A GBF-binding site and a novel AT element define the minimal sequences sufficient to direct prespore-specific expression in Dictyostelium discoideum

In order to better understand the molecular mechanisms of cellular differentiation in Dictyostelium discoideum, we have identified the minimum regulatory sequences of the prespore-specific gene SP60/cotC that are sufficient to confer cell-type-specific expression on a heterologous promoter. This region includes at least two essential cis-acting elements: a novel AT-rich element (or elements) and CAE3. The essential function of the AT element is confirmed through point mutations that decrease expression below the level of detection. CAE3 is one of three CA-rich elements (CAEs) required for the induction of SP60/cotC during development or in response to extracellular cyclic AMP. The CAEs have differential affinities for a specific developmentally induced nuclear activity (CAE1 > CAE2 >> CAE3). Here, we identify this activity as G-box-binding factor (GBF) and show that in vitro-transcribed and -translated GBF binds all three SP60/cotC CAEs in a sequence-specific manner. Previous studies have suggested that GBF mediates the induction of some prestalk genes, and these results demonstrate that it also has a specific role in prespore gene activation.

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Characterization of a novel Dictyostelium discoideum prespore-specific gene, PspB, reveals conserved regulatory sequences

Development ◽

10.1242/dev.120.6.1601 ◽

1994 ◽

Vol 120 (6) ◽

pp. 1601-1611 ◽

Cited By ~ 4

Author(s):

J.A. Powell-Coffman ◽

R.A. Firtel

Keyword(s):

Dictyostelium Discoideum ◽

Molecular Mechanisms ◽

Regulatory Element ◽

Consensus Sequence ◽

Specific Gene ◽

Regulatory Sequences ◽

Cell Type ◽

Specific Expression ◽

Regulatory Regions ◽

Cell Type Specific

While Dictyostelium discoideum has been studied as a developmental system for decades, and many regulatory proteins have been cloned, the molecular mechanisms of cell-type-specific gene expression are poorly understood. In this paper we characterize a novel prespore gene, PspB, and undertake a comparative analysis of the regulatory regions in prespore-specific D. discoideum promoters. Sequence alignment of the PSPB gene product with other prespore-specific proteins identifies a conserved, repeated 12 amino acid cysteine-containing motif that may be involved in spore coat function or assembly. Analysis of the PspB promoter identifies two domains essential for developmentally induced promoter activity. The first region includes two CA-rich elements (CAEs) that we show to be functionally homologous to the cAMP-inducible elements previously identified in the SP60 (cotC) promoter. The PspB CAEs compete with the SP60 (cotC) CAEs for binding in vitro to a developmentally regulated nuclear activity. We identify this activity as G-box Binding Factor, a developmentally induced transcription factor. The PspB CAEs and adjacent nucleotides direct a very low level of prespore-enriched expression, but high levels of cell-type-specific expression requires a second promoter region: a 46-bp AT-rich sequence that does not resemble the CAEs or any other previously described late gene promoter elements. Comparison of the PspB AT element with regulatory regions of the SP60 (cotC), SP70 (cotB), and D19 (pspA) promoters reveals an extensive consensus sequence. We suggest that these AT-rich sequences may represent a common regulatory element (or elements) required for prespore gene activation.

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GATA and Ets cis-acting sequences mediate megakaryocyte-specific expression

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.668-676.1993 ◽

1993 ◽

Vol 13 (1) ◽

pp. 668-676

Author(s):

V Lemarchandel ◽

J Ghysdael ◽

V Mignotte ◽

C Rahuel ◽

P H Roméo

Keyword(s):

Binding Site ◽

Consensus Sequence ◽

Mrna Level ◽

Point Mutations ◽

Specific Gene ◽

Cell Type Specificity ◽

Specific Expression ◽

Platelet Factor ◽

Cis Acting ◽

Dna Fragment

The human glycoprotein IIB (GPIIB) gene is expressed only in megakaryocytes, and its promoter displays cell type specificity. We show that this specificity involved two cis-acting sequences. The first one, located at -55, contains a GATA binding site. Point mutations that abolish protein binding on this site decrease the activity of the GPIIB promoter but do not affect its tissue specificity. The second one, located at -40, contains an Ets consensus sequence, and we show that Ets-1 or Ets-2 protein can interact with this -40 GPIIB sequence. Point mutations that impair Ets binding decrease the activity of the GPIIB promoter to the same extent as do mutations that abolish GATA binding. A GPIIB 40-bp DNA fragment containing the GATA and Ets binding sites can confer activity to a heterologous promoter in megakaryocytic cells. This activity is independent of the GPIIB DNA fragment orientation, and mutations on each binding site result in decreased activity. Using cotransfection assays, we show that c-Ets-1 and human GATA1 can transactive the GPIIB promoter in HeLa cells and can act additively. Northern (RNA) blot analysis indicates that the ets-1 mRNA level is increased during megakaryocyte-induced differentiation of erythrocytic/megakaryocytic cell lines. Gel retardation assays show that the same GATA-Ets association is found in the human GPIIB enhancer and the rat platelet factor 4 promoter, the other two characterized regulatory regions of megakaryocyte-specific genes. These results indicate that GATA and Ets cis-acting sequences are an important determinant of megakaryocytic specific gene expression.

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GATA and Ets cis-acting sequences mediate megakaryocyte-specific expression.

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.668 ◽

1993 ◽

Vol 13 (1) ◽

pp. 668-676 ◽

Cited By ~ 151

Author(s):

V Lemarchandel ◽

J Ghysdael ◽

V Mignotte ◽

C Rahuel ◽

P H Roméo

Keyword(s):

Binding Site ◽

Consensus Sequence ◽

Mrna Level ◽

Point Mutations ◽

Specific Gene ◽

Cell Type Specificity ◽

Specific Expression ◽

Platelet Factor ◽

Cis Acting ◽

Dna Fragment

The human glycoprotein IIB (GPIIB) gene is expressed only in megakaryocytes, and its promoter displays cell type specificity. We show that this specificity involved two cis-acting sequences. The first one, located at -55, contains a GATA binding site. Point mutations that abolish protein binding on this site decrease the activity of the GPIIB promoter but do not affect its tissue specificity. The second one, located at -40, contains an Ets consensus sequence, and we show that Ets-1 or Ets-2 protein can interact with this -40 GPIIB sequence. Point mutations that impair Ets binding decrease the activity of the GPIIB promoter to the same extent as do mutations that abolish GATA binding. A GPIIB 40-bp DNA fragment containing the GATA and Ets binding sites can confer activity to a heterologous promoter in megakaryocytic cells. This activity is independent of the GPIIB DNA fragment orientation, and mutations on each binding site result in decreased activity. Using cotransfection assays, we show that c-Ets-1 and human GATA1 can transactive the GPIIB promoter in HeLa cells and can act additively. Northern (RNA) blot analysis indicates that the ets-1 mRNA level is increased during megakaryocyte-induced differentiation of erythrocytic/megakaryocytic cell lines. Gel retardation assays show that the same GATA-Ets association is found in the human GPIIB enhancer and the rat platelet factor 4 promoter, the other two characterized regulatory regions of megakaryocyte-specific genes. These results indicate that GATA and Ets cis-acting sequences are an important determinant of megakaryocytic specific gene expression.

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Cis-regulatory variants affect gene expression dynamics in yeast

10.1101/2021.03.16.435665 ◽

2021 ◽

Author(s):

Ching-Hua Shih ◽

Justin C. Fay

Keyword(s):

Gene Expression ◽

Gene Activation ◽

Regulatory Sequences ◽

Diauxic Shift ◽

Promoter Regions ◽

Specific Expression ◽

Cis Acting ◽

Regulatory Variants ◽

Endogenous Expression ◽

Gene Expression Dynamics

Evolution of cis-regulatory sequences depends on how they effect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within species ASE is associated with intergenic variants, but ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects expression are relevant to the evolution of cis-regulatory sequences.

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Regulation of tissue-specific glycolytic isozyme genes: coordinate response to oxygen availability in myogenic cells

Canadian Journal of Zoology ◽

10.1139/z88-155 ◽

1988 ◽

Vol 66 (5) ◽

pp. 1046-1058 ◽

Cited By ~ 20

Author(s):

Keith A. Webster ◽

Brian J. Murphy

Keyword(s):

Molecular Mechanisms ◽

Gene Activation ◽

Regulatory Sequences ◽

Tissue Specific ◽

Physiological Regulation ◽

Cis Acting ◽

Evolutionary Selection ◽

Coordinated Expression ◽

Steady State Levels ◽

Primary Basis

The steady-state levels of glycolytic isozymes in higher eucaryotic cells result from the coordinated expression of multiple unlinked genes. The tissue-specific isozyme profiles that characterize the expression of these genes are the result of adaptive evolutionary selection and form the primary basis for physiological regulation of the pathway. This review addresses some of the molecular mechanisms that may contribute to the regulation of these genes, both during development and in response to physiological perturbations in mature tissues. The evidence favors mechanisms of programmed "gene activation" accompanied by the concurrent activation of tissue-specific coordinating trans-acting cellular factors that determine transcriptional efficiencies of both regulatory and nonregulatory glycolytic isozymes. Based upon data from higher and lower eucaryotes, it is predicted that tissue-specific glycolytic isozyme genes have common cis-acting regions in their promoters to bind the cellular transcription factors. These regulatory sequences allow the unlinked genes to respond coordinately to physiological and developmental signals.

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Knock-in and precise nucleotide substitution using near-PAMless engineered Cas9 variants in Dictyostelium discoideum

Scientific Reports ◽

10.1038/s41598-021-89546-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yuu Asano ◽

Kensuke Yamashita ◽

Aoi Hasegawa ◽

Takanori Ogasawara ◽

Hoshie Iriki ◽

...

Keyword(s):

Genome Editing ◽

Dictyostelium Discoideum ◽

Streptococcus Pyogenes ◽

Nucleotide Substitution ◽

Point Mutations ◽

Targeted Mutagenesis ◽

Single Amino Acid ◽

Specific Gene ◽

Knock Out ◽

Protospacer Adjacent Motif

AbstractThe powerful genome editing tool Streptococcus pyogenes Cas9 (SpCas9) requires the trinucleotide NGG as a protospacer adjacent motif (PAM). The PAM requirement is limitation for precise genome editing such as single amino-acid substitutions and knock-ins at specific genomic loci since it occurs in narrow editing window. Recently, SpCas9 variants (i.e., xCas9 3.7, SpCas9-NG, and SpRY) were developed that recognise the NG dinucleotide or almost any other PAM sequences in human cell lines. In this study, we evaluated these variants in Dictyostelium discoideum. In the context of targeted mutagenesis at an NG PAM site, we found that SpCas9-NG and SpRY were more efficient than xCas9 3.7. In the context of NA, NT, NG, and NC PAM sites, the editing efficiency of SpRY was approximately 60% at NR (R = A and G) but less than 22% at NY (Y = T and C). We successfully used SpRY to generate knock-ins at specific gene loci using donor DNA flanked by 60 bp homology arms. In addition, we achieved point mutations with efficiencies as high as 97.7%. This work provides tools that will significantly expand the gene loci that can be targeted for knock-out, knock-in, and precise point mutation in D. discoideum.

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Serial analysis of gene expression (SAGE) during porcine embryo development

Reproduction Fertility and Development ◽

10.1071/rd03081 ◽

2004 ◽

Vol 16 (2) ◽

pp. 87 ◽

Cited By ~ 12

Author(s):

Le Ann Blomberg ◽

Kurt A. Zuelke

Keyword(s):

Gene Expression ◽

Functional Genomics ◽

Embryo Development ◽

Molecular Mechanisms ◽

Physiological Role ◽

Transgenic Animals ◽

Specific Gene ◽

Research Strategies

Functional genomics provides a powerful means for delving into the molecular mechanisms involved in pre-implantation development of porcine embryos. High rates of embryonic mortality (30%), following either natural mating or artificial insemination, emphasise the need to improve the efficiency of reproduction in the pig. The poor success rate of live offspring from in vitro-manipulated pig embryos also hampers efforts to generate transgenic animals for biotechnology applications. Previous analysis of differential gene expression has demonstrated stage-specific gene expression for in vivo-derived embryos and altered gene expression for in vitro-derived embryos. However, the methods used to date examine relatively few genes simultaneously and, thus, provide an incomplete glimpse of the physiological role of these genes during embryogenesis. The present review will focus on two aspects of applying functional genomics research strategies for analysing the expression of genes during elongation of pig embryos between gestational day (D) 11 and D12. First, we compare and contrast current methodologies that are being used for gene discovery and expression analysis during pig embryo development. Second, we establish a paradigm for applying serial analysis of gene expression as a functional genomics tool to obtain preliminary information essential for discovering the physiological mechanisms by which distinct embryonic phenotypes are derived.

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Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Molecular and Cellular Biology ◽

10.1128/mcb.13.11.6866 ◽

1993 ◽

Vol 13 (11) ◽

pp. 6866-6875 ◽

Cited By ~ 20

Author(s):

D C Hagen ◽

L Bruhn ◽

C A Westby ◽

G F Sprague

Keyword(s):

Saccharomyces Cerevisiae ◽

Binding Site ◽

Dna Sequences ◽

Point Mutations ◽

Transcription Activation ◽

Specific Gene ◽

Binding Assays ◽

Weak Binding

Transcription activation of alpha-specific genes in Saccharomyces cerevisiae is regulated by two proteins, MCM1 and alpha 1, which bind to DNA sequences, called P'Q elements, found upstream of alpha-specific genes. Neither MCM1 nor alpha 1 alone binds efficiently to P'Q elements. Together, however, they bind cooperatively in a manner that requires both the P' sequence, which is a weak binding site for MCM1, and the Q sequence, which has been postulated to be the binding site for alpha 1. We analyzed a collection of point mutations in the P'Q element of the STE3 gene to determine the importance of individual base pairs for alpha-specific gene transcription. Within the 10-bp conserved Q sequence, mutations at only three positions strongly affected transcription activation in vivo. These same mutations did not affect the weak binding to P'Q displayed by MCM1 alone. In vitro DNA binding assays showed a direct correlation between the ability of the mutant sequences to form ternary P'Q-MCM1-alpha 1 complexes and the degree to which transcription was activated in vivo. Thus, the ability of alpha 1 and MCM1 to bind cooperatively to P'Q elements is critical for activation of alpha-specific genes. In all natural alpha-specific genes the Q sequence is adjacent to the degenerate side of P'. To test the significance of this geometry, we created several novel juxtapositions of P, P', and Q sequences. When the Q sequence was opposite the degenerate side, the composite QP' element was inactive as a promoter element in vivo and unable to form stable ternary QP'-MCM1-alpha 1 complexes in vitro. We also found that addition of a Q sequence to a strong MCM1 binding site allows the addition of alpha 1 to the complex. This finding, together with the observation that Q-element point mutations affected ternary complex formation but not the weak binding of MCM1 alone, supports the idea that the Q sequence serves as a binding site for alpha 1.

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Stable transfer and restricted expression of a cloned class I gene encoding a secreted transplantation-like antigen

Molecular and Cellular Biology ◽

10.1128/mcb.5.6.1295-1300.1985 ◽

1985 ◽

Vol 5 (6) ◽

pp. 1295-1300

Author(s):

Y Barra ◽

K Tanaka ◽

K J Isselbacher ◽

G Khoury ◽

G Jay

Keyword(s):

Molecular Mechanisms ◽

Cell Types ◽

Class I ◽

Regulatory Sequences ◽

Transcriptional Enhancer ◽

Gene Encoding ◽

Specific Expression ◽

Tissue Specific ◽

Functional Studies ◽

I Gene

The identification of a unique major histocompatibility complex class I gene, designated Q10, which encodes a secreted rather than a cell surface antigen has led to questions regarding its potential role in regulating immunological functions. Since the Q10 gene is specifically activated only in the liver, we sought to define the molecular mechanisms which control its expression in a tissue-specific fashion. Results obtained by transfection of the cloned Q10 gene, either in the absence or presence of a heterologous transcriptional enhancer, into a variety of cell types of different tissue derivations are consistent with the Q10 gene being regulated at two levels. The first is by a cis-dependent mechanism which appears to involve site-specific DNA methylation. The second is by a trans-acting mechanism which would include the possibility of an enhancer binding factor. The ability to efficiently express the Q10 gene in certain transfected cell lines offers an opportunity to obtain this secreted class I antigen in quantities sufficient for functional studies; this should also make it possible to define regulatory sequences which may be responsible for the tissue-specific expression of Q10.

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