Comparative Analysis of 3D Expression Patterns of Transcription Factor Genes and Digit Fate Maps in the Developing Chick Wing

NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.

Download Full-text

Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

10.1101/2021.04.23.441111 ◽

2021 ◽

Author(s):

Zhaoran Zhou ◽

Christiane Eichner ◽

Frank Nilsen ◽

Inge Jonassen ◽

Michael Dondrup

Keyword(s):

Transcription Factor ◽

Rna Interference ◽

Atlantic Salmon ◽

Expression Profiles ◽

Expression Patterns ◽

Transcriptional Level ◽

Lepeophtheirus Salmonis ◽

Salmon Louse ◽

Transcription Factor Genes ◽

Regulatory Impact

Background: The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods: Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results: Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation. Conclusions: We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

Download Full-text

Metallothionein and bZIP Transcription Factor Genes from Velvetleaf and Their Differential Expression Following Colletotrichum coccodes Infection

Phytopathology ◽

10.1094/phyto-96-1116 ◽

2006 ◽

Vol 96 (10) ◽

pp. 1116-1123 ◽

Cited By ~ 9

Author(s):

Amélie L. Dauch ◽

Suha H. Jabaji-Hare

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Leucine Zipper ◽

Expression Patterns ◽

Bzip Transcription Factor ◽

Colletotrichum Coccodes ◽

Transcription Factor Genes ◽

Pathogen Attack ◽

Fungal Genes ◽

Type 3

Colletotrichum coccodes is a biocontrol agent of velvetleaf (Abutilon theophrasti), a noxious weed of corn and soybean. Metallothioneins (MTs) and basic region/leucine zipper motif (bZIP) are heavy-metal-binding proteins and transcription factors, respectively, that have been related to several plant processes, including the responses of plants to pathogen attack. Previous investigation of the determinants involved in the velvet-leaf-C. coccodes interaction had shed light on particular plant and fungal genes expressed in this pathosystem. Here, we report on the temporal expression patterns of two distinct types (2 and 3) of MT and bZIP transcription factor genes in velvetleaf leaves following infection with C. coccodes using quantitative reverse-transcription polymerase chain reaction. Gene expression ratios were significantly upregulated 1 day after infection (DAI), a time at which velvetleaf leaves appeared symptomless. At 2 DAI, bZIP and type 3 MT expression ratios dropped to levels significantly lower than those estimated for noninfected plants. Necrotic symptoms appeared 5 DAI and increased with time, during which gene expression levels were maintained either below or at levels observed in the control. These findings indicate that C. coccodes altered the expression of type 2 and 3 MT and bZIP genes. In addition, this is the first report on induction of a type 3 MT in plants in response to a pathogen attack.

Download Full-text

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

International Journal of Molecular Sciences ◽

10.3390/ijms20143591 ◽

2019 ◽

Vol 20 (14) ◽

pp. 3591 ◽

Cited By ~ 4

Author(s):

Ming-Ming Liu ◽

Mang-Mang Wang ◽

Jin Yang ◽

Jing Wen ◽

Peng-Cheng Guo ◽

...

Keyword(s):

Transcription Factor ◽

Higher Plants ◽

Protein Complexes ◽

Expression Patterns ◽

Interaction Network ◽

Land Plants ◽

Terrestrial Plants ◽

Functional Studies ◽

Transcription Factor Genes ◽

Tcp Family

The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants’ development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.

Download Full-text

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Genes ◽

10.3390/genes11010020 ◽

2019 ◽

Vol 11 (1) ◽

pp. 20

Author(s):

Fernando Manuel Matias Hurtado ◽

Maísa de Siqueira Pinto ◽

Perla Novais de Oliveira ◽

Diego Mauricio Riaño-Pachón ◽

Laura Beatriz Inocente ◽

...

Keyword(s):

Cell Wall ◽

Transcription Factor ◽

Secondary Cell Wall ◽

Expression Patterns ◽

Wood Quality ◽

Tectona Grandis ◽

Wood Formation ◽

Xylem Differentiation ◽

Transcription Factor Genes ◽

Tectona Grandis L.F

NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.

Download Full-text

A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

BMC Genomics ◽

10.1186/s12864-021-08054-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhaoran Zhou ◽

Christiane Eichner ◽

Frank Nilsen ◽

Inge Jonassen ◽

Michael Dondrup

Keyword(s):

Transcription Factor ◽

Rna Interference ◽

Atlantic Salmon ◽

Expression Profiles ◽

Expression Patterns ◽

Transcriptional Level ◽

Lepeophtheirus Salmonis ◽

Salmon Louse ◽

Transcription Factor Genes ◽

Regulatory Impact

Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

Download Full-text

Significant Decreased in Cord Blood (CB) Versus Adult Peripheral Blood (APB) Monocyte (Mo)-Derived Dendritic Cells (DC) Gene Expression Patterns and T Cell Functional Activation: Insight into Immaturity of CB Cellular Immunity.

Blood ◽

10.1182/blood.v106.11.2210.2210 ◽

2005 ◽

Vol 106 (11) ◽

pp. 2210-2210

Author(s):

H. Jiang ◽

C. Wade-Harris ◽

L. Baxi ◽

M. S. Cairo

Keyword(s):

Gene Expression ◽

T Cells ◽

Transcription Factor ◽

T Cell ◽

Cd8 T Cells ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Surface Molecules ◽

Transcription Factor Genes ◽

Presentation Activity

Abstract It has been recognized that dysfunction of CB immunity is in part due to the immaturity of the neonatal immune system (Cairo, Blood, 1997). However, biological pathways and molecular mechanisms associated with the immaturity of CB immunity are still poorly understood. Recently we have utilized oligonucleotide microarray to examine gene expression profiling of CB versus APB Mo and have demonstrated significant differential gene expression patterns, including surface molecules, cytokines, signaling molecules, transcription factors and apoptotic genes (Jiang/Cairo, et al, J. of Immunol., 2004). We sought to examine whether there are differential expressed genes occurred in Mo-derived CB versus APB DC and their impact on DC mediated T cell activity. Briefly, Mo were purified from fresh CB or APB and cultured for 8 days with GM-CSF and IL-4 (immature DC (iDC)) and LPS for mature DC (mDC). mRNA was isolated and oligonucleotide microarray was carried out (Affymetrix, U133A). Data was analyzed by Microarray Suite Version 5.0 (Affymetrix) and GeneSpring 5.0 software (Silicon Genetics). Selected genes were analyzed by RT-PCR (SuperScript, Invetrogen). We identified gene expression patterns that were significantly lower in CB versus APB DC including surface molecules HLA-DQA1 (4F), HLA-DRB3 (5F), HLA-DRB4 (5.5F), CD80 (3F), CD38 (3.8F); cytokine/chemokine genes IL-1b (2.5F), IL6 (2.9F), IL12B (3.5F), CXCL10 (6.6F); immunoregulatory genes ISG20 (11F), IFI27 (7.6F), TNFSF10 (4.5F), SOCS3 (2.5F). Moreover, several transcription factor genes whose proteins may involve in the activation of expression of these immune regulator genes were also differentially expressed (IRF-5 (3F), IRF7 (3F), MAD (6.3F)). We therefore compared CB versus APB DC antigen presentation activity to APB CD8 T cells by ELISPOT assay for interferon-r (IFNr) production (BD Pharmagen). Briefly, the purified CD8 T cells (MHC HLA A2) were incubated with CB or APB DC that were loaded without or with influenza peptide onto ELISPOT plate (Larsson, et al, J. of Immunol., 2000). The ELISPOT plates were developed, scanned and quantitated by an ELISPOT reader (C.T.L. Technology). Our results demonstrated that, although CB or APB mDC had allogeneic effects, influenza peptide loaded CB mDC was not able to induce CD8 T cells to produce IFNr while APB mDC loaded with influenza peptide strongly induced CD8 T cells to produce IFNr. This stimulatory effect of APB mDC on CD8 T cells to produce IFNr was 3.5 fold greater than that of CB mDC. We further examined DC antigen presentation activity to CD4 T cells and observed that APB-DC had stronger effects on CD4 T cell proliferation (3 fold for mDC vs. iDC) compared with CB-DC (only 1.5 fold for mDC vs. iDC) by CFSE assay (Molecular Probe). We postulate that decreased expression of specific surface molecules and other genes resulting in lower surface protein expression in CB DC may in part be responsible for the lack of initiation of signaling events from cell surface to trigger CB-DC to stimulate activation of CD8 and CD4 T cells. The decreased expression of transcription factor genes may also in part be responsible for the lower expressed surface molecule genes. Furthermore, these decreased expressed genes in other molecular categories in LPS-CB vs. APB DC may also partially be responsible for differential innate and adaptive immune function and properties of CB vs. APB.

Download Full-text