Interference with gene regulation in living sea urchin embryos: Transcription factor Knock Out (TKO), a genetically controlled vector for blockade of specific transcription factors

Although a great deal has been elucidated concerning the mechanisms regulating muscle differentiation, little is known about transcription factor-specific gene regulation. Our understanding of the genetic mechanisms regulating cell differentiation is quite limited. Much of what has been defined centers on regulatory signaling cascades and transcription factors. Surprisingly few studies have investigated the association of genes with specific transcription factors. To address these issues, we have utilized a method coupling chromatin immunoprecipitation and CpG microarrays to characterize the genes associated with MEF2 in differentiating C2C12 cells. Results demonstrated a defined binding pattern over the course of differentiation. Filtered data demonstrated 9 clones to be elevated at 0 h, 792 at 6 h, 163 by 1 day, and 316 at 3 days. Using unbiased selection parameters, we selected a subset of 291 prospective candidates. Clones were sequenced and filtered for removal of redundancy between clones and for the presence of repetitive elements. We were able to place 50 of these on the mouse genome, and 20 were found to be located near well-annotated genes. From this list, previously undefined associations with MEF2 were discovered. Many of these genes represent proteins involved in neurogenesis, neuromuscular junctions, signaling and metabolism. The remaining clones include many full-length cDNA and represent novel gene targets. The results of this study provides for the first time, a unique look at gene regulation at the level of transcription factor binding in differentiating muscle.

Download Full-text

Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

10.1101/2021.02.05.429970 ◽

2021 ◽

Author(s):

Mingxia Zhao ◽

Zhao Peng ◽

Yang Qin ◽

Ling Zhang ◽

Bin Tian ◽

...

Keyword(s):

Gene Regulation ◽

Transcription Factor ◽

Transcription Factors ◽

Protein Delivery ◽

Graphical Model ◽

Gene Activation ◽

Cuticular Wax ◽

Host Cells ◽

Myb Transcription Factor ◽

Leaf Phenotype

ABSTRACTCellular functions are diversified through intricate transcription regulations, and an understanding gene regulation networks is essential to elucidating many developmental processes and environmental responses. Here, we employed the Transcriptional-Activator Like effectors (TALes), which represent a family of transcription factors that are synthesized by members of the γ-proteobacterium genus Xanthomonas and secreted to host cells for activation of targeted host genes. Through delivery by the maize pathogen, Xanthomonas vasicola pv. vasculorum, designer TALes (dTALes), which are synthetic TALes, were used to induce the expression of the maize gene glossy3 (gl3), a MYB transcription factor gene involved in the cuticular wax biosynthesis. RNA-Seq analysis of leaf samples identified 146 gl3 downstream genes. Eight of the nine known genes known to be involved in the cuticular wax biosynthesis were up-regulated by at least one dTALe. A top-down Gaussian graphical model predicted that 68 gl3 downstream genes were directly regulated by GL3. A chemically induced mutant of the gene Zm00001d017418 from the gl3 downstream gene, encoding aldehyde dehydrogenase, exhibited a typical glossy leaf phenotype and reduced epicuticular waxes. The bacterial protein delivery of artificial transcription factors, dTALes, proved to be a straightforward and powerful approach for the revelation of gene regulation in plants.

Download Full-text

Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

10.1101/683318 ◽

2019 ◽

Author(s):

Jonathan E. Valencia ◽

Roberto Feuda ◽

Dan O. Mellott ◽

Robert D. Burke ◽

Isabelle S. Peter

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Sea Urchin ◽

Cell Types ◽

Pigment Cells ◽

Current Evidence ◽

Regulatory State ◽

Developmental Context ◽

Immotile Cilia ◽

Retinal Determination

ABSTRACTOne of the signatures of evolutionarily related cell types is the expression of similar combinations of transcription factors in distantly related animals. Here we present evidence that sea urchin larvae possess bilateral clusters of ciliary photoreceptors that are positioned in the oral/anterior apical neurogenic domain and associated with pigment cells. The expression of synaptotagmin indicates that the photoreceptors are neurons. Immunostaining shows that the sea urchin photoreceptors express an RGR/GO-opsin, opsin3.2, which co-localizes with tubulin on immotile cilia on the cell surface. Furthermore, orthologs of several transcription factors expressed in vertebrate photoreceptors are expressed in sea urchin ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx, a transcription factor typically associated with ciliary photoreceptors. Analysis of gene expression during sea urchin development indicates that the photoreceptors derive from the anterior apical neurogenic domain. Thus, based on location, developmental origin, and transcription factor expression, sea urchin ciliary photoreceptors are likely homologous to vertebrate rods and cones. However, we found that genes typically involved in eye development in many animals, including pax6, six1/2, eya, and dac, are not expressed in sea urchin ciliary photoreceptors. Instead, all four genes are co-expressed in the hydropore canal, indicating that these genes operate as a module in an unrelated developmental context. Thus, based on current evidence, we conclude that at least within deuterostomes, ciliary photoreceptors share a common evolutionary origin and express a shared regulatory state that includes Rx, Otx, and Six3, but not transcription factors that are commonly associated with the retinal determination circuit.

Download Full-text

SpRunt-1, a New Member of the Runt Domain Family of Transcription Factors, Is a Positive Regulator of the Aboral Ectoderm-SpecificCyIIIAGene in Sea Urchin Embryos

Developmental Biology ◽

10.1006/dbio.1996.0050 ◽

1996 ◽

Vol 174 (1) ◽

pp. 43-54 ◽

Cited By ~ 39

Author(s):

James A. Coffman ◽

Carmen V. Kirchhamer ◽

Michael G. Harrington ◽

Eric H. Davidson

Keyword(s):

Transcription Factors ◽

Sea Urchin ◽

Domain Family ◽

Runt Domain ◽

Positive Regulator ◽

Sea Urchin Embryos

Download Full-text

Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites

Bioinformatics and Biology Insights ◽

10.4137/bbi.s6362 ◽

2011 ◽

Vol 5 ◽

pp. BBI.S6362 ◽

Cited By ~ 5

Author(s):

Wei-Sheng Wu

Keyword(s):

Gene Regulation ◽

Transcription Factor ◽

Spatial Distribution ◽

Transcription Factors ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Gene Clusters ◽

Functional Gene ◽

Spatial Distributions ◽

Factor Binding

Transcription factors control gene expression by binding to short specific DNA sequences, called transcription factor binding sites (TFBSs), in the promoter of a gene. Thus, studying the spatial distribution of TFBSs in the promoters may provide insights into the molecular mechanisms of gene regulation. I developed a method to construct the spatial distribution of TFBSs for any set of genes of interest. I found that different functional gene clusters have different spatial distributions of TFBSs, indicating that gene regulation mechanisms may be very different among different functional gene clusters. I also found that the binding sites for different transcription factors (TFs) may have different spatial distributions: a sharp peak, a plateau or no dominant single peak. The spatial distributions of binding sites for many TFs derived from my analyses are valuable prior information for TFBS prediction algorithm because different regions of a promoter can assign different possibilities for TFBS occurrence.

Download Full-text

SpKrl: a direct target of beta-catenin regulation required for endoderm differentiation in sea urchin embryos

Development ◽

10.1242/dev.128.3.365 ◽

2001 ◽

Vol 128 (3) ◽

pp. 365-375 ◽

Cited By ~ 1

Author(s):

E.W. Howard ◽

L.A. Newman ◽

D.W. Oleksyn ◽

R.C. Angerer ◽

L.M. Angerer

Keyword(s):

Transcription Factor ◽

Protein Synthesis ◽

Sea Urchin ◽

Antisense Oligonucleotides ◽

Beta Catenin ◽

Nuclear Entry ◽

Nuclear Function ◽

Endoderm Differentiation ◽

Sea Urchin Embryos ◽

Direct Target

Localization of nuclear beta-catenin initiates specification of vegetal fates in sea urchin embryos. We have identified SpKrl, a gene that is activated upon nuclear entry of beta-catenin. SpKrl is upregulated when nuclear beta-catenin activity is increased with LiCl and downregulated in embryos injected with molecules that inhibit beta-catenin nuclear function. LiCl-mediated SpKrl activation is independent of protein synthesis, indicating that SpKrl is a direct target of beat-catenin and TCF. Embryos in which SpKrl translation is inhibited with morpholino antisense oligonucleotides lack endoderm. Conversely, SpKrl mRNA injection rescues some vegetal structures in beta-catenin-deficient embryos. SpKrl negatively regulates expression of the animalizing transcription factor, SpSoxB1. We propose that SpKrl functions in patterning the vegetal domain by suppressing animal regulatory activities.

Download Full-text

Identification and comparison of genes differentially regulated by transcription factors and miRNAs

10.1101/803643 ◽

2019 ◽

Author(s):

Amir Asiaee ◽

Zachary B Abrams ◽

Samantha Nakayiza ◽

Deepa Sampath ◽

Kevin R. Coombes

Keyword(s):

Gene Regulation ◽

Transcription Factor ◽

Transcription Factors ◽

Linear Models ◽

Critical Role ◽

Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Coefficient Of Determination ◽

Sequencing Data ◽

Mirna Sequencing

AbstractTranscription factors and microRNAs (miRNA) both play a critical role in gene regulation and in the development of many diseases such as cancer. Understanding how transcription factors and miRNAs influence gene expression is thus important to understand, but complicated due to the large and interconnected nature of the human genome. To help better understand what genes are being regulated by transcription factors and/or miRNAs we looked at it over 8000 patient samples from 32 different cancer types collected from The Cancer Genome Atlas (TCGA). We started by clustering the transcription factors and miRNAs using Thresher to reduce the number of features. Using both the mRNA and miRNA sequencing data we constructed linear models to calculate the coefficient of determination (R2) for each mRNA based on the Thresher cluster expression. We generated three types of linear models: transcription factor, miRNA and transcription factor plus miRNA. We then determined genes that were highly explained or poorly explained by each of the three models based on the genes R2 value. We performed downstream gene enrichment analysis using ToppGene on the sets of well and poorly explained genes. This identified differences in gene regulation between transcription factors and miRNAs and showed what groups of gene are differentially regulated.

Download Full-text

Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

BMC Biology ◽

10.1186/s12915-021-01194-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Jonathan E. Valencia ◽

Roberto Feuda ◽

Dan O. Mellott ◽

Robert D. Burke ◽

Isabelle S. Peter

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Sea Urchin ◽

Evolutionary Relationship ◽

Cell Types ◽

Developmental Expression ◽

Pigment Cells ◽

Cell Type ◽

Neuronal Marker ◽

Neurogenic Ectoderm

Abstract Background The evolutionary history of cell types provides insights into how morphological and functional complexity arose during animal evolution. Photoreceptor cell types are particularly broadly distributed throughout Bilateria; however, their evolutionary relationship is so far unresolved. Previous studies indicate that ciliary photoreceptors are homologous at least within chordates, and here, we present evidence that a related form of this cell type is also present in echinoderm larvae. Results Larvae of the purple sea urchin Strongylocentrotus purpuratus have photoreceptors that are positioned bilaterally in the oral/anterior apical neurogenic ectoderm. Here, we show that these photoreceptors express the transcription factor Rx, which is commonly expressed in ciliary photoreceptors, together with an atypical opsin of the GO family, opsin3.2, which localizes in particular to the cilia on the cell surface of photoreceptors. We show that these ciliary photoreceptors express the neuronal marker synaptotagmin and are located in proximity to pigment cells. Furthermore, we systematically identified additional transcription factors expressed in these larval photoreceptors and found that a majority are orthologous to transcription factors expressed in vertebrate ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx. Based on the developmental expression of rx, these photoreceptors derive from the anterior apical neurogenic ectoderm. However, genes typically involved in eye development in bilateria, including pax6, six1/2, eya, and dac, are not expressed in sea urchin larval photoreceptors but are instead co-expressed in the hydropore canal. Conclusions Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates.

Download Full-text

EBR1, a Novel Zn2Cys6 Transcription Factor, Affects Virulence and Apical Dominance of the Hyphal Tip in Fusarium graminearum

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-06-11-0158 ◽

2011 ◽

Vol 24 (12) ◽

pp. 1407-1418 ◽

Cited By ~ 22

Author(s):

Chunzhao Zhao ◽

Cees Waalwijk ◽

Pierre J. G. M. de Wit ◽

Theo van der Lee ◽

Dingzhong Tang

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Fusarium Graminearum ◽

Apical Dominance ◽

Radial Growth ◽

Fluorescent Protein ◽

Orthologous Gene ◽

Protein Fusion ◽

Knock Out ◽

Hyphal Tip

Zn2Cys6 transcription factors are unique to fungi and have been reported to be involved in different regulatory functions. Here, we characterized EBR1 (enhanced branching 1), a novel Zn2Cys6 transcription factor of Fusarium graminearum. Knocking out EBR1 in F. graminearum PH-1 caused reduction of both radial growth and virulence. The conidia of knock-out strain PH-1Δebr1 germinated faster than those of wild-type PH-1, but the conidiation of the mutant was significantly reduced. Detailed analysis showed that the reduced radial growth might be due to reduced apical dominance of the hyphal tip, leading to increased hyphal branching. Inoculation assays on wheat heads with a green fluorescent protein (GFP)-labeled PH-1Δebr1 mutant showed that it was unable to penetrate the rachis of the spikelets. Protein fusion with GFP showed that EBR1 is localized in the nucleus of both conidia and hyphae. Knocking out the orthologous gene FOXG_05408 in F. oxysporum f. sp. lycopersici caused a much weaker phenotype than the PH-1Δebr1 mutant, which may be due to the presence of multiple orthologous genes in this fungus. Transformation of FOXG_05408 into PH-1Δebr1 restored the mutant phenotype. Similar to EBR1, FOXG_05408 is localized in the nucleus of F. oxysporum f. sp. lycopersici. Possible functions of EBR1 and its relation with other fungal transcription factors are discussed.

Download Full-text