more differentiated secretory luminal cells. However, the mechanism of prostate cancer pro-luminal differentiation is largely unknown. Through integrating analysis of the transcription factors (TFs) from 806 human prostate cancers, we have identified that ERG highly correlated with prostate cancer luminal subtyping. ERG overexpression in luminal epithelial cells inhibits its normal plasticity to transdifferentiate into basal lineage and ERG supersedes PTEN-loss which favors basal differentiation. ERG knock-out disrupted prostate cell luminal differentiation, whereas AR knock-out had no such effects. Trp63 is a known master regulator of prostate basal lineage. Through analysis of 3D chromatin architecture, we found that ERG binds and inhibits the enhancer activity and chromatin looping of a Trp63 distal enhancer, thereby silencing its gene expression. Specific deletion of the distal ERG binding site resulted in the loss of ERG-mediated inhibition of basal differentiation. Thus, ERG orchestrates chromatin interactions and regulates prostate cell lineage toward pro-luminal program, as its fundamental role on lineage differentiation in prostate cancer initiation.

scholarly journals SisterC: A novel 3C-technique to detect chromatin interactions between and along sister chromatids

2020 ◽  
Author(s):  
Marlies E. Oomen ◽  
Adam K. Hedger ◽  
Jonathan K. Watts ◽  
Job Dekker
Keyword(s):  
Cell Cycle ◽  
Single Strand ◽  
Chromosome Conformation Capture ◽  
Brdu Incorporation ◽  
Chromosome Conformation ◽  
Strand Breaks ◽  
Chromatin Interactions ◽  
Sister Chromatids ◽  
Single Strand Breaks ◽  
Capture Techniques

Abstract Current chromosome conformation capture techniques are not able to distinguish sister chromatids. Here we describe the protocol of SisterC1: a novel Hi-C technique that leverages BrdU incorporation and UV/Hoechst-induced single strand breaks to identify interactions along and between sister chromatids. By synchronizing cells, BrdU is incorporated only on the newly replicated strand, which distinguishes the two sister chromatids2,3. This is followed by Hi-C4 of cells that can be arrested in different stages of the cell cycle, e.g. in mitosis. Before final amplification of the Hi-C library, strands containing BrdU are specifically depleted by UV/Hoechst treatment. SisterC libraries are then sequenced using 50bp paired end reads, followed by mapping using standard Hi-C processing tools. Interactions can then be assigned as inter- or intra-sister interactions based on read orientation.

Abstract P221: Retinoblastoma Protein--Associated Proteins 48 and 46 Are Novel p300/GATA4-Binding Partners Involved in Hypertrophic Responses in Cardiomyocytes

2011 ◽  
Vol 109 (suppl_1) ◽  
Author(s):  
Yoichi Sunagawa ◽  
Yasufumi Katanasaka ◽  
Taishi Terada ◽  
Yuichi Watanabe ◽  
Hiromichi Wada ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Transcriptional Repression ◽  
Zinc Finger Protein ◽  
Retinoblastoma Protein ◽  
Histone Deacetylation ◽  
Hek293 Cells ◽  
Functional Protein ◽  
Nucleosome Remodeling ◽  
Transcriptional Activation Domain ◽  
Functional Relationships

Background: A zinc finger protein GATA4 is one of hypertrophy-responsive transcription factors, and increases its DNA-binding and transcriptional activities in response to hypertrophic stimuli in cardiomyocytes. Activation of GATA4 during this process is mediated, in part, through acetylation by intrinsic histone acetyltransferases such as a transcriptional coactivator p300. Here, we show that retinoblastoma protein (Rb)-associated protein 48 and 46 (RbAp48, RbAp46), components of NuRD (nucleosome remodeling and deacetylase) complex that has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation, are novel components of p300/GATA4 complex. However, the precise functional relationships among p300, GATA4, RbAp48, and RbAp46 remain unknown. Methods and Results: A series of GST pull-down assays revealed that the C-terminal domain of RbAp48/46 bound to the N-terminal transcriptional activation domain of GATA4 and C/H-3 domain of p300, respectively. Immunoprecipitation followed by western blotting demonstrated that RbAp48/46 repressed p300-induced acetylation of GATA4 and histones. While overexpressions of RbAp48/46 inhibited p300/GATA4-induced atrial natriuretic factors (ANF) and endotheline-1 (ET-1) promoter activities, knockdown of neither RbAp48 nor RbAp46 by RNAi enhanced these promoter activities in HEK293 cells. Stimulation of cardiomyocytes with phenylephrine (PE) decreased the binding of GATA4/p300 with RbAp48/46. RbAp48/46 repressed PE-induced hypertrophic responses such as myofibrillar organization, increase in cell size and promoter activation of the ANF and ET-1 in cardiomyocytes. Conclusion: These findings demonstrate that RbAp48 and RbAp46 form a functional protein complex with GATA4/p300 and regulated hypertrophic responses in cardiomyocytes.

FOG-1 Directly Binds to a Chromatin Remodeling and Deacetylase-Containing Complex To Mediate Transcriptional Repression by GATA-1.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 355-355
Author(s):  
Wei Hong ◽  
Minako Nakazawa ◽  
Ying-Yu Chen ◽  
Rajashree Kori ◽  
Carrie Rakowski ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Histone Deacetylation ◽  
Gene Repression ◽  
Single Point Mutation ◽  
Mutant Form ◽  
Erythroid Cells ◽  
Binding Studies ◽  
Nucleosome Remodeling ◽  
N Terminus

Abstract Terminal erythroid maturation requires coordinated activation of erythroid marker genes and repression of genes associated with the undifferentiated state. These gene expression patterns are mediated by the concerted action of the erythroid transcription factor GATA-1 and its cofactor FOG-1 that can activate or repress transcription depending on promoter context. We and others showed previously that one mechanism by which FOG-1 functions is to facilitate GATA-1 association with certain DNA target sites in vivo. Using gene complementation studies of GATA-1-ablated erythroid cells, we show that at several GATA-1-repressed target genes (c-kit, c-myc and GATA-2) FOG-1 is dispensable for GATA-1 occupancy in vivo but essential for gene repression and histone deacetylation. To examine how FOG-1 functions as co-repressor we performed affinity chromatography, conventional protein purification and in vitro binding studies to identify proteins that bind FOG-1. We discovered that FOG-1 directly associates with the nucleosome remodeling and histone deacetylase complex NURD. This interaction is mediated by a small conserved domain at the N-terminus of FOG-1 and the MTA-1 subunit of NURD. Association of FOG-1 with NURD occurs in vivo and depends on an intact N-terminus of FOG-1. A series of point mutations across the N-terminus of FOG-1 revealed a tight correlation between NURD binding and transcriptional repression. In particular, a single point mutation at the N-terminus of FOG-1 that abrogated NURD binding also blocked gene repression by FOG-1. Finally, the ability of GATA-1 to repress transcription was impaired in erythroid cells expressing a mutant form of FOG-1 that is defective for NURD binding. Together, these studies show that FOG-1 and very likely other FOG proteins are bona fide co-repressors that link GATA proteins to histone deacetylation and nucleosome remodeling via a novel protein interaction module.

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