scholarly journals PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations

2021 ◽  
Vol 22 (19) ◽  
pp. 10304
Author(s):  
Yang Xu ◽  
Ziqiang Zhu
Keyword(s):  
Target Genes ◽  
High Ambient Temperature ◽  
Interacting Proteins ◽  
Hormone Signaling ◽  
Helix Loop Helix ◽  
Robust Network ◽  
Global Transcriptome ◽  
Signaling Components ◽  
Reduce Gene Expression ◽  
Gene Expression Levels

Basic helix-loop-helix (bHLH) family transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is necessary for plant adaption to light or high ambient temperature. PIF4 directly associates with plenty of its target genes and modulates the global transcriptome to induce or reduce gene expression levels. However, PIF4 activity is tightly controlled by its interacting proteins. Until now, twenty-five individual proteins have been reported to physically interact with PIF4. These PIF4-interacting proteins act together with PIF4 and form a unique nexus for plant adaption to light or temperature change. In this review, we will discuss the different categories of PIF4-interacting proteins, including photoreceptors, circadian clock regulators, hormone signaling components, and transcription factors. These distinct PIF4-interacting proteins either integrate light and/or temperature cues with endogenous hormone signaling, or control PIF4 abundances and transcriptional activities. Taken together, PIF4 and PIF4-interacting proteins play major roles for exogenous and endogenous signal integrations, and therefore establish a robust network for plants to cope with their surrounding environmental alterations.

scholarly journals Id2 Promotes Apoptosis by a Novel Mechanism Independent of Dimerization to Basic Helix-Loop-Helix Factors

1998 ◽  
Vol 18 (9) ◽  
pp. 5435-5444 ◽  
Author(s):  
Monica Florio ◽  
Maria-Clemencia Hernandez ◽  
Hui Yang ◽  
Hui-Kuo Shu ◽  
John L. Cleveland ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cell Death ◽  
Target Genes ◽  
Specific Binding ◽  
Helix Loop Helix ◽  
Cell Death Pathway ◽  
Id Proteins ◽  
Enhanced Expression ◽  
Positive Regulators ◽  
Hlh Transcription Factors

ABSTRACT Members of the helix-loop-helix (HLH) family of Id proteins have demonstrated roles in the regulation of differentiation and cell proliferation. Id proteins inhibit differentiation by HLH-mediated heterodimerization with basic HLH transcription factors. This blocks their sequence-specific binding to DNA and activation of target genes that are often expressed in a tissue-specific manner. Id proteins can also act as positive regulators of cell proliferation. The different mechanisms proposed for Id-mediated promotion of entry into S phase also involve HLH-mediated interactions affecting regulators of the G1/S transition. We have found that Id2 augments apoptosis in both interleukin-3 (IL-3)-dependent 32D.3 myeloid progenitors and U2OS osteosarcoma cells. We could not detect a similar activity for Id3. In contrast to the effects of Id2 on differentiation and cell proliferation, Id2-mediated apoptosis is independent of HLH-mediated dimerization. The ability of Id2 to promote cell death resides in its N-terminal region and is associated with the enhanced expression of a known component of the programmed cell death pathway, the proapoptotic gene BAX.

scholarly journals Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging

2020 ◽  
Vol 21 (6) ◽  
pp. 1908 ◽  
Author(s):  
Hongxia Zhang ◽  
Kunlin Jin
Keyword(s):  
Target Genes ◽  
Differentially Expressed ◽  
Molecular Signaling ◽  
Slow Development ◽  
Exosomal Mirnas ◽  
Pathways Analysis ◽  
Old Rats ◽  
Underlying Mechanisms ◽  
Signaling Components ◽  
Serum Exosomes

People are living longer than ever. Consequently, they have a greater chance for developing a functional impairment or aging-related disease, such as a neurodegenerative disease, later in life. Thus, it is important to identify and understand mechanisms underlying aging as well as the potential for rejuvenation. Therefore, we used next-generation sequencing to identify differentially expressed microRNAs (miRNAs) in serum exosomes isolated from young (three-month-old) and old (22-month-old) rats and then used bioinformatics to explore candidate genes and aging-related pathways. We identified 2844 mRNAs and 68 miRNAs that were differentially expressed with age. TargetScan revealed that 19 of these miRNAs are predicated to target the 766 mRNAs. Pathways analysis revealed signaling components targeted by these miRNAs: mTOR, AMPK, eNOS, IGF, PTEN, p53, integrins, and growth hormone. In addition, the most frequently predicted target genes regulated by these miRNAs were EIF4EBP1, insulin receptor, PDK1, PTEN, paxillin, and IGF-1 receptor. These signaling pathways and target genes may play critical roles in regulating aging and lifespan, thereby validating our analysis. Understanding the causes of aging and the underlying mechanisms may lead to interventions that could reverse certain aging processes and slow development of aging-related diseases.

scholarly journals Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1793
Author(s):  
Aleša Kristan ◽  
Nataša Debeljak ◽  
Tanja Kunej
Keyword(s):  
Target Genes ◽  
Regulatory Elements ◽  
Future Research ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Pas Domain ◽  
Expression Stability ◽  
Post Translational Modifications ◽  
Oxygen Homeostasis ◽  
Cancer Types

Endothelial PAS domain-containing protein 1 (EPAS1), also HIF2α, is an alpha subunit of hypoxia-inducible transcription factor (HIF), which mediates cellular and systemic response to hypoxia. EPAS1 has an important role in the transcription of many hypoxia-responsive genes, however, it has been less researched than HIF1α. The aim of this study was to integrate an increasing number of data on EPAS1 into a map of diverse OMICs elements. Publications, databases, and bioinformatics tools were examined, including Ensembl, MethPrimer, STRING, miRTarBase, COSMIC, and LOVD. The EPAS1 expression, stability, and activity are tightly regulated on several OMICs levels to maintain complex oxygen homeostasis. In the integrative EPAS1 map we included: 31 promoter-binding proteins, 13 interacting miRNAs and one lncRNA, and 16 post-translational modifications regulating EPAS1 protein abundance. EPAS1 has been associated with various cancer types and other diseases. The development of neuroendocrine tumors and erythrocytosis was shown to be associated with 11 somatic and 20 germline variants. The integrative map also includes 12 EPAS1 target genes and 27 interacting proteins. The study introduced the first integrative map of diverse genomics, transcriptomics, proteomics, regulomics, and interactomics data associated with EPAS1, to enable a better understanding of EPAS1 activity and regulation and support future research.

scholarly journals D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 807 ◽  
Author(s):  
Pan ◽  
Liu ◽  
Wen ◽  
Liu ◽  
Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Promoter Methylation ◽  
Methylation Level ◽  
Target Genes ◽  
Gene Promoter ◽  
Support Vector ◽  
Whole Genome ◽  
Expression Levels ◽  
Gene Expression Levels

Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene expression levels capture adequate information to reconstruct the target gene expression levels. This inspired us to propose that the methylation level of the promoters in landmark genes might be adequate to reconstruct the promoter methylation level of target genes, which would eventually reduce the cost of promoter methylation profiling. Here, we propose a deep learning model called Deep-Gene Promoter Methylation (D-GPM) to predict the whole-genome promoter methylation level based on the promoter methylation profile of the landmark genes from The Cancer Genome Atlas (TCGA). D-GPM-15%-7000 × 5, the optimal architecture of D-GPM, acquires the least overall mean absolute error (MAE) and the highest overall Pearson correlation coefficient (PCC), with values of 0.0329 and 0.8186, respectively, when testing data. Additionally, the D-GPM outperforms the regression tree (RT), linear regression (LR), and the support vector machine (SVM) in 95.66%, 92.65%, and 85.49% of the target genes by virtue of its relatively lower MAE and in 98.25%, 91.00%, and 81.56% of the target genes based on its relatively higher PCC, respectively. More importantly, the D-GPM predominates in predicting 79.86% and 78.34% of the target genes according to the model distribution of the least MAE and the highest PCC, respectively.

scholarly journals The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

2019 ◽  
Vol 20 (11) ◽  
pp. 2730 ◽  
Author(s):  
Chunlai Wu ◽  
Xupo Ding ◽  
Zehong Ding ◽  
Weiwei Tie ◽  
Yan Yan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Transcriptional Control ◽  
Tandem Duplication ◽  
Target Genes ◽  
Hormone Signaling ◽  
Class Iii ◽  
Motif Analysis ◽  
Transcriptional Changes ◽  
Postharvest Physiological Deterioration ◽  
Class Iii Peroxidase

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.

ABI5 regulates ABA-induced anthocyanin biosynthesis by modulating the MYB1-bHLH3 complex in apple

2020 ◽  
Author(s):  
Jian-Ping An ◽  
Xiao-Wei Zhang ◽  
Ya-Jing Liu ◽  
Xiao-Fei Wang ◽  
Chun-Xiang You ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Target Genes ◽  
Anthocyanin Biosynthesis ◽  
Aba Signaling ◽  
Plant Growth And Development ◽  
Biochemical Tests ◽  
Positive Role ◽  
Helix Loop Helix ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Mechanisms

Abstract Abscisic acid (ABA) induces anthocyanin biosynthesis in many plant species. However, the molecular mechanism of ABA-regulated anthocyanin biosynthesis remains unclear. As a crucial regulator of ABA signaling, ABSCISIC ACID-INSENSITIVE5 (ABI5) is involved in many aspects of plant growth and development, yet its regulation of anthocyanin biosynthesis has not been elucidated. In this study, we found that MdABI5, the apple homolog of Arabidopsis ABI5, positively regulated ABA-induced anthocyanin biosynthesis. A series of biochemical tests showed that MdABI5 specifically interacts with basic helix-loop-helix 3 (MdbHLH3), a positive regulator of anthocyanin biosynthesis. MdABI5 enhanced the binding of MdbHLH3 to its target genes dihydroflavonol 4-reductase (MdDFR) and UDP flavonoid glucosyl transferase (MdUF3GT). In addition, MdABI5 directly bound to the promoter of MdbHLH3 to activate its expression. Moreover, MdABI5 enhanced ABA-promoted interaction between MdMYB1 and MdbHLH3. Finally, antisense suppression of MdbHLH3 significantly reduced anthocyanin biosynthesis promoted by MdABI5, indicating that MdABI5-promoted anthocyanin biosynthesis was dependent on MdbHLH3. Taken together, our data suggest that MdABI5 plays a positive role in ABA-induced anthocyanin biosynthesis by modulating the MdbHLH3-MdMYB1 complex. Our work broadens the regulatory network of ABA-mediated anthocyanin biosynthesis, providing new insights to further study the transcriptional regulatory mechanisms behind this process.

scholarly journals Functions of E2A-HEB Heterodimers in T-Cell Development Revealed by a Dominant Negative Mutation of HEB

2000 ◽  
Vol 20 (18) ◽  
pp. 6677-6685 ◽  
Author(s):  
Robert J. Barndt ◽  
Meifang Dai ◽  
Yuan Zhuang
Keyword(s):  
T Cell ◽  
Target Genes ◽  
T Cell Development ◽  
Cell Lineage ◽  
Cell Receptor ◽  
Cell Development ◽  
Dominant Negative ◽  
Helix Loop Helix ◽  
Dominant Negative Mutation ◽  
Bhlh Proteins

ABSTRACT Lymphocyte development and differentiation are regulated by the basic helix-loop-helix (bHLH) transcription factors encoded by theE2A and HEB genes. These bHLH proteins bind to E-box enhancers in the form of homodimers or heterodimers and, consequently, activate transcription of the target genes. E2A homodimers are the predominant bHLH proteins present in B-lineage cells and are shown genetically to play critical roles in B-cell development. E2A-HEB heterodimers, the major bHLH dimers found in thymocyte extracts, are thought to play a similar role in T-cell development. However, disruption of either the E2A or HEBgene led to only partial blocks in T-cell development. The exact role of E2A-HEB heterodimers and possibly the E2A and HEB homodimers in T-cell development cannot be distinguished in simple disruption analysis due to a functional compensation from the residual bHLH homodimers. To further define the function of E2A-HEB heterodimers, we generated and analyzed a dominant negative allele of HEB, which produces a physiological amount of HEB proteins capable of forming nonfunctional heterodimers with E2A proteins. Mice carrying this mutation show a stronger and earlier block in T-cell development than HEB complete knockout mice. The developmental block is specific to the α/β T-cell lineage at a stage before the completion of V(D)J recombination at the TCRβ gene locus. This defect is intrinsic to the T-cell lineage and cannot be rescued by expression of a functional T-cell receptor transgene. These results indicate that E2A-HEB heterodimers play obligatory roles both before and after TCRβ gene rearrangement during the α/β lineage T-cell development.

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