scholarly journals Assessing Transcriptional Responses to Light by the Dinoflagellate Symbiodinium

2019 ◽  
Vol 7 (8) ◽  
pp. 261
Author(s):  
Bahareh Zaheri ◽  
Steve Dagenais-Bellefeuille ◽  
Bo Song ◽  
David Morse
Keyword(s):  
Transcription Factors ◽  
Differential Expression ◽  
Cold Shock ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
Transcriptional Response ◽  
Rna Seq ◽  
Transcriptional Responses ◽  
Northern Blots ◽  
Cold Shock Domain

The control of transcription is poorly understood in dinoflagellates, a group of protists whose permanently condensed chromosomes are formed without histones. Furthermore, while transcriptomes contain a number of proteins annotated as transcription factors, the majority of these are cold shock domain proteins which are also known to bind RNA, meaning the number of true transcription factors is unknown. Here we have assessed the transcriptional response to light in the photosynthetic species Symbiodinium kawagutii. We find that three genes previously reported to respond to light using qPCR do not show differential expression using northern blots or RNA-Seq. Interestingly, global transcript profiling by RNA-Seq at LD 0 (dawn) and LD 12 (dusk) found only seven light-regulated genes (FDR = 0.1). qPCR using three randomly selected genes out of the seven was only able to validate differential expression of two. We conclude that there is likely to be less light regulation of gene expression in dinoflagellates than previously thought and suggest that transcriptional responses to other stimuli should also be more thoroughly evaluated in this class of organisms.

scholarly journals Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4

2021 ◽  
Vol 12 (8) ◽  
Author(s):  
Thomas Kleiber ◽  
Guillaume Davidson ◽  
Gabrielle Mengus ◽  
Igor Martianov ◽  
Irwin Davidson
Keyword(s):  
Transcription Factors ◽  
Beta Cell ◽  
Single Cell ◽  
Beta Cells ◽  
Pancreatic Beta Cells ◽  
Cell Function ◽  
Insulin Signalling ◽  
Regulation Of Gene Expression ◽  
Chromatin Remodelling ◽  
Rna Seq

AbstractRegulation of gene expression involves a complex and dynamic dialogue between transcription factors, chromatin remodelling and modification complexes and the basal transcription machinery. To address the function of the Taf4 subunit of general transcription factor TFIID in the regulation of insulin signalling, it was inactivated in adult murine pancreatic beta cells. Taf4 inactivation impacted the expression of critical genes involved in beta-cell function leading to increased glycaemia, lowered plasma insulin levels and defective glucose-stimulated insulin secretion. One week after Taf4-loss, single-cell RNA-seq revealed cells with mixed beta cell, alpha and/or delta cell identities as well as a beta cell population trans-differentiating into alpha-like cells. Computational analysis of single-cell RNA-seq defines how known critical beta cell and alpha cell determinants may act in combination with additional transcription factors and the NuRF chromatin remodelling complex to promote beta cell trans-differentiation.

scholarly journals Assessing nucleic acid binding activity of four dinoflagellate cold shock domain proteins from Symbiodinium kawagutii and Lingulodinium polyedra

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bahareh Zaheri ◽  
David Morse
Keyword(s):  
Transcription Factors ◽  
Nucleic Acid ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Binding Activity ◽  
Dependent Manner ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Double Stranded Dna ◽  
Cold Shock Domain

Abstract Background Dinoflagellates have a generally large number of genes but only a small percentage of these are annotated as transcription factors. Cold shock domain (CSD) containing proteins (CSPs) account for roughly 60% of these. CSDs are not prevalent in other eukaryotic lineages, perhaps suggesting a lineage-specific expansion of this type of transcription factors in dinoflagellates, but there is little experimental data to support a role for dinoflagellate CSPs as transcription factors. Here we evaluate the hypothesis that dinoflagellate CSPs can act as transcription factors by binding double-stranded DNA in a sequence dependent manner. Results We find that both electrophoretic mobility shift assay (EMSA) competition experiments and selection and amplification binding (SAAB) assays indicate binding is not sequence specific for four different CSPs from two dinoflagellate species. Competition experiments indicate all four CSPs bind to RNA better than double-stranded DNA. Conclusion Dinoflagellate CSPs do not share the nucleic acid binding properties expected for them to function as bone fide transcription factors. We conclude the transcription factor complement of dinoflagellates is even smaller than previously thought suggesting that dinoflagellates have a reduced dependance on transcriptional control compared to other eukaryotes.

scholarly journals A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 784
Author(s):  
Daniel E. Carlin ◽  
Kassi Kosnicki ◽  
Sara Garamszegi ◽  
Trey Ideker ◽  
Helga Thorvaldsdóttir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
User Interface ◽  
Dna Binding ◽  
Data Integration ◽  
Differential Expression ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Functional Regulation

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

scholarly journals Characterization of Two Dinoflagellate Cold Shock Domain Proteins

mSphere ◽  
2016 ◽  
Vol 1 (1) ◽  
Author(s):  
Mathieu Beauchemin ◽  
Sougata Roy ◽  
Sarah Pelletier ◽  
Alexandra Averback ◽  
Frederic Lanthier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Mobility Shift ◽  
Two Dimensional Gel Electrophoresis ◽  
Content Type ◽  
Cold Shock Domain ◽  
Cold Shock Domain Proteins ◽  
Specific Sequences

ABSTRACT Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists.

scholarly journals Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection

2021 ◽  
Author(s):  
Reo Yoo ◽  
Kevin Rychel ◽  
Saugat Poudel ◽  
Tahani Al-bulushi ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mycobacterium Tuberculosis ◽  
Transcription Factors ◽  
Environmental Changes ◽  
Transcriptional Regulatory Network ◽  
Sulfur Metabolism ◽  
Transcriptional Response ◽  
Future Research ◽  
Rna Seq ◽  
Metabolic Systems

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, a systems level characterization and analysis of interactions among the controlling transcription factors remains to be achieved. Here, we applied an unsupervised machine learning method to modularize the M. tuberculosis transcriptome and describe the role of transcription factors (TFs) in the TRN. By applying Independent Component Analysis (ICA) to over 650 transcriptomic samples, we obtained 80 independently modulated gene sets known as "iModulons", many of which correspond to known regulons. These iModulons explain 61% of the variance in the organism's transcriptional response. We show that iModulons: 1) reveal the function of previously unknown regulons, 2) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and virulence events, and 3) identify intrinsic clusters of transcriptional regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation, and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.

Nitric oxide donor induces temporal and dose-dependent reduction of gene expression in human endothelial cells

2004 ◽  
Vol 287 (5) ◽  
pp. H1977-H1986 ◽  
Author(s):  
Branko Braam ◽  
Remmert de Roos ◽  
Adele Dijk ◽  
Peter Boer ◽  
Jan Andries Post ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitric Oxide ◽  
Endothelial Cells ◽  
Transcription Factors ◽  
Prolonged Exposure ◽  
Cell Structure ◽  
Transcriptional Response ◽  
Nitric Oxide Donor ◽  
Transcriptional Responses ◽  
Deta Nonoate

The present study tested the hypothesis that acute increases in nitric oxide (NO) exert substantial influences on gene transcription in endothelial cells (ECs) via guanylyl cyclase (GC). Human umbilical veins ECs (HUVECs) were exposed to 0.1, 1, and 10 mM of sodium nitroprusside (SNP) for 4 h and to 1 mM SNP or 250 μM of ( Z)-1[ N-(2-aminoethyl)- N-(2-ammonioethyl)amino]diazen-1-ium-1,2-diolate (DETA-NONOate) for 2, 4, 8, and 24 h. Also, cells were exposed to DETA-NONOate in the presence and absence of the GC inhibitor 1 H-[1,2,4]oxadiazolo-[4,3- a]quinoxalin-1-one (ODQ; 10 μM) for 4 h. RNA was isolated, reverse transcribed, Cy3 and Cy5 labeled, and analyzed using cDNA microarrays. Increasing doses of SNP predominantly depressed gene expression in HUVECs. Gene function was related to growth, adhesion, and cell structure. DETA-NONOate evoked a wave of expression changes (maximum at 4 h), with a remarkable downregulation of the transcription factors MSX1, RELB, and Egr-1. Both SNP- and DETA-NONOate-induced gene expression had faded after 24 h, despite continued elevation of cGMP in the medium. Coadministration of ODQ decreased many, but not all, of the transcriptional responses to DETA-NONOate. NO pronouncedly depressed EC gene expression, in particular of transcription factors. The observation that many, but not all, transcriptional changes induced by NO could be inhibited by inhibition of GC indicates the presence of GC-independent NO actions on gene expression. Thus EC gene expression responds to NO; however, the transcriptional response fades during prolonged exposure. This could allow the EC to respond to increased shear, without vigorous changes in gene expression.

scholarly journals A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 784
Author(s):  
Daniel E. Carlin ◽  
Kassi Kosnicki ◽  
Sara Garamszegi ◽  
Trey Ideker ◽  
Helga Thorvaldsdóttir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
User Interface ◽  
Dna Binding ◽  
Data Integration ◽  
Differential Expression ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Functional Regulation

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identifying protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from an RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

scholarly journals NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells

2021 ◽  
Vol 22 (11) ◽  
pp. 5902
Author(s):  
Stefan Nagel ◽  
Claudia Pommerenke ◽  
Corinna Meyer ◽  
Hans G. Drexler
Keyword(s):  
Dendritic Cells ◽  
Transcription Factors ◽  
Cell Lines ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Homeobox Gene ◽  
Leukemia Cell Line ◽  
Specific Gene ◽  
Rna Seq ◽  
And Function

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

scholarly journals RNA-Seq Provides New Insights into the Molecular Events Involved in “Ball-Skin versus Bladder Effect” on Fruit Cracking in Litchi

2021 ◽  
Vol 22 (1) ◽  
pp. 454
Author(s):  
Jun Wang ◽  
Xiao Fang Wu ◽  
Yong Tang ◽  
Jian Guo Li ◽  
Ming Lei Zhao
Keyword(s):  
Transcription Factors ◽  
Plant Hormones ◽  
Fruit Development ◽  
Economic Value ◽  
Lipid Synthesis ◽  
Expression Level ◽  
Agricultural Product ◽  
Rna Seq ◽  
Fruit Cracking ◽  
Molecular Events

Fruit cracking is a disorder of fruit development in response to internal or external cues, which causes a loss in the economic value of fruit. Therefore, exploring the mechanism underlying fruit cracking is of great significance to increase the economic yield of fruit trees. However, the molecular mechanism underlying fruit cracking is still poorly understood. Litchi, as an important tropical and subtropical fruit crop, contributes significantly to the gross agricultural product in Southeast Asia. One important agricultural concern in the litchi industry is that some famous varieties with high economic value such as ‘Nuomici’ are susceptible to fruit cracking. Here, the cracking-susceptible cultivar ‘Nuomici’ and cracking-resistant cultivar ‘Huaizhi’ were selected, and the samples including pericarp and aril during fruit development and cracking were collected for RNA-Seq analysis. Based on weighted gene co-expression network analysis (WGCNA) and the “ball-skin versus bladder effect” theory (fruit cracking occurs upon the aril expanding pressure exceeds the pericarp strength), it was found that seven co-expression modules genes (1733 candidate genes) were closely associated with fruit cracking in ‘Nuomici’. Importantly, we propose that the low expression level of genes related to plant hormones (Auxin, Gibberellins, Ethylene), transcription factors, calcium transport and signaling, and lipid synthesis might decrease the mechanical strength of pericarp in ‘Nuomici’, while high expression level of genes associated with plant hormones (Auxin and abscisic acid), transcription factors, starch/sucrose metabolism, and sugar/water transport might increase the aril expanding pressure, thereby resulting in fruit cracking in ‘Nuomici’. In conclusion, our results provide comprehensive molecular events involved in the “ball-skin versus bladder effect” on fruit cracking in litchi.

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