scholarly journals Transcription factor Pit-1 affects transcriptional timing in the dual-promoter human prolactin gene

Endocrinology ◽  
2021 ◽  
Author(s):  
Anne V McNamara ◽  
Raheela Awais ◽  
Hiroshi Momiji ◽  
Lee Dunham ◽  
Karen Featherstone ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Image Data ◽  
Artificial Chromosome ◽  
Active Role ◽  
Time Lapse ◽  
Promoter Regions ◽  
Promoter Architecture ◽  
Human Prolactin ◽  
Active Transcription ◽  
Transcriptional Bursting

Abstract Gene transcription occurs in short bursts interspersed with silent periods, and these kinetics can be altered by promoter structure. The effect of alternate promoter architecture on transcription bursting is not known. We studied the human prolactin (hPRL) gene that contains two promoters, a pituitary-specific promoter that requires the transcription factor Pit-1, and displays dramatic transcriptional bursting activity, and an alternate upstream promoter that is active in non-pituitary tissues. We studied large hPRL genomic fragments with luciferase reporters, and used bacterial artificial chromosome (BAC) recombineering to manipulate critical promoter regions. Stochastic switch mathematical modelling of single-cell time-lapse luminescence image data revealed that the Pit-1-dependent promoter showed longer, higher-amplitude transcriptional bursts. Knockdown studies confirmed that the presence of Pit-1 stabilised and prolonged periods of active transcription. Pit-1 therefore plays an active role in establishing the timing of transcription cycles, in addition to its cell-specific functions.

Live imaging of Runx1 expression in the dorsal aorta tracks the emergence of blood progenitors from endothelial cells

Blood ◽  
2010 ◽  
Vol 116 (6) ◽  
pp. 909-914 ◽  
Author(s):  
Enid Yi Ni Lam ◽  
Christopher J. Hall ◽  
Philip S. Crosier ◽  
Kathryn E. Crosier ◽  
Maria Vega Flores
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Fluorescent Protein ◽  
Living Organism ◽  
Time Lapse ◽  
Dorsal Aorta ◽  
Transgenic Zebrafish ◽  
Hematopoietic Stem ◽  
Green Fluorescent

Abstract Blood cells of an adult vertebrate are continuously generated by hematopoietic stem cells (HSCs) that originate during embryonic life within the aorta-gonad-mesonephros region. There is now compelling in vivo evidence that HSCs are generated from aortic endothelial cells and that this process is critically regulated by the transcription factor Runx1. By time-lapse microscopy of Runx1-enhanced green fluorescent protein transgenic zebrafish embryos, we were able to capture a subset of cells within the ventral endothelium of the dorsal aorta, as they acquire hemogenic properties and directly emerge as presumptive HSCs. These nascent hematopoietic cells assume a rounded morphology, transiently occupy the subaortic space, and eventually enter the circulation via the caudal vein. Cell tracing showed that these cells subsequently populated the sites of definitive hematopoiesis (thymus and kidney), consistent with an HSC identity. HSC numbers depended on activity of the transcription factor Runx1, on blood flow, and on proper development of the dorsal aorta (features in common with mammals). This study captures the earliest events of the transition of endothelial cells to a hemogenic endothelium and demonstrates that embryonic hematopoietic progenitors directly differentiate from endothelial cells within a living organism.

Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics

2021 ◽  
Author(s):  
Liang Ma ◽  
Zeyue Gao ◽  
Jiegen Wu ◽  
Bijunyao Zhong ◽  
Yuchen Xie ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcriptional Bursting ◽  
Coactivator P300

DNA-binding and transcriptional properties of human transcription factor TFIID after mild proteolysis

1990 ◽  
Vol 10 (7) ◽  
pp. 3415-3420
Author(s):  
M W Van Dyke ◽  
M Sawadogo
Keyword(s):  
Transcription Factor ◽  
Transcription Initiation ◽  
Small Region ◽  
Protein Product ◽  
Differential Sensitivity ◽  
Yeast Cells ◽  
Promoter Regions ◽  
Regulatory Processes ◽  
Promoter Recognition ◽  
Transcription Complexes

The existence of separable functions within the human class II general transcription factor TFIID was probed for differential sensitivity to mild proteolytic treatment. Independent of whether TFIID was bound to DNA or free in solution, partial digestion with either one of a variety of nonspecific endoproteases generated a protease-resistant protein product that retained specific DNA recognition, as revealed by DNase I footprinting. However, in contrast to native TFIID, which interacts with the adenovirus major late (ML) promoter over a very broad DNA region, partially proteolyzed TFIID interacted with only a small region of the ML promoter immediately surrounding the TATA sequence. This novel footprint was very similar to that observed with the TATA factor purified from yeast cells. Partially proteolyzed human TFIID could form stable complexes that were resistant to challenge by exogenous templates. It could also nucleate the assembly of transcription complexes on the ML promoter with an efficiency comparable to that of native TFIID, yielding similar levels of transcription initiation. These results suggest a model in which the human TFIID protein is composed of at least two different regions or polypeptides: a protease-resistant "core," which by itself is sufficient for promoter recognition and basal transcriptional levels, and a protease-sensitive "tail," which interacts with downstream promoter regions and may be involved in regulatory processes.

scholarly journals The Role of EjSVPs in Flower Initiation in Eriobotrya japonica

2019 ◽  
Vol 20 (23) ◽  
pp. 5933 ◽  
Author(s):  
Yuanyuan Jiang ◽  
Jiangrong Peng ◽  
Zhike Zhang ◽  
Shoukai Lin ◽  
Shunquan Lin ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Expression Patterns ◽  
Active Role ◽  
Eriobotrya Japonica ◽  
Flower Initiation ◽  
Mads Box ◽  
Promoter Regions ◽  
Expression Levels ◽  
Flowering Regulation ◽  
Responsive Element

Flowering plants have evolved different flowering habits to sustain long-term reproduction. Most woody trees experience dormancy and then bloom in the warm spring, but loquat blooms in the cold autumn and winter. To explore its mechanism of flowering regulation, we cloned two SHORT VEGETATIVE PHASE (SVP) homologous genes from ‘Jiefanzhong’ loquat (Eriobotrya japonica Lindl.), namely, EjSVP1 and EjSVP2. Sequence analysis revealed that the EjSVPs were typical MADS-box transcription factors and exhibited a close genetic relationship with other plant SVP/DORMANCY-ASSOCIATED MADS-BOX (DAM) proteins. The temporal and spatial expression patterns showed that EjSVP1 and EjSVP2 were mainly expressed in the shoot apical meristem (SAM) after the initiation of flowering; after reaching their highest level, they gradually decreased with the development of the flower until they could not be detected. EjSVP1 expression levels were relatively high in young tissues, and EjSVP2 expression levels were relatively high in young to mature transformed tissues. Interestingly, EjSVP2 showed relatively high expression levels in various flower tissues. We analyzed the EjSVP promoter regions and found that they did not contain the C-repeat/dehydration-responsive element. Finally, we overexpressed the EjSVPs in wild-type Arabidopsis thaliana Col-0 and found no significant changes in the number of rosette leaves of Arabidopsis thaliana; however, overexpression of EjSVP2 affected the formation of Arabidopsis thaliana flower organs. In conclusion, EjSVPs were found to play an active role in the development of loquat flowering. These findings may provide a reference for exploring the regulation mechanisms of loquat flowering and the dormancy mechanisms of other plants.

scholarly journals An Artificially Constructed De Novo Human Chromosome Behaves Almost Identically to Its Natural Counterpart during Metaphase and Anaphase in Living Cells

2006 ◽  
Vol 26 (20) ◽  
pp. 7682-7695 ◽  
Author(s):  
Tomohiro Tsuduki ◽  
Megumi Nakano ◽  
Nao Yasuoka ◽  
Saeko Yamazaki ◽  
Teruaki Okada ◽  
...  
Keyword(s):  
Yeast Artificial Chromosome ◽  
Fluorescent Protein ◽  
De Novo ◽  
Artificial Chromosome ◽  
Time Lapse ◽  
Living Cells ◽  
Lac Repressor ◽  
Host Chromosome ◽  
Artificial Chromosomes ◽  
Spindle Midzone

ABSTRACT Human artificial chromosomes (HACs) are promising reagents for the analysis of chromosome function. While HACs are maintained stably, the segregation mechanisms of HACs have not been investigated in detail. To analyze HACs in living cells, we integrated 256 copies of the Lac operator into a precursor yeast artificial chromosome (YAC) containing α-satellite DNA and generated green fluorescent protein (GFP)-tagged HACs in HT1080 cells expressing a GFP-Lac repressor fusion protein. Time-lapse analyses of GFP-HACs and host centromeres in living mitotic cells indicated that the HAC was properly aligned at the spindle midzone and that sister chromatids of the HAC separated with the same timing as host chromosomes and moved to the spindle poles with mobility similar to that of the host centromeres. These results indicate that a HAC composed of a multimer of input α-satellite YACs retains most of the functions of the centromeres on natural chromosomes. The only difference between the HAC and the host chromosome was that the HAC oscillated more frequently, at higher velocity, across the spindle midzone during metaphase. However, this provides important evidence that an individual HAC has the capacity to maintain tensional balance in the pole-to-pole direction, thereby stabilizing its position around the spindle midzone.

scholarly journals Different SP1 binding dynamics at individual genomic loci in human cells

2020 ◽  
Author(s):  
Yuko Hasegawa ◽  
Kevin Struhl
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Time Course ◽  
Nucleosome Occupancy ◽  
Binding Kinetics ◽  
Common Mechanism ◽  
Sequence Motif ◽  
Promoter Regions ◽  
Pml Bodies ◽  
Slow Turnover

Using a tamoxifen-inducible time-course ChIP-seq approach, we show that the ubiquitous transcription factor SP1 has different binding dynamics at its target sites in the human genome that are not correlated with SP1 occupancy levels at those sites. While ~70% of SP1 binding sites are located in promoter regions, loci with slow SP1 binding turnover are enriched in enhancer and Polycomb-repressed regions. Unexpectedly, SP1 sites with fast turnover times tend to have higher quality and more copies of the SP1 sequence motif. Different co-binding factors associate near SP1 binding sites depending on their binding kinetics and on their location at promoters or enhancers. For example, NFY and FOS are preferentially associated near promoter-bound SP1 sites with fast turnover, whereas DNA motifs of ETS and homeodomain proteins are preferentially observed at sites with slow turnover. At promoters but not enhancers, proteins involved in sumoylation and PML bodies associate more strongly with slow SP1 binding sites than with the fast-binding sites. The speed of SP1 binding turnover is not associated with nucleosome occupancy, and it is not necessarily coupled to higher transcriptional activity. These results with SP1 are in contrast from those of human TBP, indicating that there is no common mechanism affecting transcription factor binding kinetics.

Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

2021 ◽  
Author(s):  
Ineke Brouwer ◽  
Emma Kerklingh ◽  
Fred van Leeuwen ◽  
Tineke L Lenstra
Keyword(s):  
Transcription Factor ◽  
Chromatin Remodeling ◽  
Single Molecule ◽  
Binding Sites ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Nucleosome Remodeling ◽  
Epistasis Analysis ◽  
Transcriptional Bursting ◽  
Kinetics Of

Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in budding yeast to measure how transcriptional bursting changes upon single and double perturbations of chromatin remodeling factors, the transcription factor Gal4 and preinitiation complex (PIC) components. Using dynamic epistasis analysis, we reveal how remodeling of different nucleosomes regulates individual transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC acts synergistically with Gal4 binding to facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. In the absence of remodelers, nucleosomes at canonical TATA boxes are displaced by TBP binding to allow for transcription activation. Overall, our results reveal how promoter nucleosome remodeling, together with transcription factor and PIC binding regulates the kinetics of transcriptional bursting.

scholarly journals Identification and characterization of the bZIP transcription factor family in yellowhorn

2020 ◽  
Vol 32 (1) ◽  
pp. 273-284 ◽  
Author(s):  
Qiaoying Chang ◽  
Xin Lu ◽  
Zhi Liu ◽  
Zhimin Zheng ◽  
Song Yu
Keyword(s):  
Transcription Factor ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Bzip Transcription Factor ◽  
Biological Functions ◽  
Transcription Factor Family ◽  
Promoter Regions ◽  
Basic Leucine Zipper ◽  
Biotic Stresses ◽  
Bzip Transcription Factor Family

AbstractThe basic leucine zipper (bZIP) transcription factor family is one of the largest and most diverse families in plants, regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses. However, little is known about the biological functions of bZIP proteins in yellowhorn (Xanthoceras sorbifolium). Recently, 64 XsbZIP genes were identified in the yellowhorn genome and found to be disproportionately distributed in linkage groups. The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP, ZmbZIP and GmbZIP proteins. Five intron patterns in the basic and hinge regions and additional conserved motifs were defined, both supporting the group classification and possibly contributing to their functional diversity. Compared to tandem duplication, the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes. In addition, most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions. Moreover, the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses, including salt (NaCl), cold and abscisic acid, with possibly different molecular mechanisms. These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.

Mechanisms of mammalian zinc-regulated gene expression

2008 ◽  
Vol 36 (6) ◽  
pp. 1262-1266 ◽  
Author(s):  
Kelly A. Jackson ◽  
Ruth A. Valentine ◽  
Lisa J. Coneyworth ◽  
John C. Mathers ◽  
Dianne Ford
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Repression ◽  
Mammalian Cells ◽  
Gene Promoter ◽  
Mrna Levels ◽  
Promoter Regions ◽  
Mrna Stabilization ◽  
Transcriptional Regulatory ◽  
Regulated Gene Expression

Mechanisms through which gene expression is regulated by zinc are central to cellular zinc homoeostasis. In this context, evidence for the involvement of zinc dyshomoeostasis in the aetiology of diseases, including Type 2 diabetes, Alzheimer's disease and cancer, highlights the importance of zinc-regulated gene expression. Mechanisms elucidated in bacteria and yeast provide examples of different possible modes of zinc-sensitive gene regulation, involving the zinc-regulated binding of transcriptional activators and repressors to gene promoter regions. A mammalian transcriptional regulatory mechanism that mediates zinc-induced transcriptional up-regulation, involving the transcription factor MTF1 (metal-response element-binding transcription factor 1), has been studied extensively. Gene responses in the opposite direction (reduced mRNA levels in response to increased zinc availability) have been observed in mammalian cells, but a specific transcriptional regulatory process responsible for such a response has yet to be identified. Examples of single zinc-sensitive transcription factors regulating gene expression in opposite directions are emerging. Although zinc-induced transcriptional repression by MTF1 is a possible explanation in some specific instances, such a mechanism cannot account for repression by zinc of all mammalian genes that show this mode of regulation, indicating the existence of as yet uncharacterized mechanisms of zinc-regulated transcription in mammalian cells. In addition, recent findings reveal a role for effects of zinc on mRNA stability in the regulation of specific zinc transporters. Our studies on the regulation of the human gene SLC30A5 (solute carrier 30A5), which codes for the zinc transporter ZnT5, have revealed that this gene provides a model system by which to study both zinc-induced transcriptional down-regulation and zinc-regulated mRNA stabilization.

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