scholarly journals Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots

2019 ◽  
Author(s):  
Birte Schwarz ◽  
Christina B. Azodi ◽  
Shin-Han Shiu ◽  
Petra Bauer
Keyword(s):  
Transcription Factor ◽  
Iron Deficiency ◽  
Large Scale ◽  
Computational Models ◽  
Regulatory Elements ◽  
Transport Systems ◽  
Fe Deficiency ◽  
Grass Species ◽  
Bhlh Transcription Factor ◽  
Fe Uptake

AbstractIron (Fe) is a key cofactor in many cellular redox processes, including respiration and photosynthesis. Plant Fe deficiency (-Fe) activates a complex regulatory network which coordinates root Fe uptake and distribution to sink tissues, while avoiding over-accumulation of Fe and other metals to toxic levels. In Arabidopsis (Arabidopsis thaliana), FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR), a bHLH transcription factor (TF), is required for up-regulation of root Fe acquisition genes. However, other root and shoot -Fe-induced genes involved in Fe allocation and signaling are FIT-independent. The cis-regulatory code, i.e. the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis genome and transcriptome data, we identified over 100 putative CREs (pCREs) that were predictive of -Fe-induced up-regulation of genes in root tissue. We used large-scale in vitro TF binding data, association with FIT-dependent or FIT-independent co-expression clusters, positional bias, and evolutionary conservation to assess pCRE properties and possible functions. In addition to bHLH and MYB TFs, also B3, NAC, bZIP, and TCP TFs might be important regulators for -Fe responses. Our approach uncovered IDE1 (Iron Deficiency-responsive Element 1), a -Fe response CRE in grass species, to be conserved in regulating genes for biosynthesis of Fe-chelating compounds also in Arabidopsis. Our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes, that advances our mechanistic understanding and informs future efforts in engineering plants with more efficient Fe uptake or transport systems.One sentence summary>100 putative cis-regulatory elements robustly predict Arabidopsis root Fe deficiency-responses in computational models, and shed light on the mechanisms of transcriptional regulation.

scholarly journals FIT, a regulatory hub for iron deficiency and stress signaling in roots, and FIT-dependent and -independent gene signatures

2020 ◽  
Vol 71 (5) ◽  
pp. 1694-1705 ◽  
Author(s):  
Birte Schwarz ◽  
Petra Bauer
Keyword(s):  
Transcription Factor ◽  
Protein Interactions ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Root Cells ◽  
Gene Signatures ◽  
Helix Loop Helix ◽  
Independent Gene ◽  
Fe Uptake ◽  
Fe Acquisition

Abstract Iron (Fe) is vital for plant growth. Plants balance the beneficial and toxic effects of this micronutrient, and tightly control Fe uptake and allocation. Here, we review the role of the basic helix–loop–helix (bHLH) transcription factor FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) in Fe acquisition. FIT is not only essential, it is also a central regulatory hub in root cells to steer and adjust the rate of Fe uptake by the root in a changing environment. FIT regulates a subset of root Fe deficiency (–Fe) response genes. Based on a combination of co-expression network and FIT-dependent transcriptome analyses, we defined a set of FIT-dependent and FIT-independent gene expression signatures and co-expression clusters that encode specific functions in Fe regulation and Fe homeostasis. These gene signatures serve as markers to integrate novel regulatory factors and signals into the –Fe response cascade. FIT forms a complex with bHLH subgroup Ib transcription factors. Furthermore, it interacts with key regulators from different signaling pathways that either activate or inhibit FIT function to adjust Fe acquisition to growth and environmental constraints. Co-expression clusters and FIT protein interactions suggest a connection of –Fe with ABA responses and root cell elongation processes that can be explored in future studies.

scholarly journals Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

2020 ◽  
Author(s):  
Xiao-Yong Zhang ◽  
Jie-Ya Qiu ◽  
Qiu-Ling Hui ◽  
Yuan-Yuan Xu ◽  
Yi-Zhong He ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Iron Deficiency ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Sequencing Data ◽  
Systematic Analysis ◽  
Go Annotation ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Proteins

Abstract Background Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results In this study, we identified a total of 128 CgbHLHs from pummelo ( Citrus grandis ) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

scholarly journals FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT) interacts with OsIRO2 to regulate iron homeostasis

2020 ◽  
Author(s):  
Gang Liang ◽  
Huimin Zhang ◽  
Yang Li ◽  
Mengna Pu ◽  
Yujie Yang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Oryza Sativa ◽  
Iron Homeostasis ◽  
Transcription Activation ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Loss Of Function ◽  
Deficiency Symptoms ◽  
Fe Uptake ◽  
Fe Homeostasis

ABSTRACTThere are two Fe-uptake strategies for maintaining Fe homeostasis in plants. As a special graminaceous plant, rice applies both strategies. However, it remains unclear how these two strategies are regulated in rice. IRON-RELATED BHLH TRANSCRIPTION FACTOR 2 (OsIRO2) is critical for regulating Fe uptake in rice. In this study, we identified an interacting partner of OsIRO2, Oryza sativa FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT), which encodes a bHLH transcription factor. The OsIRO2 protein is localized in the cytoplasm and nucleus, but OsFIT facilitates the accumulation of OsIRO2 in the nucleus. Loss-of-function mutations to OsFIT result in decreased Fe accumulation, severe Fe-deficiency symptoms, and disrupted expression of Fe-uptake genes. In contrast, OsFIT overexpression promotes Fe accumulation and the expression of Fe-uptake genes. Genetic analyses indicated that OsFIT and OsIRO2 function in the same genetic node. Further analysis suggested that OsFIT and OsIRO2 form a functional transcription activation complex to initiate the expression of Fe-uptake genes. Our findings provide a mechanism understanding of how rice maintains Fe homeostasis.One-sentence summaryOsFIT interacts with and facilitates the accumulation of OsIRO2 in the nucleus where the OsFIT-OsIRO2 transcription complex initiates the transcription of Fe deficiency responsive genes.

scholarly journals Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

2019 ◽  
Author(s):  
Xiao-Yong Zhang ◽  
Jie-Ya Qiu ◽  
Qiu-Ling Hui ◽  
Yuan-Yuan Xu ◽  
Yi-Zhong He ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Iron Deficiency ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Sequencing Data ◽  
Systematic Analysis ◽  
Go Annotation ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Proteins

Abstract Background Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results In this study, we identified a total of 128 CgbHLHs from pummelo ( Citrus grandis ) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

scholarly journals Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

2020 ◽  
Author(s):  
Xiao-Yong Zhang ◽  
Jie-Ya Qiu ◽  
Qiu-Ling Hui ◽  
Yuan-Yuan Xu ◽  
Yi-Zhong He ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Iron Deficiency ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Sequencing Data ◽  
Systematic Analysis ◽  
Go Annotation ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Proteins

Abstract Background Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results In this study, we identified a total of 128 CgbHLHs from pummelo ( Citrus grandis ) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

scholarly journals Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression

2020 ◽  
Vol 126 (7) ◽  
pp. 875-888 ◽  
Author(s):  
Samir Sissaoui ◽  
Jun Yu ◽  
Aimin Yan ◽  
Rui Li ◽  
Onur Yukselen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Transcription Factor ◽  
Deep Sequencing ◽  
Chromatin Immunoprecipitation ◽  
Regulatory Elements ◽  
Bhlh Transcription Factor ◽  
Genome Wide ◽  
A Genome

Rationale: Significant progress has revealed transcriptional inputs that underlie regulation of artery and vein endothelial cell fates. However, little is known concerning genome-wide regulation of this process. Therefore, such studies are warranted to address this gap. Objective: To identify and characterize artery- and vein-specific endothelial enhancers in the human genome, thereby gaining insights into mechanisms by which blood vessel identity is regulated. Methods and Results: Using chromatin immunoprecipitation and deep sequencing for markers of active chromatin in human arterial and venous endothelial cells, we identified several thousand artery- and vein-specific regulatory elements. Computational analysis revealed that NR2F2 (nuclear receptor subfamily 2, group F, member 2) sites were overrepresented in vein-specific enhancers, suggesting a direct role in promoting vein identity. Subsequent integration of chromatin immunoprecipitation and deep sequencing data sets with RNA sequencing revealed that NR2F2 regulated 3 distinct aspects related to arteriovenous identity. First, consistent with previous genetic observations, NR2F2 directly activated enhancer elements flanking cell cycle genes to drive their expression. Second, NR2F2 was essential to directly activate vein-specific enhancers and their associated genes. Our genomic approach further revealed that NR2F2 acts with ERG (ETS-related gene) at many of these sites to drive vein-specific gene expression. Finally, NR2F2 directly repressed only a small number of artery enhancers in venous cells to prevent their activation, including a distal element upstream of the artery-specific transcription factor, HEY2 (hes related family bHLH transcription factor with YRPW motif 2). In arterial endothelial cells, this enhancer was normally bound by ERG, which was also required for arterial HEY2 expression. By contrast, in venous endothelial cells, NR2F2 was bound to this site, together with ERG, and prevented its activation. Conclusions: By leveraging a genome-wide approach, we revealed mechanistic insights into how NR2F2 functions in multiple roles to maintain venous identity. Importantly, characterization of its role at a crucial artery enhancer upstream of HEY2 established a novel mechanism by which artery-specific expression can be achieved.

scholarly journals Identification of the Novel Tooth-Specific Transcription Factor AmeloD

2018 ◽  
Vol 98 (2) ◽  
pp. 234-241 ◽  
Author(s):  
B. He ◽  
Y. Chiba ◽  
H. Li ◽  
S. de Vega ◽  
K. Tanaka ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Epithelial Cell ◽  
Tooth Development ◽  
Tooth Germ ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Epithelial Cell Line ◽  
Bhlh Transcription Factor ◽  
Specific Cell ◽  
E Cadherin

Basic-helix-loop-helix (bHLH) transcription factors play an important role in various organs’ development; however, a tooth-specific bHLH factor has not been reported. In this study, we identified a novel tooth-specific bHLH transcription factor, which we named AmeloD, by screening a tooth germ complementary DNA (cDNA) library using a yeast 2-hybrid system. AmeloD was mapped onto the mouse chromosome 1q32. Phylogenetic analysis showed that AmeloD belongs to the achaete-scute complex-like ( ASCL) gene family and is a homologue of ASCL5. AmeloD was uniquely expressed in the inner enamel epithelium (IEE), but its expression was suppressed after IEE cell differentiation into ameloblasts. Furthermore, AmeloD expression showed an inverse expression pattern with the epithelial cell-specific cell–cell adhesion molecule E-cadherin in the dental epithelium. Overexpression of AmeloD in dental epithelial cell line CLDE cells resulted in E-cadherin suppression. We found that AmeloD bound to E-box cis-regulatory elements in the proximal promoter region of the E-cadherin gene. These results reveal that AmeloD functions as a suppressor of E-cadherin transcription in IEE cells. Our study demonstrated that AmeloD is a novel tooth-specific bHLH transcription factor that may regulate tooth development through the suppression of E-cadherin in IEE cells.

scholarly journals The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots

2010 ◽  
Vol 22 (7) ◽  
pp. 2219-2236 ◽  
Author(s):  
Terri A. Long ◽  
Hironaka Tsukagoshi ◽  
Wolfgang Busch ◽  
Brett Lahner ◽  
David E. Salt ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Iron Deficiency ◽  
Bhlh Transcription Factor

scholarly journals A Novel Negative Fe-Deficiency-Responsive Element and a TGGCA-Type-Like FeRE Control the Expression ofFTR1inChlamydomonas reinhardtii

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Xiaowen Fei ◽  
Mats Eriksson ◽  
Yajun Li ◽  
Xiaodong Deng
Keyword(s):  
Iron Deficiency ◽  
Chlamydomonas Reinhardtii ◽  
Mutational Analysis ◽  
Transcriptional Start Site ◽  
Regulatory Elements ◽  
Fe Deficiency ◽  
Start Site ◽  
Response Elements ◽  
Responsive Element ◽  
Necessary And Sufficient

We have reported three Fe-deficiency-responsive elements (FEREs),FOX1, ATX1,andFEA1, all of which are positive regulatory elements in response to iron deficiency inChlamydomonas reinhardtii. Here we describeFTR1, another iron regulated gene and mutational analysis of its promoter. Our results reveal that the FeREs ofFTR1distinguish itself from other iron response elements by containing bothnegativeandpositiveregulatory regions. InFTR1, the−291/−236 region from the transcriptional start site is necessary and sufficient for Fe-deficiency-inducible expression. This region contains two positive FeREs with a TGGCA-like core sequence: the FtrFeRE1 (ATGCAGGCT) at−287/−279 and the FtrFeRE2 (AAGCGATTGCCAGAGCGC) at−253/−236. Furthermore, we identified a novel FERE, FtrFeRE3 (AGTAACTGTTAAGCC) localized at−319/−292, which negatively influences the expression ofFTR1.

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