scholarly journals Human Slug Is a Repressor That Localizes to Sites of Active Transcription

2000 ◽  
Vol 20 (14) ◽  
pp. 5087-5095 ◽  
Author(s):  
Kirugaval Hemavathy ◽  
Siradanahalli C. Guru ◽  
John Harris ◽  
J. Don Chen ◽  
Y. Tony Ip
Keyword(s):  
Dna Binding ◽  
Cell Fate ◽  
Histone Deacetylases ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Protein Localization ◽  
Zinc Fingers ◽  
Cell Movement ◽  
Left Right Asymmetry ◽  
And Function

ABSTRACT Snail/Slug family proteins have been identified in diverse species of both vertebrates and invertebrates. The proteins contain four to six zinc fingers and function as DNA-binding transcriptional regulators. Various members of the family have been demonstrated to regulate cell movement, neural cell fate, left-right asymmetry, cell cycle, and apoptosis. However, the molecular mechanisms of how these regulators function and the target genes involved are largely unknown. In this report, we demonstrate that human Slug (hSlug) is a repressor and modulates both activator-dependent and basal transcription. The repression depends on the C-terminal DNA-binding zinc fingers and on a separable repression domain located in the N terminus. This domain may recruit histone deacetylases to modify the chromatin and effect repression. Protein localization study demonstrates that hSlug is present in discrete foci in the nucleus. This subnuclear pattern does not colocalize with the PML foci or the coiled bodies. Instead, the hSlug foci overlap extensively with areas of the SC-35 staining, some of which have been suggested to be sites of active splicing or transcription. These results lead us to postulate that hSlug localizes to target promoters, where activation occurs, to repress basal and activator-mediated transcription.

scholarly journals Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Marina Farkas ◽  
Hideharu Hashimoto ◽  
Yingtao Bi ◽  
Ramana V. Davuluri ◽  
Lois Resnick-Silverman ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Cell Cycle Arrest ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Binding Modes ◽  
Cell Fate Decisions ◽  
Cycle Arrest

AbstractThe tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate decisions (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to 20-bp response elements (REs) in the genome (RRRCWWGYYYN0-13RRRCWWGYYY). In general, REs at cell cycle arrest targets (e.g. p21) are of higher affinity than those at apoptosis targets (e.g., BAX). However, the RE sequence code underlying selectivity remains undeciphered. Here, we identify molecular mechanisms mediating p53 binding to high- and low-affinity REs by showing that key determinants of the code are embedded in the DNA shape. We further demonstrate that differences in minor/major groove widths, encoded by G/C or A/T bp content at positions 3, 8, 13, and 18 in the RE, determine distinct p53 DNA-binding modes by inducing different Arg248 and Lys120 conformations and interactions. The predictive capacity of this code was confirmed in vivo using genome editing at the BAX RE to interconvert the DNA-binding modes, transcription pattern, and cell fate outcome.

scholarly journals Mechanosensation and Mechanotransduction by Lymphatic Endothelial Cells Act as Important Regulators of Lymphatic Development and Function

2021 ◽  
Vol 22 (8) ◽  
pp. 3955
Author(s):  
László Bálint ◽  
Zoltán Jakus
Keyword(s):  
Endothelial Cells ◽  
Endothelial Cell ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Mechanical Forces ◽  
Lymphatic Endothelial Cells ◽  
Lymphatic Development ◽  
And Function ◽  
The Impact

Our understanding of the function and development of the lymphatic system is expanding rapidly due to the identification of specific molecular markers and the availability of novel genetic approaches. In connection, it has been demonstrated that mechanical forces contribute to the endothelial cell fate commitment and play a critical role in influencing lymphatic endothelial cell shape and alignment by promoting sprouting, development, maturation of the lymphatic network, and coordinating lymphatic valve morphogenesis and the stabilization of lymphatic valves. However, the mechanosignaling and mechanotransduction pathways involved in these processes are poorly understood. Here, we provide an overview of the impact of mechanical forces on lymphatics and summarize the current understanding of the molecular mechanisms involved in the mechanosensation and mechanotransduction by lymphatic endothelial cells. We also discuss how these mechanosensitive pathways affect endothelial cell fate and regulate lymphatic development and function. A better understanding of these mechanisms may provide a deeper insight into the pathophysiology of various diseases associated with impaired lymphatic function, such as lymphedema and may eventually lead to the discovery of novel therapeutic targets for these conditions.

scholarly journals Differential regulation of gastrulation and neuroectodermal gene expression by Snail in the Drosophila embryo

Development ◽  
1997 ◽  
Vol 124 (19) ◽  
pp. 3683-3691 ◽  
Author(s):  
K. Hemavathy ◽  
X. Meng ◽  
Y.T. Ip
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Expression Patterns ◽  
Cell Movement ◽  
Drosophila Embryo ◽  
Intermediate Phenotype ◽  
Gene Products ◽  
Mesodermal Cell ◽  
Possible Cause ◽  
Mesodermal Lineage

The initiation of mesoderm differentiation in the Drosophila embryo requires the gene products of twist and snail. In either mutant, the ventral cell invagination during gastrulation is blocked and no mesoderm-derived tissue is formed. One of the functions of Snail is to repress neuroectodermal genes and restrict their expressions to the lateral regions. The derepression of the neuroectodermal genes into the ventral region in snail mutant is a possible cause of defects in gastrulation and in mesoderm differentiation. To investigate such possibility, we analysed a series of snail mutant alleles. We found that different neuroectodermal genes respond differently in various snail mutant background. Due to the differential response of target genes, one of the mutant alleles, V2, that has reduced Snail function showed an intermediate phenotype. In V2 embryos, neuroectodermal genes, such as single-minded and rhomboid, are derepressed while ventral invagination proceeds normally. However, the differentiation of these invaginated cells into mesodermal lineage is disrupted. The results suggest that the establishment of mesodermal cell fate requires the proper restriction of neuroectodermal genes, while the ventral cell movement is independent of the expression patterns of these genes. Together with the data showing that the expression of some ventral genes disappear in snail mutants, we propose that Snail may repress or activate another set of target genes that are required specifically for gastrulation.

scholarly journals Multilevel regulation of the glass locus during Drosophila eye development

2019 ◽  
Author(s):  
Cornelia Fritsch ◽  
F. Javier Bernardo-Garcia ◽  
Tim-Henning Humberg ◽  
Sara Miellet ◽  
Silvia Almeida ◽  
...  
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Eye Development ◽  
Fruit Fly ◽  
Protein Isoforms ◽  
Critical Feature ◽  
Reading Frame ◽  
Cis Acting ◽  
Temporal Gene Expression ◽  
And Function

ABSTRACTDevelopment of eye tissue is initiated by a conserved set of transcripton factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control idendity of photoreceptor as well as non-photoreceptors cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintainance of differentiated tissues. The molecular mechanisms that control expression of glass, however remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alterantive small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is surprisingly robust and appears buffered to targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.

scholarly journals Nkx3.1 binds and negatively regulates the transcriptional activity of Sp-family members in prostate-derived cells

2005 ◽  
Vol 393 (1) ◽  
pp. 397-409 ◽  
Author(s):  
Steven O. Simmons ◽  
Jonathan M. Horowitz
Keyword(s):  
Dna Binding ◽  
Histone Deacetylases ◽  
Target Genes ◽  
Protein Complexes ◽  
Trichostatin A ◽  
Prostate Gland ◽  
Specific Antigen ◽  
Family Members ◽  
Early Event ◽  
Prostate Tumorigenesis

Nkx3.1 is a homeodomain-containing transcription factor that is expressed early in the development of the prostate gland and is believed to play an important role in the differentiation of prostatic epithelia. Loss of Nkx3.1 protein expression is often an early event in prostate tumorigenesis, and the abundance of Nkx3.1-negative epithelial cells increases with disease progression. In a number of systems, homeodomain proteins collaborate with zinc-finger-containing transcription factors to bind and regulate target genes. In the present paper, we report that Nkx3.1 collaborates with Sp-family members in the regulation of PSA (prostate-specific antigen) in prostate-derived cells. Nkx3.1 forms protein complexes with Sp proteins that are dependent on their respective DNA-binding domains and an N-terminal segment of Nkx3.1, and Nkx3.1 negatively regulates Sp-mediated transcription via Trichostatin A-sensitive and -insensitive mechanisms. A distal 1000 bp portion of the PSA promoter is required for transrepression by Nkx3.1, although Nkx3.1 DNA-binding activity is itself not required. We conclude that Nkx3.1 negatively regulates Sp-mediated transcription via the tethering of histone deacetylases and/or by inhibiting the association of Sp proteins with co-activators.

scholarly journals Temperature regulates NF-κB dynamics and function through timing of A20 transcription

2018 ◽  
Vol 115 (22) ◽  
pp. E5243-E5249 ◽  
Author(s):  
C. V. Harper ◽  
D. J. Woodcock ◽  
C. Lam ◽  
M. Garcia-Albornoz ◽  
A. Adamson ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Early Response ◽  
Strong Temperature Dependence ◽  
Necrosis Factor Alpha ◽  
Factor Alpha ◽  
Multidimensional Information ◽  
Dynamics And Function ◽  
And Function ◽  
Necrosis Factor

NF-κB signaling plays a pivotal role in control of the inflammatory response. We investigated how the dynamics and function of NF-κB were affected by temperature within the mammalian physiological range (34 °C to 40 °C). An increase in temperature led to an increase in NF-κB nuclear/cytoplasmic oscillation frequency following Tumor Necrosis Factor alpha (TNFα) stimulation. Mathematical modeling suggested that this temperature sensitivity might be due to an A20-dependent mechanism, and A20 silencing removed the sensitivity to increased temperature. The timing of the early response of a key set of NF-κB target genes showed strong temperature dependence. The cytokine-induced expression of many (but not all) later genes was insensitive to temperature change (suggesting that they might be functionally temperature-compensated). Moreover, a set of temperature- and TNFα-regulated genes were implicated in NF-κB cross-talk with key cell-fate–controlling pathways. In conclusion, NF-κB dynamics and target gene expression are modulated by temperature and can accurately transmit multidimensional information to control inflammation.

Regulation of cell survival and proliferation by the FOXO (Forkhead box, class O) subfamily of Forkhead transcription factors

2003 ◽  
Vol 31 (1) ◽  
pp. 292-297 ◽  
Author(s):  
K.U. Birkenkamp ◽  
P.J. Coffer
Keyword(s):  
Transcription Factors ◽  
Cell Survival ◽  
Cell Fate ◽  
Nuclear Export ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Acute Lymphocytic Leukaemia ◽  
Cell Fate Decisions ◽  
Forkhead Transcription Factors ◽  
Forkhead Box

Recently, the FOXO (Forkhead box, class O) subfamily of Forkhead transcription factors has been identified as direct targets of phosphoinositide 3-kinase-mediated signal transduction. The AFX (acute-lymphocytic-leukaemia-1 fused gene from chromosome X), FKHR (Forkhead in rhabdomyosarcoma) and FKHR-L1 (FKHR-like 1) transcription factors are directly phosphorylated by protein kinase B, resulting in nuclear export and inhibition of transcription. This signalling pathway was first identified in the nematode worm Caenorhabditis elegans, where it has a role in regulation of the life span of the organism. Studies have shown that this evolutionarily conserved signalling module has a role in regulation of both cell-cycle progression and cell survival in higher eukaryotes. These effects are co-ordinated by FOXO-mediated induction of a variety of specific target genes that are only now beginning to be identified. Interestingly, FOXO transcription factors appear to be able to regulate transcription through both DNA-binding-dependent and -independent mechanisms. Our understanding of the regulation of FOXO activity, and defining specific transcriptional targets, may provide clues to the molecular mechanisms controlling cell fate decisions to divide, differentiate or die.

scholarly journals The effect of human GATA4 gene mutations on the activity of target gonadal promoters

2008 ◽  
Vol 42 (2) ◽  
pp. 149-160 ◽  
Author(s):  
Marie France Bouchard ◽  
Hiroaki Taniguchi ◽  
Robert S Viger
Keyword(s):  
Dna Binding ◽  
Gene Transcription ◽  
Transcriptional Activity ◽  
Target Genes ◽  
Heart Defects ◽  
Gene Mutations ◽  
Significant Loss ◽  
Specific Gene ◽  
Mutant Proteins ◽  
And Function

GATA transcription factors are crucial regulators of cell-specific gene expression in many tissues including the gonads. Although clinical cases of reproductive dysfunction have yet to be formally linked to GATA gene mutations, they have begun to be reported in other systems. Heterozygous GATA4 mutations have been associated with cases of congenital heart defects. Little is known, however, about the effect of these mutations on gonadal gene transcription. Since individuals carrying these mutations do not appear to suffer from gross reproductive defects, we hypothesized that this might be due to the differential transcriptional properties of the mutant proteins on heart versus gonadal target genes. Five mutations (S52F, E215D, G295S, V266M, and E359X) were recreated in the rat GATA4 protein. Several parameters were used to analyze the transcriptional properties of the mutants: activation of known gonadal target promoters (Star, Cyp19a1, and Inha), DNA binding, and interaction with GATA4 transcriptional partners. Three mutations (S52F, G295S, and E359X) reduced GATA4 transcriptional activity on the different gonadal promoters. With the exception of the G295S mutant, which showed a significant loss of DNA-binding affinity, the decrease in activity of the other GATA4 mutants was not associated with a change in DNA binding. All GATA4 mutants retained their ability to interact and cooperate with their major gonadal partners (NR5A1 and NR5A2) thereby compensating in part for the loss in intrinsic GATA4 transcriptional activity. Thus, unlike the heart, where the GATA4 mutations have deleterious effects, our data suggest that they would have a lesser impact on gonadal gene transcription and function.

scholarly journals Ecology and molecular targets of hypermutation in the global microbiome

2020 ◽  
Author(s):  
Simon Roux ◽  
Blair G. Paul ◽  
Sarah C. Bagby ◽  
Michelle A. Allen ◽  
Graeme Attwood ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
Distinct Type ◽  
Raw Material ◽  
Read Mapping ◽  
A Genome ◽  
And Function ◽  
Natural Communities ◽  
Cellular Genome

AbstractChanges in the sequence of an organism’s genome, i.e. mutations, are the raw material of evolution1. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as Diversity-generating retroelements (DGRs)2–4. DGRs introduce mutations in specific target genes, and were characterized from several cultivated bacteria and bacteriophages2. Whilst a larger diversity of DGR loci has been identified in genomic data from environmental samples, i.e. metagenomes, the ecological role of these DGRs and their associated evolutionary drivers remain poorly understood5–7. Here we built and analyzed an extensive dataset of >30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment.

Prospero distinguishes sibling cell fate without asymmetric localization in the Drosophila adult external sense organ lineage

Development ◽  
1999 ◽  
Vol 126 (10) ◽  
pp. 2063-2071 ◽  
Author(s):  
L. Manning ◽  
C.Q. Doe
Keyword(s):  
Cell Fate ◽  
Asymmetric Cell Division ◽  
Protein Localization ◽  
Sense Organ ◽  
Cell Loss ◽  
Sense Organs ◽  
Cell Fates ◽  
Dendrite Morphology ◽  
And Function ◽  
Sheath Cells

The adult external sense organ precursor (SOP) lineage is a model system for studying asymmetric cell division. Adult SOPs divide asymmetrically to produce IIa and IIb daughter cells; IIa generates the external socket (tormogen) and hair (trichogen) cells, while IIb generates the internal neuron and sheath (thecogen) cells. Here we investigate the expression and function of prospero in the adult SOP lineage. Although Prospero is asymmetrically localized in embryonic SOP lineage, this is not observed in the adult SOP lineage: Prospero is first detected in the IIb nucleus and, during IIb division, it is cytoplasmic and inherited by both neuron and sheath cells. Subsequently, Prospero is downregulated in the neuron but maintained in the sheath cell. Loss of prospero function leads to ‘double bristle’ sense organs (reflecting a IIb-to-IIa transformation) or ‘single bristle’ sense organs with abnormal neuronal differentiation (reflecting defective IIb development). Conversely, ectopic prospero expression results in duplicate neurons and sheath cells and a complete absence of hair/socket cells (reflecting a IIa-to-IIb transformation). We conclude that (1) despite the absence of asymmetric protein localization, prospero expression is restricted to the IIb cell but not its IIa sibling, (2) prospero promotes IIb cell fate and inhibits IIa cell fate, and (3) prospero is required for proper axon and dendrite morphology of the neuron derived from the IIb cell. Thus, prospero plays a fundamental role in establishing binary IIa/IIb sibling cell fates without being asymmetrically localized during SOP division. Finally, in contrast to previous studies, we find that the IIb cell divides prior to the IIa cell in the SOP lineage.

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