scholarly journals Interaction of the CCAAT displacement protein with shared regulatory elements required for transcription of paired histone genes.

1995 ◽  
Vol 15 (7) ◽  
pp. 3587-3596 ◽  
Author(s):  
H M el-Hodiri ◽  
M Perry
Keyword(s):  
Bidirectional Promoter ◽  
Regulatory Elements ◽  
Histone Gene ◽  
Single Element ◽  
Gene Promoters ◽  
Histone Genes ◽  
Ccaat Displacement Protein ◽  
Intergenic Dna ◽  
Specific Complex

The H2A and H2B genes of the Xenopus xlh3 histone gene cluster are transcribed in opposite directions from initiation points located approximately 235 bp apart. The close proximity of these genes to one another suggests that their expression may be controlled by either a single bidirectional promoter or by separate promoters. Our analysis of the transcription of histone gene pairs containing deletions and site-specific mutations of intergenic DNA revealed that both promoters are distinct but that they overlap physically and share multiple regulatory elements, providing a possible basis for the coordinate regulation of their in vivo activities. Using the intergenic DNA fragment as a probe and extracts from mammalian and amphibian cells, we observed the formation of a specific complex containing the CCAAT displacement protein (CDP). The formation of the CDP-containing complex was not strictly dependent on any single element in the intergenic region but instead required the presence of at least two of the three CCAAT motifs. Interestingly, similar CDP-containing complexes were formed on the promoters from the three other histone genes. The binding of CDP to histone gene promoters may contribute to the coordination of their activities during the cell cycle and early development.

scholarly journals Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal

2021 ◽  
Author(s):  
Tina R. Lynch ◽  
Mingyu Xue ◽  
Cazza W. Czerniak ◽  
ChangHwan Lee ◽  
Judith Kimble
Keyword(s):  
Stem Cell ◽  
Regulatory Elements ◽  
Single Element ◽  
Developmental Context ◽  
C Elegans ◽  
Stem Cell Maintenance ◽  
Nascent Transcripts ◽  
Functional Analyses ◽  
Dose Dependent

A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. The use of reporter constructs, cell culture and computational modeling has made enormous contributions to understanding this fundamental question, but analysis of regulatory elements in their natural developmental context is an essential but rarely used complement. Here, we edited Notch-dependent cis-regulatory elements in the endogenous C. elegans sygl-1 gene, which encodes a key stem cell regulator. We then analyzed the in vivo consequences of those mutations – on both gene expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of a single element in a three-element homotypic cluster reduced expression as well as stem cell pool size by about half, while mutation of two elements essentially abolished them. We find that LBS number and LBS neighborhood are both important to activity: elements on separate chromosomes function additively, while elements in the same cluster act synergistically. Our approach of precise CRISPR/Cas9 gene editing coupled with quantitation of both molecular and biological readouts establishes a powerful model for in vivo functional analyses of DNA cis-regulatory elements.

The bidirectional promoter of the divergently transcribed mouse Surf-1 and Surf-2 genes

1991 ◽  
Vol 11 (3) ◽  
pp. 1281-1294
Author(s):  
A C Lennard ◽  
M Fried
Keyword(s):  
Binding Site ◽  
Dimethyl Sulfate ◽  
Ribosomal Protein Gene ◽  
Bidirectional Promoter ◽  
Gene Promoters ◽  
Accurate Expression ◽  
Bona Fide ◽  
Efficient Expression

The ubiquitously expressed mouse Surf-1 and Surf-2 genes are divergently transcribed, and their heterogeneous start sites are separated by up to a maximum of only 73 bp. By using in vitro DNase I, dimethyl sulfate methylation, and gel retardation assays, we have identified five putative promoter control elements between and around the Surf-1 and Surf-2 start sites. The effects of each site on the regulation of Surf-1 and Surf-2 transcription have been studied in vivo, and four sites were found to be functional promoter elements. A novel binding site is required for efficient use of the intermediate but not the major start site of Surf-1. Three elements function in a bidirectional manner and are shared for efficient and accurate expression of both Surf-1 and Surf-2. One is an UEF (USF, MLTF) binding site which had a small effect on the use of the intermediate start sites of Surf-1 and also affected the major start sites of Surf-2. Another has sequence homology to the RPG alpha binding site associated with some ribosomal protein gene promoters and is required for efficient expression of the major but not intermediate start sites of Surf-1 and all start sites of Surf-2. The third, an RPG alpha-like site, is used for all start sites of both Surf-1 and Surf-2. Dissection of this cellular promoter region showed that different binding sites affect the use of different start sites and revealed a complex interaction between multiple elements that constitute a bona fide bidirectional promoter.

scholarly journals Transcription factor MBF-I interacts with metal regulatory elements of higher eucaryotic metallothionein genes.

1989 ◽  
Vol 9 (12) ◽  
pp. 5315-5323 ◽  
Author(s):  
J Imbert ◽  
M Zafarullah ◽  
V C Culotta ◽  
L Gedamu ◽  
D Hamer
Keyword(s):  
Gene Transcription ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Direct Role ◽  
Transcription In Vitro ◽  
Mouse Cells ◽  
Affinity Reagent

Metallothionein (MT) gene promoters in higher eucaryotes contain multiple metal regulatory elements (MREs) that are responsible for the metal induction of MT gene transcription. We identified and purified to near homogeneity a 74-kilodalton mouse nuclear protein that specifically binds to certain MRE sequences. This protein, MBF-I, was purified employing as an affinity reagent a trout MRE that is shown to be functional in mouse cells but which lacks the G+C-rich and SP1-like sequences found in many mammalian MT gene promoters. Using point-mutated MREs, we showed that there is a strong correlation between DNA binding in vitro and MT gene regulation in vivo, suggesting a direct role of MBF-I in MT gene transcription. We also showed that MBF-I can induce MT gene transcription in vitro in a mouse extract and that this stimulation requires zinc.

scholarly journals Hepatic gene expression patterns in thyroid hormone-treated hypothyroid rats

2003 ◽  
Vol 31 (2) ◽  
pp. 291-303 ◽  
Author(s):  
JM Weitzel ◽  
S Hamann ◽  
M Jauk ◽  
M Lacey ◽  
A Filbry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thyroid Hormone ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Activation Mechanism ◽  
Gene Expression Patterns ◽  
Peroxisome Proliferator ◽  
Gene Promoters ◽  
Protein Levels

Thyroid hormone (T3) is essential for normal development, differentiation and metabolic balance. We have performed DNA microarray experiments using hepatic RNA from hypothyroid and T3-treated hypothyroid rats in order to characterize T3-induced gene expression patterns after various time points (6, 24 and 48 h after the administration of the hormone). Sixty-two of 4608 different genes displayed a reproducible T3-response, and cluster analysis divided these differentially regulated genes into six expression patterns. Thirty-six genes were not significantly regulated within the first 24 h. Transient transfection experiments of eight late-induced gene promoters failed to detect a thyroid hormone response element within their regulatory elements, suggesting an indirect activation mechanism(s). In search for an intermediate factor of T3 action, we examined whether various rather ubiquitous transcription factors, peroxisome proliferator-activated receptors (PPARs) and coactivators of the PPARgamma coactivator 1 family (PGC-1) are regulated by T3. Only PPARgamma and PERC/PGC-1beta exhibit a significant T3-response within the first 6 h after treatment, identifying these factors as candidate components for mediating the late-induced expression pattern. Regulation of early-induced genes within the first 6 h after administration of T3 on transcript levels correlates with altered protein levels after 24 and 48 h in vivo.

Transcription factor MBF-I interacts with metal regulatory elements of higher eucaryotic metallothionein genes

1989 ◽  
Vol 9 (12) ◽  
pp. 5315-5323
Author(s):  
J Imbert ◽  
M Zafarullah ◽  
V C Culotta ◽  
L Gedamu ◽  
D Hamer
Keyword(s):  
Gene Transcription ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Direct Role ◽  
Transcription In Vitro ◽  
Mouse Cells ◽  
Affinity Reagent

Metallothionein (MT) gene promoters in higher eucaryotes contain multiple metal regulatory elements (MREs) that are responsible for the metal induction of MT gene transcription. We identified and purified to near homogeneity a 74-kilodalton mouse nuclear protein that specifically binds to certain MRE sequences. This protein, MBF-I, was purified employing as an affinity reagent a trout MRE that is shown to be functional in mouse cells but which lacks the G+C-rich and SP1-like sequences found in many mammalian MT gene promoters. Using point-mutated MREs, we showed that there is a strong correlation between DNA binding in vitro and MT gene regulation in vivo, suggesting a direct role of MBF-I in MT gene transcription. We also showed that MBF-I can induce MT gene transcription in vitro in a mouse extract and that this stimulation requires zinc.

scholarly journals The bidirectional promoter of the divergently transcribed mouse Surf-1 and Surf-2 genes.

1991 ◽  
Vol 11 (3) ◽  
pp. 1281-1294 ◽  
Author(s):  
A C Lennard ◽  
M Fried
Keyword(s):  
Binding Site ◽  
Dimethyl Sulfate ◽  
Ribosomal Protein Gene ◽  
Bidirectional Promoter ◽  
Gene Promoters ◽  
Accurate Expression ◽  
Bona Fide ◽  
Efficient Expression

The ubiquitously expressed mouse Surf-1 and Surf-2 genes are divergently transcribed, and their heterogeneous start sites are separated by up to a maximum of only 73 bp. By using in vitro DNase I, dimethyl sulfate methylation, and gel retardation assays, we have identified five putative promoter control elements between and around the Surf-1 and Surf-2 start sites. The effects of each site on the regulation of Surf-1 and Surf-2 transcription have been studied in vivo, and four sites were found to be functional promoter elements. A novel binding site is required for efficient use of the intermediate but not the major start site of Surf-1. Three elements function in a bidirectional manner and are shared for efficient and accurate expression of both Surf-1 and Surf-2. One is an UEF (USF, MLTF) binding site which had a small effect on the use of the intermediate start sites of Surf-1 and also affected the major start sites of Surf-2. Another has sequence homology to the RPG alpha binding site associated with some ribosomal protein gene promoters and is required for efficient expression of the major but not intermediate start sites of Surf-1 and all start sites of Surf-2. The third, an RPG alpha-like site, is used for all start sites of both Surf-1 and Surf-2. Dissection of this cellular promoter region showed that different binding sites affect the use of different start sites and revealed a complex interaction between multiple elements that constitute a bona fide bidirectional promoter.

Defects inSPT16orPOB3(yFACT) inSaccharomyces cerevisiaeCause Dependence on the Hir/Hpc Pathway: Polymerase Passage May Degrade Chromatin Structure

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1557-1571 ◽  
Author(s):  
Tim Formosa ◽  
Susan Ruone ◽  
Melissa D Adams ◽  
Aileen E Olsen ◽  
Peter Eriksson ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Histone Gene ◽  
Transcriptional Elongation ◽  
Histone Genes ◽  
Elongation Factors ◽  
Genes Encoding ◽  
Paf1 Complex ◽  
Transcription And Replication

AbstractSpt16/Cdc68, Pob3, and Nhp6 collaborate in vitro and in vivo as the yeast factor SPN, which is homologous to human FACT. SPN/FACT complexes mediate passage of polymerases through nucleosomes and are important for both transcription and replication. An spt16 mutation was found to be intolerable when combined with a mutation in any member of the set of functionally related genes HIR1, HIR2/SPT1, HIR3/HPC1, or HPC2. Mutations in POB3, but not in NHP6A/B, also display strong synthetic defects with hir/hpc mutations. A screen for other mutations that cause dependence on HIR/HPC genes revealed genes encoding members of the Paf1 complex, which also promotes transcriptional elongation. The Hir/Hpc proteins affect the expression of histone genes and also promote normal deposition of nucleosomes; either role could explain an interaction with elongation factors. We show that both spt16 and pob3 mutants respond to changes in histone gene numbers, but in opposite ways, suggesting that Spt16 and Pob3 each interact with histones but perhaps with different subsets of these proteins. Supporting this, spt16 and pob3 mutants also display different sensitivities to mutations in the N-terminal tails of histones H3 and H4 and to mutations in enzymes that modulate acetylation of these tails. Our results support a model in which SPN/FACT has two functions: it disrupts nucleosomes to allow polymerases to access DNA, and it reassembles the nucleosomes afterward. Mutations that impair the reassembly activity cause chromatin to accumulate in an abnormally disrupted state, imposing a requirement for a nucleosome reassembly function that we propose is provided by Hir/Hpc proteins.

scholarly journals Transcriptional Activation of Histone Genes Requires NPAT-Dependent Recruitment of TRRAP-Tip60 Complex to Histone Promoters during the G1/S Phase Transition

2007 ◽  
Vol 28 (1) ◽  
pp. 435-447 ◽  
Author(s):  
Michael DeRan ◽  
Mary Pulvino ◽  
Eriko Greene ◽  
Chuan Su ◽  
Jiyong Zhao
Keyword(s):  
Phase Transition ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
S Phase ◽  
Histone Gene ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Histone Genes ◽  
Transactivation Domain ◽  
Histone H4 Acetylation

ABSTRACT Transcriptional activation of histone subtypes is coordinately regulated and tightly coupled with the onset of DNA replication during S-phase entry. The underlying molecular mechanisms for such coordination and coupling are not well understood. The cyclin E-Cdk2 substrate NPAT has been shown to play an essential role in the transcriptional activation of histone genes at the G1/S-phase transition. Here, we show that NPAT interacts with components of the Tip60 histone acetyltransferase complex through a novel amino acid motif, which is functionally conserved in E2F and adenovirus E1A proteins. In addition, we demonstrate that transformation/transactivation domain-associated protein (TRRAP) and Tip60, two components of the Tip60 complex, associate with histone gene promoters at the G1/S-phase boundary in an NPAT-dependent manner. In correlation with the association of the TRRAP-Tip60 complex, histone H4 acetylation at histone gene promoters increases at the G1/S-phase transition, and this increase involves NPAT function. Suppression of TRRAP or Tip60 expression by RNA interference inhibits histone gene activation. Thus, our data support a model in which NPAT recruits the TRRAP-Tip60 complex to histone gene promoters to coordinate the transcriptional activation of multiple histone genes during the G1/S-phase transition.

scholarly journals Identification and characterization of a chicken alpha-globin enhancer.

1989 ◽  
Vol 9 (3) ◽  
pp. 893-901 ◽  
Author(s):  
J A Knezetic ◽  
G Felsenfeld
Keyword(s):  
Globin Gene ◽  
Regulatory Elements ◽  
Dnase I ◽  
Specific Factor ◽  
Gene Promoters ◽  
Globin Genes ◽  
Mobility Shift ◽  
Enhancer Element ◽  
Alpha Globin

We identify and describe the properties of an enhancer within the chicken alpha-globin gene cluster. This cluster consists of one gene (pi) expressed only in primitive erythrocytes and two (alpha A and alpha D) expressed in both primitive and definitive cell lineages. The genes are linked together in the order 5'-pi-alpha D-alpha A-3' and occupy a region about 10 kilobase pairs long. The enhancer is located at the 3' end of the cluster, about 750 base pairs 3' to the alpha A translation stop site. When assayed by transfection into either primitive or definitive primary chicken erythrocytes, this element stimulated expression from plasmids containing the alpha D- or alpha A-globulin gene promoters. Except for sites in the alpha-globin promoters, no other stimulatory activity was observed in DNA taken from other regions of the alpha-globin locus. Moderate resolution DNase I hypersensitivity studies as well as DNase I footprinting revealed three regions of protein binding, each containing a similar core DNA sequence within the enhancer element. Gel mobility shift studies demonstrated that all three regions bind the recently identified erythrocyte-specific factor, EryfI, which has binding sites in the regulatory regions of all chicken globin genes. Our data suggest that the enhancer we have identified may act in vivo only on the alpha A gene; expression of the alpha D gene is affected by another EryfI site located in the alpha D promoter. Such a mechanism would be consistent with the observed relative abundances of alpha A- and alpha D-globin in vivo. The simplicity of these regulatory elements may reflect the limited repertoire of expression of these genes during development.

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