An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses

AbstractArsenic stress causes rapid transcriptional responses in plants. However, transcriptional regulators of arsenic-induced gene expression in plants remain less well known. To date, forward genetic screens have proven limited for dissecting arsenic response mechanisms. We hypothesized that this may be due to the extensive genetic redundancy present in plant genomes. To overcome this limitation, we pursued a forward genetics screen for arsenite tolerance using a randomized library of plants expressing >2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants, and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance.

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DksA-dependent regulation of RpoS contributes to Borrelia burgdorferi tick-borne transmission and mammalian infectivity

PLoS Pathogens ◽

10.1371/journal.ppat.1009072 ◽

2021 ◽

Vol 17 (2) ◽

pp. e1009072

Author(s):

William K. Boyle ◽

Crystal L. Richards ◽

Daniel P. Dulebohn ◽

Amanda K. Zalud ◽

Jeff A. Shaw ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Rna Polymerase ◽

Nutrient Limitation ◽

Pathogenic Bacteria ◽

Transcriptional Control ◽

Ixodes Scapularis ◽

Stringent Response ◽

Transcriptional Responses

Throughout its enzootic cycle, the Lyme disease spirochete Borreliella (Borrelia) burgdorferi, senses and responds to changes in its environment using a small repertoire of transcription factors that coordinate the expression of genes required for infection of Ixodes ticks and various mammalian hosts. Among these transcription factors, the DnaK suppressor protein (DksA) plays a pivotal role in regulating gene expression in B. burgdorferi during periods of nutrient limitation and is required for mammalian infectivity. In many pathogenic bacteria, the gene regulatory activity of DksA, along with the alarmone guanosine penta- and tetra-phosphate ((p)ppGpp), coordinate the stringent response to various environmental stresses, including nutrient limitation. In this study, we sought to characterize the role of DksA in regulating the transcriptional activity of RNA polymerase and its role in the regulation of RpoS-dependent gene expression required for B. burgdorferi infectivity. Using in vitro transcription assays, we observed recombinant DksA inhibits RpoD-dependent transcription by B. burgdorferi RNA polymerase independent of ppGpp. Additionally, we determined the pH-inducible expression of RpoS-dependent genes relies on DksA, but this relationship is independent of (p)ppGpp produced by Relbbu. Subsequent transcriptomic and western blot assays indicate DksA regulates the expression of BBD18, a protein previously implicated in the post-transcriptional regulation of RpoS. Moreover, we observed DksA was required for infection of mice following intraperitoneal inoculation or for transmission of B. burgdorferi by Ixodes scapularis nymphs. Together, these data suggest DksA plays a central role in coordinating transcriptional responses in B. burgdorferi required for infectivity through DksA’s interactions with RNA polymerase and post-transcriptional control of RpoS.

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Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions

Genes ◽

10.3390/genes12050640 ◽

2021 ◽

Vol 12 (5) ◽

pp. 640

Author(s):

Ming-Kun Huang ◽

Ling Zhang ◽

Li-Meng Zhou ◽

Wai-Shing Yung ◽

Man-Wah Li ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Glycine Soja ◽

Gene Activation ◽

Wild Soybean ◽

Plant Genome ◽

Homologous Gene ◽

Open Chromatin ◽

Gene Expressions ◽

In The Wild

Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.

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Specific Regulation of TCP genes by miR319

10.1101/747790 ◽

2019 ◽

Author(s):

Javier F. Palatnik ◽

Detlef Weigel

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Mirna Family ◽

Gene Families ◽

Evolutionarily Conserved ◽

Genes Encoding ◽

Specific Regulation ◽

Multicellular Organisms ◽

Sequence Similarities

AbstractMicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. Many of the evolutionarily conserved miRNAs in plants are encoded by small gene families. The miR159/miR319 family has six members of similar sequences sharing 17 nucleotides in Arabidopsis thaliana. The members of this miRNA family regulate genes encoding TCP (TEOSINTE BRANCHED1, CYCLOIDEA and PCF1/2) and MYB transcription factors. However, despite their sequence similarities, genetic evidence indicates that miR159 and miR319 fulfil different roles in vivo. Here, we confirm previous findings showing that TCP genes are not targeted by miR159. Thus, specific small sequence differences between the miRNAs allow for the specific regulation of TCP transcription factors by miR319 miRNAs.

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In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation

10.1101/808402 ◽

2019 ◽

Author(s):

Nathan J. VanDusen ◽

Julianna Y. Lee ◽

Weiliang Gu ◽

Isha Sethi ◽

Yanjiang Zheng ◽

...

Keyword(s):

Gene Expression ◽

Regenerative Medicine ◽

Forward Genetics ◽

Transcriptional Networks ◽

Epigenetic Mark ◽

High Resource ◽

Organ Systems ◽

Forward Genetic Screens ◽

Somatic Mutagenesis

ABSTRACTBetween birth and adulthood cardiomyocytes (CMs) undergo dramatic changes in size, ultrastructure, metabolism, and gene expression, in a process collectively referred to as CM maturation. The transcriptional network that coordinates CM maturation is poorly understood, creating a bottleneck for cardiac regenerative medicine. Forward genetic screens are a powerful, unbiased method to gain novel insights into transcriptional networks, yet this approach has rarely been used in vivo in mammals because of high resource demands. Here we utilized somatic mutagenesis to perform the first reported in vivo CRISPR genetic screen within a mammalian heart. We discovered and validated several novel transcriptional regulators of CM maturation. Among them were RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicated that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.

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Identification and Evolution Analysis of the JAZ Gene Family in Maize

10.21203/rs.3.rs-144271/v1 ◽

2021 ◽

Author(s):

Yang Han ◽

Dawn Luthe

Keyword(s):

Gene Expression ◽

Gene Family ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Gene Families ◽

Defense Responses ◽

Maize Genome ◽

Synteny Analysis ◽

Genetic Redundancy ◽

Duplication Events

Abstract Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

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Molecular diversity and gene expression of cotton ERF transcription factors reveal that group IXa members are responsive to jasmonate, ethylene andXanthomonas

Molecular Plant Pathology ◽

10.1111/j.1364-3703.2009.00549.x ◽

2009 ◽

Vol 10 (4) ◽

pp. 471-485 ◽

Cited By ~ 32

Author(s):

ANTONY CHAMPION ◽

EUGENIE HEBRARD ◽

BENOIT PARRA ◽

CAROLINE BOURNAUD ◽

PHILIPPE MARMEY ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Molecular Diversity ◽

Erf Transcription Factors

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Modeling the transport of nuclear proteins along single skeletal muscle cells

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1919600117 ◽

2020 ◽

Vol 117 (6) ◽

pp. 2978-2986 ◽

Cited By ~ 9

Author(s):

Hermes Taylor-Weiner ◽

Christopher L. Grigsby ◽

Duarte M. S. Ferreira ◽

José M. Dias ◽

Molly M. Stevens ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Molecular Weight ◽

Transcription Factors ◽

Protein Transport ◽

Muscle Cells ◽

Skeletal Muscle Cells ◽

Nuclear Proteins ◽

Transcriptional Responses

Skeletal muscle cells contain hundreds of myonuclei within a shared cytoplasm, presenting unique challenges for regulating gene expression. Certain transcriptional programs (e.g., postsynaptic machinery) are segregated to specialized domains, while others (e.g., contractile proteins) do not show spatial confinement. Furthermore, local stimuli, such as denervation, can induce transcriptional responses that are propagated along the muscle cells. Regulated transport of nuclear proteins (e.g., transcription factors) between myonuclei represents a potential mechanism for coordinating gene expression. However, the principles underlying the transport of nuclear proteins within multinucleated cells remain poorly defined. Here we used a mosaic transfection model to create myotubes that contained exactly one myonucleus expressing a fluorescent nuclear reporter and monitored its distribution among all myonuclei. We found that the transport properties of these model nuclear proteins in myotubes depended on molecular weight and nuclear import rate, as well as on myotube width. Interestingly, muscle hypertrophy increased the transport of high molecular weight nuclear proteins, while atrophy restricted the transport of smaller nuclear proteins. We have developed a mathematical model of nuclear protein transport within a myotube that recapitulates the results of our in vitro experiments. To test the relevance to nuclear proteins expressed in skeletal muscle, we studied the transport of two transcription factors—aryl hydrocarbon receptor nuclear translocator and sine oculis homeobox 1—and found that their distributions were similar to the reporter proteins with corresponding molecular weights. Together, these results define a set of variables that can be used to predict the spatial distributions of nuclear proteins within a myotube.

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

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.00323.2004 ◽

2004 ◽

Vol 287 (5) ◽

pp. H1977-H1986 ◽

Cited By ~ 28

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.

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Towards an understanding of cell-specific functions of signal-dependent transcription factors

Journal of Molecular Endocrinology ◽

10.1530/jme-13-0216 ◽

2013 ◽

Vol 51 (3) ◽

pp. T37-T50 ◽

Cited By ~ 18

Author(s):

Dawn X Zhang ◽

Christopher K Glass

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Hormone Receptors ◽

Wide Spectrum ◽

Transcriptional Responses ◽

Natural Genetic Variation ◽

Surface Receptors ◽

A Genome ◽

And Function

The ability to regulate gene expression in a cell-specific manner is a feature of many broadly expressed signal-dependent transcription factors (SDTFs), including nuclear hormone receptors and transcription factors that are activated by cell surface receptors for extracellular signals. As the most plastic cells of the hematopoietic system, macrophages are responsive to a wide spectrum of regulatory molecules and provide a robust model system for investigation of the basis for cell-specific transcriptional responses at a genome-wide level. Here, focusing on recent studies in macrophages, we review the evidence suggesting a model in which cell-specific actions of SDTFs are the consequence of priming functions of lineage determining transcription factors. We also discuss recent findings relating lineage-determining and SDTF activity to alterations in the epigenetic landscape as well as the production and function of enhancer RNAs. These findings have implications for the understanding of how natural genetic variation impacts cell-specific programs of gene expression and suggest new approaches for altering gene expressionin vivo.

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Identification and evolution analysis of the JAZ gene family in maize

BMC Genomics ◽

10.1186/s12864-021-07522-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yang Han ◽

Dawn Luthe

Keyword(s):

Gene Expression ◽

Gene Family ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Gene Families ◽

Defense Responses ◽

Maize Genome ◽

Synteny Analysis ◽

Genetic Redundancy ◽

Duplication Events

Abstract Background Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds. Conclusions Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

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