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Trends in Cell Biology Mar 2009As major regulators of the cell cycle, apoptosis and differentiation, E2F transcription factors have been studied extensively in a broad range of organisms. The recent... (Review)
Review
As major regulators of the cell cycle, apoptosis and differentiation, E2F transcription factors have been studied extensively in a broad range of organisms. The recent identification of atypical E2F family members further expands our structural, functional and molecular view of the cellular E2F activity. Unlike other family members, atypical E2Fs have a duplicated DNA-binding domain and control gene expression without heterodimerization with dimerization partner proteins. Recently, knockout strategies in plants and mammals have pinpointed that atypical E2Fs have a crucial role in plant cell size control, endocycle regulation, proliferation and apoptotic response upon DNA stress. Their position at the crossroads of proliferation and DNA stress response marks these novel E2F proteins as interesting study objects in the field of tumor biology.
Topics: Animals; Arabidopsis; Arabidopsis Proteins; E2F Transcription Factors; E2F7 Transcription Factor; Humans; Multigene Family; Repressor Proteins
PubMed: 19201609
DOI: 10.1016/j.tcb.2009.01.002 -
Developmental Cell Oct 2002A recent study has demonstrated that an external coincidence mechanism, based on the endogenous circadian control of a transcription factor expression (CO) and the... (Review)
Review
A recent study has demonstrated that an external coincidence mechanism, based on the endogenous circadian control of a transcription factor expression (CO) and the modulation of CO function by light, constitutes the molecular basis for the regulation of flowering time by photoperiod.
Topics: Animals; Circadian Rhythm; Photoperiod; Transcription Factors
PubMed: 12408794
DOI: 10.1016/s1534-5807(02)00296-4 -
Genes Dec 2022Ethyl acetate is an important flavor element that is a vital component of . To date, the transcription factors that can help identify the molecular mechanisms involved...
Ethyl acetate is an important flavor element that is a vital component of . To date, the transcription factors that can help identify the molecular mechanisms involved in the synthesis of ethyl acetate have not been studied. In the present study, we sequenced and assembled the strain YF1503 transcriptomes to identify transcription factors. We identified 307 transcription factors in YF1503 using high-throughput RNA sequencing. Some transcription factors, such as C2H2, bHLH, MYB, and bZIP, were up-regulated, and these might play a role in ethyl acetate synthesis. According to the trend of ethyl acetate content, heat map results and STEM, twelve genes were selected for verification of expression levels using quantitative real-time PCR. This dynamic transcriptome analysis presents fundamental information on the transcription factors and pathways that are involved in the synthesis of ethyl acetate in aroma-producing yeast. Of significant interest is the discovery of the roles of various transcription factor genes in the synthesis of ethyl acetate.
Topics: Transcription Factors; Odorants; Yeasts; Gene Expression Profiling
PubMed: 36553608
DOI: 10.3390/genes13122341 -
Genes & Development Jul 1993
Review
Topics: Animals; DNA-Directed RNA Polymerases; Humans; Protein Conformation; Transcription Factor TFIID; Transcription Factors; Transcription, Genetic
PubMed: 8330735
DOI: 10.1101/gad.7.7b.1291 -
Nucleic Acids Research Oct 2002Multifunctional proteins challenge the conventional 'one protein-one function' paradigm. Here we note apparent multifunctional proteins with nucleic acid partners,... (Review)
Review
Multifunctional proteins challenge the conventional 'one protein-one function' paradigm. Here we note apparent multifunctional proteins with nucleic acid partners, tabulating eight examples. We then focus on eight additional cases of transcription factors that bind double-stranded DNA with sequence specificity, but that also appear to lead alternative lives as RNA-binding proteins. Exemplified by the prototypic Xenopus TFIIIA protein, and more recently by mammalian p53, this list of transcription factors includes WT-1, TRA-1, bicoid, the bacterial sigma(70) subunit, STAT1 and TLS/FUS. The existence of transcription factors that bind both DNA and RNA provides an interesting puzzle. Little is known concerning the biological roles of these alternative protein-nucleic acid interactions, and even less is known concerning the structural basis for dual nucleic acid specificity. We discuss how these natural examples have motivated us to identify artificial RNA sequences that competitively inhibit a DNA-binding transcription factor not known to have a natural RNA partner. The identification of such RNAs raises the possibility that RNA binding by DNA-binding proteins is more common than currently appreciated.
Topics: Animals; Base Sequence; DNA; DNA-Binding Proteins; Homeodomain Proteins; Humans; Models, Molecular; Molecular Sequence Data; Protein Binding; RNA; STAT1 Transcription Factor; Trans-Activators; Transcription Factor TFIIIA; Transcription Factors; Tumor Suppressor Protein p53
PubMed: 12364590
DOI: 10.1093/nar/gkf512 -
International Journal of Molecular... May 2022Transcription factors play crucial roles in the regulation of heart induction, formation, growth and morphogenesis. Zinc finger GATA transcription factors are among the... (Review)
Review
Transcription factors play crucial roles in the regulation of heart induction, formation, growth and morphogenesis. Zinc finger GATA transcription factors are among the critical regulators of these processes. , and genes are expressed in a partially overlapping manner in developing hearts, and and continue their expression in adult cardiac myocytes. Using different experimental models, GATA4, 5 and 6 were shown to work together not only to ensure specification of cardiac cells but also during subsequent heart development. The complex involvement of these related gene family members in those processes is demonstrated through the redundancy among them and crossregulation of each other. Our recent identification at the genome-wide level of genes specifically regulated by each of the three family members and our earlier discovery that and function upstream, while functions downstream of noncanonical Wnt signalling during cardiac differentiation, clearly demonstrate the functional differences among the cardiogenic GATA factors. Such suspected functional differences are worth exploring more widely. It appears that in the past few years, significant advances have indeed been made in providing a deeper understanding of the mechanisms by which each of these molecules function during heart development. In this review, I will therefore discuss current evidence of the role of individual cardiogenic GATA factors in the process of heart development and emphasize the emerging central role of
Topics: GATA Transcription Factors; GATA4 Transcription Factor; GATA5 Transcription Factor; GATA6 Transcription Factor; Gene Expression Regulation, Developmental; Heart; Myocytes, Cardiac
PubMed: 35563646
DOI: 10.3390/ijms23095255 -
BMC Molecular Biology Dec 2018NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to...
BACKGROUND
NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in Npas3 knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH-PAS transcription factors. Here we set out to characterize NPAS3 as a transcription factor, and to confirm whether NPAS3 acts as predicted for a Class 1 bHLH-PAS family member.
RESULTS
Through these studies we have experimentally demonstrated that NPAS3 behaves as a true transcription factor, capable of gene regulation through direct association with DNA. NPAS3 and ARNT are confirmed to directly interact in human cells through both bHLH and PAS dimerization domains. The C-terminus of NPAS3 was found to contain a functional transactivation domain. Further, the NPAS3::ARNT heterodimer was shown to directly regulate the expression of VGF and TXNIP through binding of their proximal promoters. Finally, we assessed the effects of three human variants of NPAS3 on gene regulatory function and do not observe significant deficits.
CONCLUSIONS
NPAS3 is a true transcription factor capable of regulating expression of target genes through their promoters by directly cooperating with ARNT. The tested human variants of NPAS3 require further characterization to identify their effects on NPAS3 expression and function in the individuals that carry them. These data enhance our understanding of the molecular function of NPAS3 and the mechanism by which it contributes to normal and abnormal neurodevelopment and neural function.
Topics: Basic Helix-Loop-Helix Transcription Factors; Carrier Proteins; Cell Line; Gene Expression Regulation; Genes, Reporter; Genetic Variation; Humans; Nerve Tissue Proteins; Promoter Regions, Genetic; Protein Binding; Protein Interaction Domains and Motifs; Protein Transport; Transcription Factors
PubMed: 30509165
DOI: 10.1186/s12867-018-0117-4 -
Molecular Cell Jun 2022Chong et al. (2022) show how the propensity of transcription factors (TFs) to associate into hubs must be finely regulated for optimal transcription.
Chong et al. (2022) show how the propensity of transcription factors (TFs) to associate into hubs must be finely regulated for optimal transcription.
Topics: Gene Expression; Gene Expression Regulation; Transcription Factors
PubMed: 35659322
DOI: 10.1016/j.molcel.2022.05.015 -
The Journal of Clinical Investigation Dec 1997
Topics: Animals; Humans; NF-kappa B; Neoplasms; Proto-Oncogene Proteins; Transcription Factor RelA; Transcription Factor RelB; Transcription Factors
PubMed: 9399935
DOI: 10.1172/JCI119843 -
PLoS Biology Oct 2023The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way...
The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections-known as rewiring-that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system with the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify 3 key properties-high activation, high expression, and preexisting low-level affinity for novel target genes-that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by preexisting GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.
Topics: Transcription Factors; Gene Expression Regulation; Gene Regulatory Networks; Models, Theoretical
PubMed: 37871011
DOI: 10.1371/journal.pbio.3002348