scholarly journals LEAFY, a Pioneer Transcription Factor in Plants: A Mini-Review

2021 ◽  
Vol 12 ◽  
Author(s):  
Nobutoshi Yamaguchi
Keyword(s):  
Eukaryotic Transcription ◽  
Linker Histones ◽  
Complex Functions ◽  
Terminal Flower 1 ◽  
Pioneer Factor ◽  
Meristem Identity ◽  
Pioneer Factors ◽  
Pioneer Transcription Factor ◽  
Insight Into ◽  
Meristem Identity Gene

A subset of eukaryotic transcription factors (TFs) possess the ability to reprogram one cell type into another. Genes important for cellular reprograming are typically located in closed chromatin, which is covered by nucleosomes. Pioneer factors are a special class of TFs that can initially engage their target sites in closed chromatin prior to the engagement with, opening of, or modification of the sites by other factors. Although many pioneer factors are known in animals, a few have been characterized in plants. The TF LEAFY (LFY) acts as a pioneer factor specifying floral fate in Arabidopsis. In response to endogenous and environmental cues, plants produce appropriate floral inducers (florigens). During the vegetative phase, LFY is repressed by the TERMINAL FLOWER 1 (TFL1)–FD complex, which functions as a floral inhibitor, or anti-florigen. The florigen FLOWERING LOCUS T (FT) competes with TFL1 to prevent the binding of the FD TF to the LFY locus. The resulting FT–FD complex functions as a transient stimulus to activate its targets. Once LFY has been transcribed in the appropriate spatiotemporal manner, LFY binds to nucleosomes in closed chromatin regions. Subsequently, LFY opens the chromatin by displacing H1 linker histones and recruiting the SWI/SNF chromatin-remodeling complex. Such local changes permit the binding of other TFs, leading to the expression of the floral meristem identity gene APETALA1. This mini-review describes the latest advances in our understanding of the pioneer TF LFY, providing insight into the establishment of gene expression competence through the shaping of the plant epigenetic landscape.

Separation of shoot and floral identity in Arabidopsis

Development ◽  
1999 ◽  
Vol 126 (6) ◽  
pp. 1109-1120 ◽  
Author(s):  
O.J. Ratcliffe ◽  
D.J. Bradley ◽  
E.S. Coen
Keyword(s):  
Shoot Apex ◽  
Floral Meristem ◽  
Floral Meristem Identity ◽  
Terminal Flower ◽  
Terminal Flower 1 ◽  
Type Pattern ◽  
Meristem Identity ◽  
Floral Meristems ◽  
Arabidopsis Plant ◽  
Meristem Identity Gene

The overall morphology of an Arabidopsis plant depends on the behaviour of its meristems. Meristems derived from the shoot apex can develop into either shoots or flowers. The distinction between these alternative fates requires separation between the function of floral meristem identity genes and the function of an antagonistic group of genes, which includes TERMINAL FLOWER 1. We show that the activities of these genes are restricted to separate domains of the shoot apex by different mechanisms. Meristem identity genes, such as LEAFY, APETALA 1 and CAULIFLOWER, prevent TERMINAL FLOWER 1 transcription in floral meristems on the apex periphery. TERMINAL FLOWER 1, in turn, can inhibit the activity of meristem identity genes at the centre of the shoot apex in two ways; first by delaying their upregulation, and second, by preventing the meristem from responding to LEAFY or APETALA 1. We suggest that the wild-type pattern of TERMINAL FLOWER 1 and floral meristem identity gene expression depends on the relative timing of their upregulation.

scholarly journals Flowering time and the identification of floral marker genes in Solanum tuberosum ssp. andigena

2019 ◽  
Vol 71 (3) ◽  
pp. 986-996 ◽  
Author(s):  
Tanja Seibert ◽  
Christin Abel ◽  
Vanessa Wahl
Keyword(s):  
Flowering Time ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Marker Genes ◽  
Flower Meristem ◽  
Growth Regime ◽  
Long Day ◽  
Storage Organs ◽  
Meristem Identity ◽  
Meristem Identity Gene

Abstract Solanaceae is a family of flowering plants that includes agricultural species such as tomato (Solanum lycopersicum), eggplant (S. melongena), pepper (Capsicum annuum), and potato (S. tuberosum). The transition from the vegetative to reproductive stage has been extensively investigated in tomato as it affects fruit yield. While potato has mainly been studied with regards to the formation of storage organs, control of flowering time is a subject of increasing interest as development of true seeds is becoming more important for future breeding strategies. Here, we describe a robust growth regime for synchronized development of S. tuberosum ssp. andigena. Using SEM to analyse the developmental stages of the shoot apical meristem (SAM) throughout the floral transition, we show that andigena is a facultative long-day plant with respect to flowering. In addition, we identify the flower meristem identity gene MACROCALYX (StMC) as a marker to distinguish between the vegetative and reproductive stages. We show that the expression of WUSCHEL HOMEOBOX 9 (StWOX9) and ANANTHA (StAN) are specific to the inflorescence meristem and flower meristems in the cyme, respectively. The expression patterns of homologs of Arabidopsis flowering-time regulators were studied, and indicated that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (StSOC1) and StFD might regulate flowering similar to other plant species.

scholarly journals GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Marissa M Gaskill ◽  
Tyler J Gibson ◽  
Elizabeth D Larson ◽  
Melissa M Harrison
Keyword(s):  
Chromatin Accessibility ◽  
Drosophila Embryo ◽  
Gaga Factor ◽  
Zygotic Transcription ◽  
Early Drosophila Embryo ◽  
Zygotic Gene ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Genome Activation ◽  
Development Proceeds

Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.

scholarly journals Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated

2019 ◽  
Author(s):  
Markus Nevil ◽  
Tyler J. Gibson ◽  
Constantine Bartolutti ◽  
Anusha Iyengar ◽  
Melissa M Harrison
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Accessibility ◽  
Mitotic Chromosomes ◽  
Developmentally Regulated ◽  
Regulatory Modules ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Coordinate Changes ◽  
Accessible Chromatin

AbstractThe dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor, Grainy head (Grh). Grh is expressed throughout Drosophila development and functions as a pioneer factor in the larvae. We demonstrated that Grh remains bound to condensed mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking either maternal or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and is likely influenced by additional factors expressed at a given developmental stage.

scholarly journals Nuclear Mobility and Activity of FOXA1 with Androgen Receptor Are Regulated by SUMOylation

2014 ◽  
Vol 28 (10) ◽  
pp. 1719-1728 ◽  
Author(s):  
Päivi Sutinen ◽  
Vesa Rahkama ◽  
Miia Rytinki ◽  
Jorma J. Palvimo
Keyword(s):  
Androgen Receptor ◽  
Dna Binding ◽  
Specific Antigen ◽  
Hek293 Cells ◽  
Lncap Cells ◽  
Post Translational Modification ◽  
Transactivation Domains ◽  
Pioneer Factor ◽  
Important Regulator ◽  
Pioneer Transcription Factor

Forkhead box (FOX) protein A1 has been dubbed a pioneer transcription factor because it binds target sites in DNA, thereby displacing nucleosomes to loosen chromatin and facilitating steroid receptor DNA binding nearby. FOXA1 is an important regulator of prostate development, collaborating with androgen receptor (AR). Post-translational modifications regulating FOXA1 are thus far poorly understood. SUMOylation, post-translational modification of proteins by small ubiquitin-like modifier (SUMO) proteins, has emerged as an important regulatory mechanism in transcriptional regulation. In this work, we show by SUMOylation assays in COS-1 cells that the FOXA1 is modified at least in two of its three lysines embedded in SUMOylation consensus, K6 and K389, in proximity to its transactivation domains and K267 proximal to its DNA-binding domain. We also provide evidence for SUMO-2/3 modification of endogenous FOXA1 in LNCaP prostate cancer cells. Based on fluorescence recovery after photobleaching assays with mCherry-fused FOXA1 and EGFP-fused AR in HEK293 cells, the presence of FOXA1 retards the nuclear mobility of agonist-bound AR. Interestingly, mutation of the FOXA1 SUMOylation sites slows down the mobility of the pioneer factor, further retarding the nuclear mobility of the AR. Chromatin immunoprecipitation and gene expression assays suggest that the mutation enhances FOXA1's chromatin occupancy as well as its activity on AR-regulated prostate-specific antigen (PSA) locus in LNCaP cells. Moreover, the mutation altered the ability of FOXA1 to influence proliferation of LNCaP cells. Taken together, these results strongly suggest that the SUMOylation can regulate the transcriptional activity of FOXA1 with the AR.

scholarly journals Enhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
I. Cody MacDonald ◽  
Travis R. Seamons ◽  
Jonathan C. Emmons ◽  
Shwan B. Javdan ◽  
Tara L. Deans
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Activation ◽  
Dynamic Range ◽  
Current Trend ◽  
Medical Science ◽  
Genetic Circuits ◽  
Eukaryotic Transcription ◽  
Complex Functions ◽  
Eukaryotic Gene

AbstractExpanding the genetic toolbox for prokaryotic synthetic biology is a promising strategy for enhancing the dynamic range of gene expression and enabling new engineered applications for research and biomedicine. Here, we reverse the current trend of moving genetic parts from prokaryotes to eukaryotes and demonstrate that the activating eukaryotic transcription factor QF and its corresponding DNA-binding sequence can be moved to E. coli to introduce transcriptional activation, in addition to tight off states. We further demonstrate that the QF transcription factor can be used in genetic devices that respond to low input levels with robust and sustained output signals. Collectively, we show that eukaryotic gene regulator elements are functional in prokaryotes and establish a versatile and broadly applicable approach for constructing genetic circuits with complex functions. These genetic tools hold the potential to improve biotechnology applications for medical science and research.

scholarly journals Effectors of Root-Knot Nematodes: An Arsenal for Successful Parasitism

2021 ◽  
Vol 12 ◽  
Author(s):  
Shounak Jagdale ◽  
Uma Rao ◽  
Ashok P. Giri
Keyword(s):  
Plant Immunity ◽  
Plant Defence ◽  
Giant Cells ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Root Knot Nematodes ◽  
Feeding Sites ◽  
The Past ◽  
Complex Functions ◽  
Insight Into

Root-knot nematodes (RKNs) are notorious plant-parasitic nematodes first recorded in 1855 in cucumber plants. They are microscopic, obligate endoparasites that cause severe losses in agriculture and horticulture. They evade plant immunity, hijack the plant cell cycle, and metabolism to modify healthy cells into giant cells (GCs) – RKN feeding sites. RKNs secrete various effector molecules which suppress the plant defence and tamper with plant cellular and molecular biology. These effectors originate mainly from sub-ventral and dorsal oesophageal glands. Recently, a few non-oesophageal gland secreted effectors have been discovered. Effectors are essential for the entry of RKNs in plants, subsequently formation and maintenance of the GCs during the parasitism. In the past two decades, advanced genomic and post-genomic techniques identified many effectors, out of which only a few are well characterized. In this review, we provide molecular and functional details of RKN effectors secreted during parasitism. We list the known effectors and pinpoint their molecular functions. Moreover, we attempt to provide a comprehensive insight into RKN effectors concerning their implications on overall plant and nematode biology. Since effectors are the primary and prime molecular weapons of RKNs to invade the plant, it is imperative to understand their intriguing and complex functions to design counter-strategies against RKN infection.

scholarly journals Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Theodora Koromila ◽  
Fan Gao ◽  
Yasuno Iwasaki ◽  
Peng He ◽  
Lior Pachter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Accessibility ◽  
Secondary Wave ◽  
Genome Wide ◽  
Zygotic Transcription ◽  
Early Embryos ◽  
Zygotic Gene ◽  
Pioneer Factor ◽  
Pioneer Factors

Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.

scholarly journals Temporal Control of Transcription by Zelda in living Drosophila embryos

2018 ◽  
Author(s):  
Jeremy Dufourt ◽  
Antonio Trullo ◽  
Jennifer Hunter ◽  
Carola Fernandez ◽  
Jorge Lazaro ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Gene Activation ◽  
Correlation Spectroscopy ◽  
Temporal Control ◽  
Control Of Gene Expression ◽  
The Awakening ◽  
Nucleosomal Dna ◽  
Pioneer Factor ◽  
Pioneer Factors

Abstract/introPioneer factors have the exquisite ability to engage their target sites at nucleosomal DNA, which leads to a local remodeling of chromatin and the establishment of a transcriptional competence. However, the direct impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains elusive. In Drosophila embryos, the maternally deposited activator Zelda (Zld) exhibits key pioneer factor properties and indeed regulates the awakening of the zygotic genome. The analysis of thousands of endogenous Zld bound regions in various genetic contexts, as well as the study of isolated synthetic enhancers with static approaches, led to the proposal that Zld could act as a quantitative developmental timer. Here we employ quantitative live imaging methods and mathematical modeling to directly test the effect of Zld on temporal coordination in gene activation and on mitotic memory. Using an automatic tracking software, we quantified the timing of activation in hundreds of nuclei and their progeny in Drosophila embryos. We demonstrate that increasing the number of Zld binding sites accelerates the kinetics of transcriptional activation regardless of their past transcriptional state. In spite of its known pioneering activities, we show that Zld is not a mitotic bookmarker and is neither necessary nor sufficient to foster mitotic memory. Fluorescent recovery after photo-bleaching and fluorescent correlation spectroscopy experiments reveal that, Zld is highly dynamic and exhibits transient binding to chromatin. We propose that Zld low binding rates could be compensated for by local accumulation of Zld in nuclear microenvironments in vivo, thus allowing rapid and coordinated gene activation.

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