scholarly journals Cross-Species Root Transcriptional Network Analysis Highlights Conserved Modules in Response to Nitrate between Maize and Sorghum

2020 ◽  
Vol 21 (4) ◽  
pp. 1445
Author(s):  
Hongyang Du ◽  
Lihua Ning ◽  
Bing He ◽  
Yuancong Wang ◽  
Min Ge ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Target Genes ◽  
Affinity Purification ◽  
Hormone Signaling ◽  
Transcriptional Repressors ◽  
Nutrient Metabolism ◽  
Available Nitrogen ◽  
Genetic Mechanisms ◽  
Root Morphogenesis

Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO3−-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO3− treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO3− and involved in nitrogen and carbohydrate metabolism, including NRT, NIR, NIA, FNR, and G6PD2. Two G2-like transcription factors (ZmNIGT1 and SbNIGT1), induced by NO3− stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO3−-regulatory network containing a set of conserved modules and transcription factors.

scholarly journals EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Fctors of a gene group

2020 ◽  
Author(s):  
Sangrea Shim ◽  
Pil Joon Seo
Keyword(s):  
Transcription Factors ◽  
Open Source ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Affinity Purification ◽  
Enrichment Analysis ◽  
Analysis Tool ◽  
Gene Group ◽  
Genome Wide ◽  
One Step

SummaryEAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a gene group) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of cis-motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target [email protected] or [email protected]://github.com/sangreashim/EAT-UpTF

scholarly journals Global analysis of the RpaB regulon based on the positional distribution of HLR1 sequences and comparative differential RNA-Seq data

2018 ◽  
Author(s):  
Matthias Riediger ◽  
Taro Kadowaki ◽  
Ryuta Nagayama ◽  
Jens Georg ◽  
Yukako Hihara ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Global Analysis ◽  
Affinity Purification ◽  
Electron Flow ◽  
Positional Distribution ◽  
State Transitions ◽  
Northern Hybridization

ABSTRACTThe transcription factor RpaB regulates the expression of genes encoding photosynthesis-associated proteins during light acclimation. The binding site of RpaB is the HLR1 motif, a pair of imperfect octameric direct repeats, separated by two random nucleotides. Here, we used high-resolution mapping data of transcriptional start sites (TSSs) in the modelSynechocystissp. PCC 6803 in conjunction with the positional distribution of HLR1 sites for the global prediction of the RpaB regulon. The results demonstrate that RpaB regulates the expression of more than 150 promoters, driving the transcription of protein-coding and non-coding genes and antisense transcripts under low light and upon the shift to high light when DNA binding activity is lost. Transcriptional activation by RpaB is achieved when the HLR1 motif is located 66 to 45 nt upstream, repression occurs when it is close to or overlapping the TSS. Selected examples were validated by multiple experimental approaches, including chromatin affinity purification, reporter gene, northern hybridization and electrophoretic mobility shift assays. We found that RpaB controlsssr2016/pgr5, which is involved in cyclic electron flow and state transitions; six out of nine ferredoxins; three of four FtsH proteases;gcvP/slr0293, encoding a crucial photorespiratory protein; andnirAandisiAfor which we suggest cross-regulation with the transcription factors NtcA or FurA, respectively. In addition to photosynthetic gene functions, RpaB contributes to the control of genes affiliated with nitrogen assimilation, cofactor biosyntheses, the CRISPR system and the circadian clock, making it one of the most versatile regulators in cyanobacteria.Significance StatementRpaB is a transcription factor in cyanobacteria and in the chloroplasts of several lineages of eukaryotic algae. Like other important transcription factors, the gene encoding RpaB cannot be deleted, making the study of deletion mutants impossible. Based on a bioinformatic approach, we increased the number of known genes controlled by RpaB by a factor of 5. Depending on the distance to the TSS, RpaB mediates transcriptional activation or repression. The high number and functional diversity among its target genes and co-regulation with other transcriptional regulators characterize RpaB as a regulatory hub.

scholarly journals Different DNA-binding specificities of NLP and NIN transcription factors underlie nitrate-induced control of root nodulation

2021 ◽  
Author(s):  
Hanna Nishida ◽  
Shohei Nosaki ◽  
Takamasa Suzuki ◽  
Momoyo Ito ◽  
Takuya Miyakawa ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Dna Binding ◽  
Target Genes ◽  
Affinity Purification ◽  
Lotus Japonicus ◽  
Adaptive Strategy ◽  
Nodule Development ◽  
Symbiotic Genes ◽  
Leguminous Plants

Abstract Leguminous plants produce nodules for nitrogen fixation; however, nodule production incurs an energy cost. Therefore, as an adaptive strategy, leguminous plants halt root nodule development when sufficient amounts of nitrogen nutrients, such as nitrate, are present in the environment. Although legume NODULE INCEPTION (NIN)-LIKE PROTEIN (NLP) transcription factors have recently been identified, understanding how nodulation is controlled by nitrate, a fundamental question for nitrate-mediated transcriptional regulation of symbiotic genes, remains elusive. Here, we show that two Lotus japonicus NLPs, NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1)/LjNLP4 and NRSYM2/LjNLP1, have overlapping functions in the nitrate-induced control of nodulation and act as master regulators for nitrate-dependent gene expression. We further identify candidate target genes of LjNLP4 by combining transcriptome analysis with a DNA affinity purification (DAP)-seq approach. We then demonstrate that LjNLP4 and LjNIN, a key nodulation-specific regulator and paralogue of LjNLP4, have different DNA-binding specificities. Moreover, LjNLP4-LjNIN dimerization underlies LjNLP4-mediated bifunctional transcriptional regulation. These data provide a basic principle for how nitrate controls nodulation through positive and negative regulation of symbiotic genes.

scholarly journals Network analysis of microRNAs, transcription factors, target genes and host genes in human anaplastic astrocytoma

2016 ◽  
Vol 12 (1) ◽  
pp. 437-444 ◽  
Author(s):  
LUCHEN XUE ◽  
ZHIWEN XU ◽  
KUNHAO WANG ◽  
NING WANG ◽  
XIAOXU ZHANG ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Anaplastic Astrocytoma ◽  
Target Genes ◽  
Host Genes

ZmCLA4 regulates leaf angle through multiple hormone signaling pathways in maize

2020 ◽  
Author(s):  
Dandan Dou ◽  
Shengbo Han ◽  
Liru Cao ◽  
Lixia Ku ◽  
Huafeng Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Target Genes ◽  
Acid Metabolism ◽  
Affinity Purification ◽  
Underlying Mechanism ◽  
Leaf Angle ◽  
Hormone Signaling ◽  
Transport Pathway ◽  
Close Relationship ◽  
Plant Hormone Signaling

Abstract Leaf angle (LA) is an important agronomic trait in cereals that shares a close relationship with crop architecture and grain yield. Although it has been previously reported that ZmCLA4 can influence LA, the underlying mechanism of it remains unclear. In this study, we used Gal4-LexA/UAS system and transactivation analysis to demonstrate that ZmCLA4 is a transcriptional repressor that regulates LA. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmCLA4 mainly binds to the promoters containing the EAR motif (CACCGGAC) as well as two motifs (CCGARGS and CDTCNTC) to inhibit the expression of its target genes. Further analysis of ZmCLA4 target genes indicated that ZmCLA4 functions as a hub of multiple plant hormone signaling pathways because ZmCLA4 was found to directly bind to the promoters of multiple genes including ZmARF22 and ZmIAA26 in the auxin transport pathway, ZmBZR3 in the brassinosteroid signaling pathway, two ZmWRKY genes involved in abscisic acid metabolism, ZmCYP genes (ZmCYP75B1, ZmCYP93D1) related to jasmonic acid metabolism, and ZmABI3 involved in the ethylene response pathway. Overall, our work provides deep insights into the regulatory network of ZmCLA4 in controlling LA in maize.

scholarly journals Network analysis of microRNAs, transcription factors, target genes and host genes in nasopharyngeal carcinoma

2016 ◽  
Vol 11 (6) ◽  
pp. 3821-3828 ◽  
Author(s):  
HAO WANG ◽  
ZHIWEN XU ◽  
MENGYAO MA ◽  
NING WANG ◽  
KUNHAO WANG
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Nasopharyngeal Carcinoma ◽  
Target Genes ◽  
Host Genes

scholarly journals Network analysis of microRNAs, transcription factors, and target genes involved in axon regeneration

2018 ◽  
Vol 19 (4) ◽  
pp. 293-304 ◽  
Author(s):  
Li-ning Su ◽  
Xiao-qing Song ◽  
Zhan-xia Xue ◽  
Chen-qing Zheng ◽  
Hai-feng Yin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Target Genes ◽  
Axon Regeneration

scholarly journals The Transcriptional Network in the Arabidopsis Circadian Clock System

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1284
Author(s):  
Norihito Nakamichi
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Circadian Clock ◽  
Feedback Loop ◽  
Target Genes ◽  
Transcriptional Network ◽  
Transcriptional Repressors ◽  
Clock System ◽  
Molecular Studies ◽  
Key Genes

The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

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