A Semi-In Vivo Transcriptional Assay to Dissect Plant Defense Regulatory Modules

2021 ◽  
pp. 203-214
Author(s):  
Fatimah Aljedaani ◽  
Naganand Rayapuram ◽  
Ikram Blilou
Keyword(s):  
Plant Defense ◽  
Regulatory Modules

scholarly journals Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons

2017 ◽  
Author(s):  
Jérôme Zervudacki ◽  
Agnès Yu ◽  
Delase Amesefe ◽  
Jingyu Wang ◽  
Jan Drouaud ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Defense ◽  
Transcriptional Control ◽  
Plant Immunity ◽  
Disease Resistance Gene ◽  
Loss Of Function ◽  
Long Terminal Repeats ◽  
Protein Coding ◽  
Regulatory Modules ◽  
Microrna Genes

ABSTRACTMobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In this study, we employed anATCOPIA93Long terminal repeats (LTR) promoter-GUSfusion to show that this retrotransposon behaves like an immune-responsive gene during plant defense in Arabidopsis. We also showed that the reactivation of the endogenousATCOPIA93copy“EVD”, in the presence of bacterial stress, is not only negatively regulated by DNA methylation but also by Polycomb-mediated silencing—a mode of repression typically found at protein-coding and microRNA genes. Interestingly, one of theATCOPIA93-derived soloLTRs is located upstream of the disease resistance geneRPP4and is devoid of either DNA methylation or H3K27m3 marks. Through loss-of-function experiments, we demonstrated that this soloLTR is required for proper expression ofRPP4during plant defense, thus linking the responsiveness ofATCOPIA93to biotic stress and the co-option of its LTR for plant immunity.

scholarly journals Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding

2017 ◽  
Author(s):  
Noa Katz ◽  
Roni Cohen ◽  
Oz Solomon ◽  
Beate Kaufmann ◽  
Orna Atar ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Cooperative Behavior ◽  
Transcriptional Level ◽  
Rna Molecules ◽  
Regulatory Modules ◽  
Regulatory Circuits ◽  
Rna Hairpins ◽  
Gene Regulatory ◽  
Gene Regulatory Circuits

SUMMARYThe construction of complex gene regulatory networks requires both inhibitory and up-regulatory modules. However, the vast majority of RNA-based regulatory “parts” are inhibitory. Using a synthetic biology approach combined with SHAPE-Seq, we explored the regulatory effect of RBP-RNA interactions in bacterial 5’-UTRs. By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational stimulation, translational repression, and cooperative behavior. Our combined approach revealed three distinct states in-vivo: in the absence of RBPs, the RNA molecules can be found either in a molten state that is amenable to translation, or a structured phase that inhibits translation. In the presence of RBPs, the RNA molecules are in a semi-structured phase with partial translational capacity. Our work provides new insight into RBP-based regulation and a blueprint for designing complete gene regulatory circuits at the post-transcriptional level.

scholarly journals A map of direct TF–DNA interactions in the human genome

2018 ◽  
Vol 47 (4) ◽  
pp. e21-e21 ◽  
Author(s):  
Marius Gheorghe ◽  
Geir Kjetil Sandve ◽  
Aziz Khan ◽  
Jeanne Chèneby ◽  
Benoit Ballester ◽  
...  
Keyword(s):  
Human Genome ◽  
Protein Interaction Data ◽  
Data Sets ◽  
Dna Interactions ◽  
Regulatory Modules ◽  
Protein Protein Interaction ◽  
Protein Binding Microarray ◽  
Bona Fide ◽  
Genomic Regions

Abstract Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most popular assay to identify genomic regions, called ChIP-seq peaks, that are bound in vivo by transcription factors (TFs). These regions are derived from direct TF–DNA interactions, indirect binding of the TF to the DNA (through a co-binding partner), nonspecific binding to the DNA, and noise/bias/artifacts. Delineating the bona fide direct TF–DNA interactions within the ChIP-seq peaks remains challenging. We developed a dedicated software, ChIP-eat, that combines computational TF binding models and ChIP-seq peaks to automatically predict direct TF–DNA interactions. Our work culminated with predicted interactions covering >2% of the human genome, obtained by uniformly processing 1983 ChIP-seq peak data sets from the ReMap database for 232 unique TFs. The predictions were a posteriori assessed using protein binding microarray and ChIP-exo data, and were predominantly found in high quality ChIP-seq peaks. The set of predicted direct TF–DNA interactions suggested that high-occupancy target regions are likely not derived from direct binding of the TFs to the DNA. Our predictions derived co-binding TFs supported by protein-protein interaction data and defined cis-regulatory modules enriched for disease- and trait-associated SNPs. We provide this collection of direct TF–DNA interactions and cis-regulatory modules through the UniBind web-interface (http://unibind.uio.no).

scholarly journals Intrinsic control of muscle attachment sites matching

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Alexandre Carayon ◽  
Laetitia Bataillé ◽  
Gaëlle Lebreton ◽  
Laurence Dubois ◽  
Aurore Pelletier ◽  
...  
Keyword(s):  
Live Imaging ◽  
Muscle Attachment ◽  
Regulatory Modules ◽  
Transcriptional Reprogramming ◽  
Attachment Sites ◽  
Tendon Cells ◽  
Evolutionarily Conserved ◽  
Selection Of ◽  
Muscle Attachment Sites

Myogenesis is an evolutionarily conserved process. Little known, however, is how the morphology of each muscle is determined, such that movements relying upon contraction of many muscles are both precise and coordinated. Each Drosophila larval muscle is a single multinucleated fibre whose morphology reflects expression of distinctive identity Transcription Factors (iTFs). By deleting transcription cis-regulatory modules of one iTF, Collier, we generated viable muscle identity mutants, allowing live imaging and locomotion assays. We show that both selection of muscle attachment sites and muscle/muscle matching is intrinsic to muscle identity and requires transcriptional reprogramming of syncytial nuclei. Live-imaging shows that the staggered muscle pattern involves attraction to tendon cells and heterotypic muscle-muscle adhesion. Unbalance leads to formation of branched muscles, and this correlates with locomotor behavior deficit. Thus, engineering Drosophila muscle identity mutants allows to investigate, in vivo, physiological and mechanical properties of abnormal muscles.

scholarly journals Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina

Development ◽  
2020 ◽  
Vol 147 (14) ◽  
pp. dev187922 ◽  
Author(s):  
Candace S. Y. Chan ◽  
Nicolas Lonfat ◽  
Rong Zhao ◽  
Alexander E. Davis ◽  
Liang Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Cell Types ◽  
Retinal Cell ◽  
Mouse Retina ◽  
Cell Type ◽  
Specific Expression ◽  
Regulatory Modules ◽  
A Cell

ABSTRACTTranscription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.

scholarly journals Deciphering human ribonucleoprotein regulatory networks

2018 ◽  
Author(s):  
Neelanjan Mukherjee ◽  
Hans-Hermann Wessels ◽  
Svetlana Lebedeva ◽  
Marcin Sajek ◽  
Mahsa Ghanbari ◽  
...  
Keyword(s):  
Cell Line ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Human Cell Line ◽  
Regulatory Function ◽  
Regulatory Modules ◽  
Binding Preference ◽  
Rna Interaction

RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules encoded functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.

scholarly journals Cell type- and stage-specific expression of Otx2 is coordinated by a cohort of transcription factors and multiple cis-regulatory modules in the retina

2019 ◽  
Author(s):  
Candace Chan ◽  
Nicolas Lonfat ◽  
Rong Zhao ◽  
Alexander Davis ◽  
Liang Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Cell Types ◽  
Retinal Cell ◽  
Cell Type ◽  
Specific Expression ◽  
Regulatory Modules ◽  
Specific Manner ◽  
A Cell

AbstractTranscription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is an advantageous strategy. However, the mechanisms that control the activation of TFs in different cell types and at different stages of development remain unclear. The neural retina serves as a model of the development of a complex tissue. We used this system to analyze how expression of the homeobox TF, Orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during retinogenesis. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. These include mature bipolar interneurons, photoreceptors, and retinal progenitor/precursor cells. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages, as revealed by ATAC-seq and DNase-seq analyses. We conclude that retinal cells utilize a cohort of TFs with different expression patterns, and multiple CRMs with different chromatin configurations, to precisely regulate the expression of Otx2 in a cell type- and stage-specific manner in the retina.

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