Transcription Factors in Poplar Growth and Development

2011 ◽  
pp. 192-230
Author(s):  
Amy Brunner ◽  
Eric Beers
Keyword(s):  
Transcription Factors ◽  
Growth And Development ◽  
Poplar Growth

scholarly journals Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9551
Author(s):  
Lidong Hao ◽  
Shubing Shi ◽  
Haibin Guo ◽  
Ming Li ◽  
Pan Hu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Growth And Development ◽  
Expression Profiles ◽  
Vital Role ◽  
Ethylene Response Factor ◽  
Plant Growth And Development ◽  
Element Analysis ◽  
Genome Wide ◽  
Genes Expression

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

scholarly journals Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

2021 ◽  
Vol 8 ◽  
Author(s):  
Weiwei Miao ◽  
Zeqiang Ma ◽  
Zhanyang Tang ◽  
Lin Yu ◽  
Siqi Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Signaling Pathway ◽  
Growth And Development ◽  
Muscle Development ◽  
Muscle Fibers ◽  
Muscle Growth ◽  
Rna Seq ◽  
Accessible Chromatin

Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

scholarly journals Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon

2021 ◽  
Vol 5 ◽  
Author(s):  
Zejun Tang ◽  
Na Song ◽  
Weiye Peng ◽  
Yang Yang ◽  
Tian Qiu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Disease Resistance ◽  
Growth And Development ◽  
Brachypodium Distachyon ◽  
Gras Family ◽  
Qrt Pcr ◽  
Physiological Processes ◽  
Plant Pathogen Interactions ◽  
Insight Into

GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.

scholarly journals Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton

2021 ◽  
Vol 22 (2) ◽  
pp. 898
Author(s):  
Muhammad Sajjad ◽  
Xi Wei ◽  
Lisen Liu ◽  
Fuguang Li ◽  
Xiaoyang Ge
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Plant Growth ◽  
Growth And Development ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Regulatory Pathways ◽  
Vascular Growth

Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.

scholarly journals β-Amylase–Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development

2011 ◽  
Vol 23 (4) ◽  
pp. 1391-1403 ◽  
Author(s):  
Heike Reinhold ◽  
Sebastian Soyk ◽  
Klára Šimková ◽  
Carmen Hostettler ◽  
John Marafino ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Growth And Development ◽  
Shoot Growth

scholarly journals Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 294 ◽  
Author(s):  
Zhengwu Fang ◽  
Wenqiang Jiang ◽  
Yiqin He ◽  
Dongfang Ma ◽  
Yike Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Growth And Development ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Structure Characterization ◽  
Sequence Length ◽  
Pcr Analysis ◽  
Segmental Duplications ◽  
Biotic And Abiotic Stress

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

scholarly journals Transcription Factors in the Fungus Aspergillus nidulans: Markers of Genetic Innovation, Network Rewiring and Conflict between Genomics and Transcriptomics

2021 ◽  
Vol 7 (8) ◽  
pp. 600
Author(s):  
Oier Etxebeste
Keyword(s):  
Transcription Factors ◽  
Aspergillus Nidulans ◽  
Growth And Development ◽  
Regulatory Networks ◽  
Regulatory Sequences ◽  
Sequence Evolution ◽  
Genomic Annotation ◽  
Associated Proteins ◽  
Duplication Events ◽  
Gain Loss

Gene regulatory networks (GRNs) are shaped by the democratic/hierarchical relationships among transcription factors (TFs) and associated proteins, together with the cis-regulatory sequences (CRSs) bound by these TFs at target promoters. GRNs control all cellular processes, including metabolism, stress response, growth and development. Due to the ability to modify morphogenetic and developmental patterns, there is the consensus view that the reorganization of GRNs is a driving force of species evolution and differentiation. GRNs are rewired through events including the duplication of TF-coding genes, their divergent sequence evolution and the gain/loss/modification of CRSs. Fungi (mainly Saccharomycotina) have served as a reference kingdom for the study of GRN evolution. Here, I studied the genes predicted to encode TFs in the fungus Aspergillus nidulans (Pezizomycotina). The analysis of the expansion of different families of TFs suggests that the duplication of TFs impacts the species level, and that the expansion in Zn2Cys6 TFs is mainly due to dispersed duplication events. Comparison of genomic annotation and transcriptomic data suggest that a significant percentage of genes should be re-annotated, while many others remain silent. Finally, a new regulator of growth and development is identified and characterized. Overall, this study establishes a novel theoretical framework in synthetic biology, as the overexpression of silent TF forms would provide additional tools to assess how GRNs are rewired.

scholarly journals GrgA controls Chlamydia trachomatis growth and development by regulating expression of transcription factors Euo and HrcA

2020 ◽  
Author(s):  
Wurihan Wurihan ◽  
Yi Zou ◽  
Alec M. Weber ◽  
Korri Weldon ◽  
Yehong Huang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Chlamydia Trachomatis ◽  
Virulence Factor ◽  
Growth And Development ◽  
Developmental Cycle ◽  
Mrna Levels ◽  
Late Genes ◽  
Transcriptomic Changes

ABSTRACTThe obligate intracellular bacterium Chlamydia trachomatis is an important human pathogen whose biphasic developmental cycle consists of an infectious elementary body and a replicative reticulate body. Whereas σ66, the primary sigma factor, is necessary for transcription of most chlamydial genes throughout the developmental cycle, σ28 is required for expression of some late genes. We previously showed that the Chlamydia-specific transcription factor GrgA physically interacts with both of these sigma factors and activates transcription from σ66- and σ28-dependent promoters in vitro. Here, we investigate the organismal functions of GrgA. We show that GrgA overexpression decreased RB proliferation via time-dependent transcriptomic changes. Significantly, σ66-dependent genes that code for two important transcription repressors are among the direct targets of GrgA. One of these repressors is Euo, which prevents the expression of late genes during early phases. The other is HrcA, which regulates gene expression in response to heat shock. The direct regulon of GrgA also includes a σ28-dependent gene that codes for the putative virulence factor PmpI. Conditional overexpression of Euo and HrcA also inhibited chlamydial growth and affected GrgA expression. Transcriptomic studies suggest that GrgA, Euo, and HrcA have distinct but overlapping indirect regulons. Furthermore, overexpression of either GrgA leads to decreased expression of numerous tRNAs. These findings indicate that a GrgA-mediated transcriptional regulatory network controls C. trachomatis growth and development.IMPORTANCEChlamydia trachomatis is the most prevalent sexually transmitted bacterial pathogen worldwide and is a leading cause of preventable blindness in under-developed areas as well as developed countries. Previous studies showed that the novel transcription factor GrgA activated chlamydial gene transcription in vitro, but did not addressed the organismal function of GrgA. Here, we demonstrate growth inhibition in C. trachomatis engineered to conditionally overexpress GrgA. GrgA overexpression immediately increases the expression of two other critical transcription factors (Euo and HrcA) and a candidate virulence factor (PmpI), among several other genes. We also reveal chlamydial growth reduction and transcriptomic changes including decreased GrgA mRNA levels in response to either Euo or HrcA overexpression. Thus, the transcription network controlled by GrgA likely plays a crucial role in chlamydial growth and pathogenesis.

scholarly journals Identification and analysis of Chrysanthemum nankingense NAC transcription factors and an expression analysis of OsNAC7 subfamily members

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11505
Author(s):  
Hai Wang ◽  
Tong Li ◽  
Wei Li ◽  
Wang Wang ◽  
Huien Zhao
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Plant Breeding ◽  
Stress Resistance ◽  
Growth And Development ◽  
Vital Role ◽  
Plant Growth And Development ◽  
Nac Transcription Factors ◽  
Comprehensive Information ◽  
New Ideas

NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play a vital role in plant growth and development, as well as in plant response to biotic and abiotic stressors (Duan et al., 2019; Guerin et al., 2019). Chrysanthemum is a plant with strong stress resistance and adaptability; therefore, a systematic study of NAC TFs in chrysanthemum is of great significance for plant breeding. In this study, 153 putative NAC TFs were identified based on the Chrysanthemum nankingense genome. According to the NAC family in Arabidopsis and rice, a rootless phylogenetic tree was constructed, in which the 153 CnNAC TFs were divided into two groups and 19 subfamilies. Moreover, the expression levels of 12 CnNAC TFs belonging to the OsNAC7 subfamily were analyzed in C. nankingense under osmotic and salt stresses, and different tissues were tested during different growth periods. The results showed that these 12 OsNAC7 subfamily members were involved in the regulation of root and stem growth, as well as in the regulation of drought and salt stresses. Finally, we investigated the function of the CHR00069684 gene, and the results showed that CHR00069684 could confer improved salt and low temperature resistance, enhance ABA sensitivity, and lead to early flowering in tobacco. It was proved that members of the OsNAC7 subfamily have dual functions including the regulation of resistance and the mediation of plant growth and development. This study provides comprehensive information on analyzing the function of CnNAC TFs, and also reveals the important role of OsNAC7 subfamily genes in response to abiotic stress and the regulation of plant growth. These results provide new ideas for plant breeding to control stress resistance and growth simultaneously.

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