scholarly journals Genome-Wide Analysis Reveals Transcription Factors Regulated by Spider-Mite Feeding in Cucumber (Cucumis sativus)

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1014
Author(s):  
Jun He ◽  
Harro J. Bouwmeester ◽  
Marcel Dicke ◽  
Iris F. Kappers
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Spider Mite ◽  
Induced Defense ◽  
Regulatory Elements ◽  
Spider Mites ◽  
Promoter Regions ◽  
Cis Acting ◽  
Genes Encoding ◽  
Mite Feeding

To gain insight into the regulatory networks that underlie the induced defense in cucumber against spider mites, genes encoding transcription factors (TFs) were identified in the cucumber (Cucumissativus) genome and their regulation by two-spotted spider mite (Tetranychusurticae) herbivory was analyzed using RNA-seq. Of the total 1212 annotated TF genes in the cucumber genome, 119 were differentially regulated upon spider-mite herbivory during a period of 3 days. These TF genes belong to different categories but the MYB, bHLH, AP2/ERF and WRKY families had the highest relative numbers of differentially expressed genes. Correlation analysis of the expression of TF genes with defense-associated genes during herbivory and pathogen infestation, and in different organs resulted in the putative identification of regulators of herbivore-induced terpenoid and green-leaf-volatile biosynthesis. Analysis of the cis-acting regulatory elements (CAREs) present in the promoter regions of the genes responsive to spider-mite feeding revealed potential TF regulators. This study describes the TF genes in cucumber that are potentially involved in the regulation of induced defense against herbivory by spider mites.

scholarly journals Rewiring of the Transcription Factor Network in Acute Myeloid Leukemia

2019 ◽  
Vol 18 ◽  
pp. 117693511985986 ◽  
Author(s):  
Salam A Assi ◽  
Constanze Bonifer ◽  
Peter N Cockerill
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Transcription Factors ◽  
Myeloid Leukemia ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Genes Encoding ◽  
Myeloid Development ◽  
Mitogen Activated Protein ◽  
Acute Myeloid

Acute myeloid leukemia (AML) is a highly heterogeneous cancer associated with different patterns of gene expression determined by the nature of their DNA mutations. These mutations mostly act to deregulate gene expression by various mechanisms at the level of the nucleus. By performing genome-wide epigenetic profiling of cis-regulatory elements, we found that AML encompasses different mutation-specific subclasses associated with the rewiring of the gene regulatory networks that drive differentiation into different directions away from normal myeloid development. By integrating epigenetic profiles with gene expression and chromatin conformation data, we defined pathways within gene regulation networks that were differentially rewired within each mutation-specific subclass of AML. This analysis revealed 2 major classes of AML: one class defined by mutations in signaling molecules that activate AP-1 via the mitogen-activated protein (MAP) kinase pathway and a second class defined by mutations within genes encoding transcription factors such as RUNX1/CBFβ and C/EBPα. By identifying specific DNA motifs protected from DNase I digestion at cis-regulatory elements, we were able to infer candidate transcription factors bound to these motifs. These integrated analyses allowed the identification of AML subtype-specific core regulatory networks that are required for AML development and maintenance, which could now be targeted in personalized therapies.

scholarly journals High-resolution analysis of cis -acting regulatory networks at the α-globin locus

2013 ◽  
Vol 368 (1620) ◽  
pp. 20120361 ◽  
Author(s):  
Jim R. Hughes ◽  
Karen M. Lower ◽  
Ian Dunham ◽  
Stephen Taylor ◽  
Marco De Gobbi ◽  
...  
Keyword(s):  
High Resolution ◽  
Gene Cluster ◽  
Regulatory Networks ◽  
Single Gene ◽  
Regulatory Elements ◽  
Circular Chromosome ◽  
Chromosome Conformation ◽  
Cis Acting ◽  
High Resolution Analysis ◽  
Resolution Analysis

We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis -acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10–1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis -regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster.

scholarly journals Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1669
Author(s):  
Angelo De Paolis ◽  
Sofia Caretto ◽  
Angela Quarta ◽  
Gian-Pietro Di Sansebastiano ◽  
Irene Sbrocca ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Antimalarial Activity ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

scholarly journals Molecular Analysis of the Pathway for the Synthesis of Thiol Tripeptides in the Model Legume Lotus japonicus

2003 ◽  
Vol 16 (11) ◽  
pp. 1039-1046 ◽  
Author(s):  
Manuel A. Matamoros ◽  
Maria R. Clemente ◽  
Shusei Sato ◽  
Erika Asamizu ◽  
Satoshi Tabata ◽  
...  
Keyword(s):  
Lotus Japonicus ◽  
Regulatory Elements ◽  
Chromosome 1 ◽  
Glutathione Synthetase ◽  
Promoter Regions ◽  
Model Legume ◽  
Cis Acting ◽  
Glutamylcysteine Synthetase ◽  
Exon 1 ◽  
Legume Symbiosis

The thiol tripeptides, glutathione (GSH) and homoglu-tathione (hGSH), perform multiple roles in legumes, including protection against toxicity of free radicals and heavy metals. The three genes involved in the synthesis of GSH and hGSH in the model legume, Lotus japonicus, have been fully characterized and appear to be present as single copies in the genome. The γ-glutamylcysteine synthetase (γecs) gene was mapped on the long arm of chromosome 4 (70.0 centimorgans [cM]) and consists of 15 exons, whereas the glutathione synthetase (gshs) and homoglutathione synthetase (hgshs) genes were mapped on the long arm of chromosome 1 (81.3 cM) and found to be arranged in tandem with a separation of approximately 8 kb. Both genes consist of 12 exons of exactly the same size (except exon 1, which is similar). Two types of transcripts were detected for the gshs gene, which putatively encode proteins localized in the plastids and cytosol. Promoter regions contain cis-acting regulatory elements that may be involved in the plant's response to light, hormones, and stress. Determination of transcript levels, enzyme activities, and thiol contents in nodules, roots, and leaves revealed that γecs and hgshs are expressed in all three plant organs, whereas gshs is significantly functional only in nodules. This strongly suggests an important role of GSH in the rhizobia-legume symbiosis.

Regulation of the ANF and BNP promoters by GATA factors: Lessons learned for cardiac transcription

2001 ◽  
Vol 79 (8) ◽  
pp. 673-681 ◽  
Author(s):  
Kevin McBride ◽  
Mona Nemer
Keyword(s):  
Transcription Factors ◽  
Natriuretic Peptide ◽  
Regulatory Networks ◽  
Current Knowledge ◽  
Lessons Learned ◽  
Clinical Markers ◽  
Gata Factors ◽  
Major Mechanism ◽  
Genes Encoding ◽  
Cardiac Gene

The identification and molecular cloning of the cardiac transcription factors GATA-4, -5, and -6 has greatly contributed to our understanding of how tissue-specific transcription is achieved during cardiac growth and development. Through analysis of their interacting partners, it has also become apparent that a major mechanism underlying spatial and temporal specificity within the heart as well as in the response to cardiogenic regulators is the combinatorial interaction between cardiac-restricted and inducible transcription factors. The cardiac GATA factors appear to be fundamental contributors to these regulatory networks. Two of the first targets identified for the cardiac GATA factors were the natriuretic peptide genes encoding atrial natriuretic factor (ANF) and B-type natriuretic peptide (BNP), the major heart secretory products that are also accepted clinical markers of the diseased heart. Studies using the ANF and BNP promoters as models of cardiac-specific transcription have unraveled the pivotal role that GATA proteins play in cardiac gene expression. We review the current knowledge on the modulation of the natriuretic peptide promoters by GATA factors, including examples of combinatorial interactions between GATA proteins and diverse transcription factors.Key words: ANF, BNP, GATA factors, cardiac transcription.

scholarly journals Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information

2021 ◽  
Vol 12 ◽  
Author(s):  
Julian Droste ◽  
Christian Rückert ◽  
Jörn Kalinowski ◽  
Mohamed Belal Hamed ◽  
Jozef Anné ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Regulatory Networks ◽  
Streptomyces Coelicolor ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Streptomyces Lividans ◽  
Model Organisms ◽  
Promoter Regions ◽  
Gene Characterization ◽  
Novel Transcripts

Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5′-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5′ untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5′-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5′-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.

scholarly journals The SEEL Motif and Members of the MYB-related REVEILLE Transcription Factor Family are Important for the Expression of LORELEI in the Synergid Cells of the Arabidopsis Female Gametophyte

2021 ◽  
Author(s):  
Jennifer A. Noble ◽  
Alex Seddon ◽  
Sahra Uygun ◽  
Steven E. Smith ◽  
Shin-Han Shiu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Pollen Tube ◽  
Female Gametophyte ◽  
Regulatory Networks ◽  
Clock Genes ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Loss Of Function ◽  
Seed Formation ◽  
Synergid Cell

Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs (TAATATCT) in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of a cis-regulatory element and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells and investigate the potential connection between circadian rhythm and fertilization.

scholarly journals Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 441 ◽  
Author(s):  
Ho ◽  
Geisler
Keyword(s):  
Transcription Factors ◽  
Dna Sequences ◽  
Developmental Stages ◽  
Experimental Testing ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Model Systems ◽  
Whole Genome Sequence ◽  
Cis Acting ◽  
Biotic Stresses

The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene’s expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some—but not all—CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.

scholarly journals AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

2006 ◽  
Vol 140 (3) ◽  
pp. 818-829 ◽  
Author(s):  
Saranyan K. Palaniswamy ◽  
Stephen James ◽  
Hao Sun ◽  
Rebecca S. Lamb ◽  
Ramana V. Davuluri ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Regulatory Elements

scholarly journals Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs

2020 ◽  
Author(s):  
Swann Floc’hlay ◽  
Emily Wong ◽  
Bingqing Zhao ◽  
Rebecca R. Viales ◽  
Morgane Thomas-Chollier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cis Acting ◽  
Dna Mutations ◽  
Allele Specific ◽  
Regulatory Dna ◽  
The Impact

AbstractPrecise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequence, and chromatin. How DNA mutations affecting any one of these regulatory ‘layers’ is buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses, at three embryonic stages, yielding a comprehensive dataset of 240 samples spanning multiple regulatory layers. Genetic variation in cis-regulatory elements is common, highly heritable, and surprisingly consistent in its effects across embryonic stages. Much of this variation does not propagate to gene expression. When it does, it acts through H3K4me3 or alternatively through chromatin accessibility and H3K27ac. The magnitude and evolutionary impact of mutations is influenced by a genes’ regulatory complexity (i.e. enhancer number), with transcription factors being most robust to cis-acting, and most influenced by trans-acting, variation. Overall, the impact of genetic variation on regulatory phenotypes appears context-dependent even within the constraints of embryogenesis.

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