Regulatory role of the G alpha 1 subunit in controlling cellular morphogenesis in Dictyostelium

Development ◽  
1994 ◽  
Vol 120 (12) ◽  
pp. 3549-3561 ◽  
Author(s):  
S. Dharmawardhane ◽  
A.B. Cubitt ◽  
A.M. Clark ◽  
R.A. Firtel
Keyword(s):  
Negative Regulator ◽  
Specific Gene ◽  
Wild Type ◽  
Cell Type ◽  
Lacz Reporter ◽  
Specific Expression ◽  
Multicellular Development ◽  
Cell Type Specific Expression ◽  
Cell Type Specific ◽  
Constitutively Active

To determine the function of the Dictyostelium G alpha 1 subunit during aggregation and multicellular development, we analyzed the phenotypes of g alpha 1 null cells and strains overexpressing either wild-type G alpha 1 or two putative constitutively active mutations of G alpha 1. Strains overexpressing the wild-type or mutant G alpha 1 proteins showed very abnormal culmination with an aberrant stalk differentiation. The similarity of the phenotypes between G alpha 1 overexpression and expression of a putative constitutively active G alpha 1 subunit suggests that these phenotypes are due to increased G alpha 1 activity rather than resulting from a non-specific interference of other pathways. In contrast, g alpha 1 null strains showed normal morphogenesis except that the stalks were thinner and longer than those of wild-type culminants. Analysis of cell-type-specific gene expression using lacZ reporter constructs indicated that strains overexpressing G alpha 1 show a loss of ecmB expression in the central core of anterior prestalk AB cells. However, expression of ecmB in anterior-like cells and the expression of prestalk A-specific gene ecmA and the prespore-specific gene SP60/cotC appeared normal. Using a G alpha 1/lacZ reporter construct, we show that G alpha 1 expression is cell-type-specific during the multicellular stages, with a pattern of expression similar to ecmB, being preferentially expressed in the anterior prestalk AB cells and anterior-like cells. The developmental and molecular phenotypes of G alpha 1 overexpression and the cell-type-specific expression of G alpha 1 suggest that G alpha 1-mediated signaling pathways play an essential role in regulating multicellular development by controlling prestalk morphogenesis, possibly by acting as a negative regulator of prestalk AB cell differentiation. During the aggregation phase of development, g alpha 1 null cells display a delayed peak in cAMP-stimulated accumulation of cGMP compared to wild-type cells, while G alpha 1 overexpressors and dominant activating mutants show parallel kinetics of activation but decreased levels of cGMP accumulation compared to that seen in wild-type cells. These data suggest that G alpha 1 plays a role in the regulation of the activation and/or adaptation of the guanylyl cyclase pathway. In contrast, the activation of adenylyl cyclase, another pathway activated by cAMP stimulation, was unaffected in g alpha 1 null cells and cell lines overexpressing wild-type G alpha 1 or the G alpha 1 (Q206L) putative dominant activating mutation.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals Positive and negative elements regulate a melanocyte-specific promoter

1992 ◽  
Vol 12 (8) ◽  
pp. 3653-3662
Author(s):  
P Lowings ◽  
U Yavuzer ◽  
C R Goding
Keyword(s):  
Protein Interactions ◽  
Regulatory Element ◽  
Basal Layer ◽  
Regulatory Elements ◽  
Hair Follicles ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

Melanocytes are specialized cells residing in the hair follicles, the eye, and the basal layer of the human epidermis whose primary function is the production of the pigment melanin, giving rise to skin, hair, and eye color. Melanogenesis, a process unique to melanocytes that involves the processing of tyrosine by a number of melanocyte-specific enzymes, including tyrosinase and tyrosinase-related protein 1 (TRP-1), occurs only after differentiation from the melanocyte precursor, the melanoblast. In humans, melanogenesis is inducible by UV irradiation, with melanin being transferred from the melanocyte in the epidermis to the surrounding keratinocytes as protection from UV-induced damage. Excessive exposure to UV, however, is the primary cause of malignant melanoma, an increasingly common and highly aggressive disease. As an initial approach to understanding the regulation of melanocyte differentiation and melanocyte-specific transcription, we have isolated the gene encoding TRP-1 and examined the cis- and trans-acting factors required for cell-type-specific expression. We find that the TRP-1 promoter comprises both positive and negative regulatory elements which confer efficient expression in a TRP-1-expressing, pigmented melanoma cell line but not in NIH 3T3 or JEG3 cells and that a minimal promoter extending between -44 and +107 is sufficient for cell-type-specific expression. Assays for DNA-protein interactions coupled with extensive mutagenesis identified three factors, whose binding correlated with the function of two positive and one negative regulatory element. One of these factors, termed M-box-binding factor 1, binds to an 11-bp motif, the M box, which acts as a positive regulatory element both in TRP-1-expressing and -nonexpressing cell lines, despite being entirely conserved between the melanocyte-specific tyrosinase and TRP-1 promoters. The possible mechanisms underlying melanocyte-specific gene expression are discussed.

scholarly journals A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders

2020 ◽  
Author(s):  
Abolfazl Doostparast Torshizi ◽  
Jubao Duan ◽  
Kai Wang
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Complex Diseases ◽  
Specific Gene ◽  
Cellular Composition ◽  
Rna Seq ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractThe importance of cell type-specific gene expression in disease-relevant tissues is increasingly recognized in genetic studies of complex diseases. However, the vast majority of gene expression studies are conducted on bulk tissues, necessitating computational approaches to infer biological insights on cell type-specific contribution to diseases. Several computational methods are available for cell type deconvolution (that is, inference of cellular composition) from bulk RNA-Seq data, but cannot impute cell type-specific expression profiles. We hypothesize that with external prior information such as single cell RNA-seq (scRNA-seq) and population-wide expression profiles, it can be a computationally tractable and identifiable to estimate both cellular composition and cell type-specific expression from bulk RNA-Seq data. Here we introduce CellR, which addresses cross-individual gene expression variations by employing genome-wide tissue-wise expression signatures from GTEx to adjust the weights of cell-specific gene markers. It then transforms the deconvolution problem into a linear programming model while taking into account inter/intra cellular correlations, and uses a multi-variate stochastic search algorithm to estimate the expression level of each gene in each cell type. Extensive analyses on several complex diseases such as schizophrenia, Alzheimer’s disease, Huntington’s disease, and type 2 diabetes validated efficiency of CellR, while revealing how specific cell types contribute to different diseases. We conducted numerical simulations on human cerebellum to generate pseudo-bulk RNA-seq data and demonstrated its efficiency in inferring cell-specific expression profiles. Moreover, we inferred cell-specific expression levels from bulk RNA-seq data on schizophrenia and computed differentially expressed genes within certain cell types. Using predicted gene expression profile on excitatory neurons, we were able to reproduce our recently published findings on TCF4 being a master regulator in schizophrenia and showed how this gene and its targets are enriched in excitatory neurons. In summary, CellR compares favorably (both accuracy and stability of inference) against competing approaches on inferring cellular composition from bulk RNA-seq data, but also allows direct imputation of cell type-specific gene expression, opening new doors to re-analyze gene expression data on bulk tissues in complex diseases.

scholarly journals Cell-type specific expression of constitutively-active Rheb promotes regeneration of bulbospinal respiratory axons following cervical SCI

2018 ◽  
Vol 303 ◽  
pp. 108-119 ◽  
Author(s):  
Mark W. Urban ◽  
Biswarup Ghosh ◽  
Laura R. Strojny ◽  
Cole G. Block ◽  
Sara M. Blazejewski ◽  
...  
Keyword(s):  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific ◽  
Constitutively Active

scholarly journals Positive and negative elements regulate a melanocyte-specific promoter.

1992 ◽  
Vol 12 (8) ◽  
pp. 3653-3662 ◽  
Author(s):  
P Lowings ◽  
U Yavuzer ◽  
C R Goding
Keyword(s):  
Protein Interactions ◽  
Regulatory Element ◽  
Basal Layer ◽  
Regulatory Elements ◽  
Hair Follicles ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

Melanocytes are specialized cells residing in the hair follicles, the eye, and the basal layer of the human epidermis whose primary function is the production of the pigment melanin, giving rise to skin, hair, and eye color. Melanogenesis, a process unique to melanocytes that involves the processing of tyrosine by a number of melanocyte-specific enzymes, including tyrosinase and tyrosinase-related protein 1 (TRP-1), occurs only after differentiation from the melanocyte precursor, the melanoblast. In humans, melanogenesis is inducible by UV irradiation, with melanin being transferred from the melanocyte in the epidermis to the surrounding keratinocytes as protection from UV-induced damage. Excessive exposure to UV, however, is the primary cause of malignant melanoma, an increasingly common and highly aggressive disease. As an initial approach to understanding the regulation of melanocyte differentiation and melanocyte-specific transcription, we have isolated the gene encoding TRP-1 and examined the cis- and trans-acting factors required for cell-type-specific expression. We find that the TRP-1 promoter comprises both positive and negative regulatory elements which confer efficient expression in a TRP-1-expressing, pigmented melanoma cell line but not in NIH 3T3 or JEG3 cells and that a minimal promoter extending between -44 and +107 is sufficient for cell-type-specific expression. Assays for DNA-protein interactions coupled with extensive mutagenesis identified three factors, whose binding correlated with the function of two positive and one negative regulatory element. One of these factors, termed M-box-binding factor 1, binds to an 11-bp motif, the M box, which acts as a positive regulatory element both in TRP-1-expressing and -nonexpressing cell lines, despite being entirely conserved between the melanocyte-specific tyrosinase and TRP-1 promoters. The possible mechanisms underlying melanocyte-specific gene expression are discussed.

scholarly journals Neuronal cell type–specific alternative splicing is regulated by the KH domain protein SLM1

2014 ◽  
Vol 204 (3) ◽  
pp. 331-342 ◽  
Author(s):  
Takatoshi Iijima ◽  
Yoko Iijima ◽  
Harald Witte ◽  
Peter Scheiffele
Keyword(s):  
Alternative Splicing ◽  
Neuronal Cell ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Splicing Regulators ◽  
Cell Type Specific Expression ◽  
Kh Domain ◽  
Cell Type Specific

The unique functional properties and molecular identity of neuronal cell populations rely on cell type–specific gene expression programs. Alternative splicing represents a powerful mechanism for expanding the capacity of genomes to generate molecular diversity. Neuronal cells exhibit particularly extensive alternative splicing regulation. We report a highly selective expression of the KH domain–containing splicing regulators SLM1 and SLM2 in the mouse brain. Conditional ablation of SLM1 resulted in a severe defect in the neuronal isoform content of the polymorphic synaptic receptors neurexin-1, -2, and -3. Thus, cell type–specific expression of SLM1 provides a mechanism for shaping the molecular repertoires of synaptic adhesion molecules in neuronal populations in vivo.

Cell-type-specific expression of the rat thyroperoxidase promoter indicates common mechanisms for thyroid-specific gene expression

1992 ◽  
Vol 12 (2) ◽  
pp. 576-588
Author(s):  
H Francis-Lang ◽  
M Price ◽  
M Polycarpou-Schwarz ◽  
R Di Lauro
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Proximal Region ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific ◽  
Rat Thyroid

A 420-bp fragment from the 5' end of the rat thyroperoxidase (TPO) gene was fused to a luciferase reporter and shown to direct cell-type-specific expression when transfected into rat thyroid FRTL-5 cells. Analysis of this DNA fragment revealed four regions of the promoter which interact with DNA-binding proteins present in FRTL-5 cells. Mutation of the DNA sequence within any of these regions reduced TPO promoter activity. The trans-acting factors binding to these sequences were compared with thyroid transcription factor 1 (TTF-1) and TTF-2, previously identified as transcriptional activators of another thyroid-specific gene, the thyroglobulin (Tg) gene. Purified TTF-1 binds to three regions of TPO which are protected by FRTL-5 proteins. Two of the binding sites overlap with recognition sites for other DNA-binding proteins. One TTF-1 site can also bind a protein (UFB) present in the nuclei of both expressing and nonexpressing cells. TTF-1 binding to the proximal region overlaps with that for a novel protein present in FRTL-5 cells which can also recognize the promoter-proximal region of Tg. Using a combination of techniques, the factor binding to the fourth TPO promoter site was shown to be TTF-2. We conclude, therefore, that the FRTL-5-specific expression of two thyroid restricted genes, encoding TPO and Tg, relies on a combination of the same trans-acting factors present in thyroid cells.

scholarly journals A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Abolfazl Doostparast Torshizi ◽  
Jubao Duan ◽  
Kai Wang
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Complex Diseases ◽  
Specific Gene ◽  
Cellular Composition ◽  
Rna Seq ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

Abstract The importance of cell type-specific gene expression in disease-relevant tissues is increasingly recognized in genetic studies of complex diseases. However, most gene expression studies are conducted on bulk tissues, without examining cell type-specific expression profiles. Several computational methods are available for cell type deconvolution (i.e. inference of cellular composition) from bulk RNA-Seq data, but few of them impute cell type-specific expression profiles. We hypothesize that with external prior information such as single cell RNA-seq and population-wide expression profiles, it can be computationally tractable to estimate both cellular composition and cell type-specific expression from bulk RNA-Seq data. Here we introduce CellR, which addresses cross-individual gene expression variations to adjust the weights of cell-specific gene markers. It then transforms the deconvolution problem into a linear programming model while taking into account inter/intra cellular correlations and uses a multi-variate stochastic search algorithm to estimate the cell type-specific expression profiles. Analyses on several complex diseases such as schizophrenia, Alzheimer’s disease, Huntington’s disease and type 2 diabetes validated the efficiency of CellR, while revealing how specific cell types contribute to different diseases. In summary, CellR compares favorably against competing approaches, enabling cell type-specific re-analysis of gene expression data on bulk tissues in complex diseases.

scholarly journals Cell-type-specific expression of the rat thyroperoxidase promoter indicates common mechanisms for thyroid-specific gene expression.

1992 ◽  
Vol 12 (2) ◽  
pp. 576-588 ◽  
Author(s):  
H Francis-Lang ◽  
M Price ◽  
M Polycarpou-Schwarz ◽  
R Di Lauro
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Proximal Region ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific ◽  
Rat Thyroid

A 420-bp fragment from the 5' end of the rat thyroperoxidase (TPO) gene was fused to a luciferase reporter and shown to direct cell-type-specific expression when transfected into rat thyroid FRTL-5 cells. Analysis of this DNA fragment revealed four regions of the promoter which interact with DNA-binding proteins present in FRTL-5 cells. Mutation of the DNA sequence within any of these regions reduced TPO promoter activity. The trans-acting factors binding to these sequences were compared with thyroid transcription factor 1 (TTF-1) and TTF-2, previously identified as transcriptional activators of another thyroid-specific gene, the thyroglobulin (Tg) gene. Purified TTF-1 binds to three regions of TPO which are protected by FRTL-5 proteins. Two of the binding sites overlap with recognition sites for other DNA-binding proteins. One TTF-1 site can also bind a protein (UFB) present in the nuclei of both expressing and nonexpressing cells. TTF-1 binding to the proximal region overlaps with that for a novel protein present in FRTL-5 cells which can also recognize the promoter-proximal region of Tg. Using a combination of techniques, the factor binding to the fourth TPO promoter site was shown to be TTF-2. We conclude, therefore, that the FRTL-5-specific expression of two thyroid restricted genes, encoding TPO and Tg, relies on a combination of the same trans-acting factors present in thyroid cells.

scholarly journals A cell type‐specific expression map of NCoR1 and SMRT transcriptional co‐repressors in the mouse brain

2020 ◽  
Vol 528 (13) ◽  
pp. 2218-2238 ◽  
Author(s):  
Attilio Iemolo ◽  
Patricia Montilla‐Perez ◽  
I‐Chi Lai ◽  
Yinuo Meng ◽  
Syreeta Nolan ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
A Cell ◽  
Cell Type Specific
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