Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements

Hajheidari, Mohsen; Huang, Shao‐shan Carol

doi:10.1016/j.pbi.2022.102232

Cited by 23 publications

(13 citation statements)

References 73 publications

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“…until the 3′ end of the next gene's 3′ UTR, assuming that conservation indicates CREs. CREs may include promoters, enhancers, silencers, and insulators; they may affect gene expression via recruitment of trans -acting factors such as TFs, chromatin remodelers, and RNA polymerase II ( Hajheidari and Huang 2022 ). It is reasonable to assume that many CREs are TFBSs when comparing the PURRs of ABS -like s.s. and GOA -like genes.…”

Section: Resultsmentioning

confidence: 99%

Conservation of the Restricted Expression of Brassicaceae Bsister-Like Genes in Seeds Requires a Transposable Element in Arabidopsis thaliana

Roessner

Bhide

Hoffmeier

et al. 2023

Molecular Biology and Evolution

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Changes in transcription factor binding sites (TFBSs) can alter the spatio-temporal expression pattern and transcript abundance of genes. Loss and gain of TFBSs were shown to cause shifts in expression patterns in numerous cases. However, we know little about the evolution of extended regulatory sequences incorporating many TFBSs. We compare, across the crucifers (Brassicaceae, cabbage family), the sequences between the translated regions of Arabidopsis Bsister- (ABS-) like MADS-box genes (including paralogous GOA-like genes) and the next gene upstream, as an example of family wide evolution of putative regulatory regions (PURRs). ABS-like genes are essential for integument development of ovules and endothelium formation in seeds of Arabidopsis thaliana. A combination of motif based GO-enrichment and reporter gene analysis using A. thaliana as common trans-regulatory environment allows analysis of selected Brassicaceae Bsister gene PURRs. Comparison of TFBS of transcriptionally active ABS-like genes with those of transcriptionally largely inactive GOA-like genes shows that the number of in silico predicted TF binding sites (TFBSs) is similar between paralogs, emphasizing the importance of experimental verification for in silico characterization of TFBS activity and analysis of their evolution. Further, our data show highly conserved expression of Brassicaceae ABS-like genes almost exclusively in the chalazal region of ovules. The Arabidopsis-specific insertion of a transposable element (TE) into the ABS PURRs is required for stabilizing this spatially restricted expression, while other Brassicaceae achieve chalaza-specific expression without TE insertion. We hypothesize that the chalaza-specific expression of ABS is regulated by CREs provided by the TE.

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Section: Resultsmentioning

confidence: 99%

Conservation of the Restricted Expression of Brassicaceae Bsister-Like Genes in Seeds Requires a Transposable Element in Arabidopsis thaliana

Roessner

Bhide

Hoffmeier

et al. 2023

Molecular Biology and Evolution

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“…Comprehending gene regulation necessitates the exploration of DNA–protein interactions and hydrogen bonding, which influences stability and specificity. Transcription factors (TFs) linked to cis -acting elements with strong hydrogen bonds play a crucial role in gene regulation . Docking findings reveal that hydrogen bonds stabilize interactions between TFs and regulatory elements, contributing to the regulation of the expression of the Os GLP12-3 gene expression.…”

Section: Resultsmentioning

confidence: 99%

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

Ahmad,

Ullah,

Ullah

et al. 2024

ACS Omega

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Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.

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“…However, wether genes of A2 and A6 have similar functions needs further verification. Promoters are one of the most important regulatory elements, determining the temporal and spatial expression of developmentally and physiologically significant genes ( Mohsen and Huang, 2022 ). Several cis-regulatory elements were identified in the AgHSFa6-1 promoter sequence, especially ARE and STRE elements, that are related to abiotic stress.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of HSF genes from celery (Apium graveolens L.) and functional characterization of AgHSFa6-1 in response to heat stress

Zhang

Zhou

et al. 2023

Front. Plant Sci.

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High temperature stress is regarded as one of the significant abiotic stresses affecting the composition and distribution of natural habitats and the productivity of agriculturally significant plants worldwide. The HSF family is one of the most important transcription factors (TFs) families in plants and capable of responding rapidly to heat and other abiotic stresses. In this study, 29 AgHSFs were identified in celery and classified into three classes (A, B, and C) and 14 subgroups. The gene structures of AgHSFs in same subgroups were conserved, whereas in different classes were varied. AgHSF proteins were predicted to be involved in multiple biological processes by interacting with other proteins. Expression analysis revealed that AgHSF genes play a significant role in response to heat stress. Subsequently, AgHSFa6-1, which was significantly induced by high temperature, was selected for functional validation. AgHSFa6-1 was identified as a nuclear protein, and can upregulate the expression of certain downstream genes (HSP98.7, HSP70-1, BOB1, CPN60B, ADH2, APX1, GOLS1) in response to high-temperature treatment. Overexpression of AgHSFa6-1 in yeast and Arabidopsis displayed higher thermotolerance, both morphologically and physiologically. In response to heat stress, the transgenic plants produced considerably more proline, solute protein, antioxidant enzymes, and less MDA than wild-type (WT) plants. Overall, this study revealed that AgHSF family members perform a key role in response to high temperature, and AgHSFa6-1 acts as a positive regulator by augmenting the ROS-scavenging system to maintain membrane integrity, reducing stomatal apertures to control water loss, and upregulating the expression level of heat-stress sensitive genes to improve celery thermotolerance.

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Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements

Cited by 23 publications

References 73 publications

Conservation of the Restricted Expression of Brassicaceae Bsister-Like Genes in Seeds Requires a Transposable Element in Arabidopsis thaliana

Conservation of the Restricted Expression of Brassicaceae Bsister-Like Genes in Seeds Requires a Transposable Element in Arabidopsis thaliana

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

Comprehensive analysis of HSF genes from celery (Apium graveolens L.) and functional characterization of AgHSFa6-1 in response to heat stress

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