Expression patterns of the coe/ebf transcription factor genes during chicken and mouse limb development

During limb development, chondrocytes located at the epiphyseal tip of long bone models give rise to articular tissue, whereas the more numerous chondrocytes in the shaft undergo maturation, hypertrophy, and mineralization and are replaced by bone cells. It is not understood how chondrocytes follow these alternative pathways to distinct fates and functions. In this study we describe the cloning of C-1-1, a novel variant of the ets transcription factor ch-ERG. C-1-1 lacks a short 27–amino acid segment located ∼80 amino acids upstream of the ets DNA binding domain. We found that in chick embryo long bone anlagen, C-1-1 expression characterizes developing articular chondrocytes, whereas ch-ERG expression is particularly prominent in prehypertrophic chondrocytes in the growth plate. To analyze the function of C-1-1 and ch-ERG, viral vectors were used to constitutively express each factor in developing chick leg buds and cultured chondrocytes. We found that virally driven expression of C-1-1 maintained chondrocytes in a stable and immature phenotype, blocked their maturation into hypertrophic cells, and prevented the replacement of cartilage with bone. It also induced synthesis of tenascin-C, an extracellular matrix protein that is a unique product of developing articular chondrocytes. In contrast, virally driven expression of ch-ERG significantly stimulated chondrocyte maturation in culture, as indicated by increases in alkaline phosphatase activity and deposition of a mineralized matrix; however, it had modest effects in vivo. The data show that C-1-1 and ch-ERG have diverse biological properties and distinct expression patterns during skeletogenesis, and are part of molecular mechanisms by which limb chondrocytes follow alternative developmental pathways. C-1-1 is the first transcription factor identified to date that appears to be instrumental in the genesis and function of epiphyseal articular chondrocytes.

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Desrt, an AT-rich interaction domain family transcription factor gene, is an early marker for nephrogenic mesoderm and is expressed dynamically during mouse limb development

Mechanisms of Development ◽

10.1016/s0925-4773(01)00370-7 ◽

2001 ◽

Vol 104 (1-2) ◽

pp. 139-142 ◽

Cited By ~ 5

Author(s):

Sika Ristevski ◽

Patrick P.L Tam ◽

Ismail Kola ◽

Paul Hertzog

Keyword(s):

Transcription Factor ◽

Limb Development ◽

Domain Family ◽

Transcription Factor Gene ◽

Interaction Domain ◽

Factor Gene ◽

Early Marker ◽

Mouse Limb ◽

Rich Interaction

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Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

PeerJ ◽

10.7717/peerj.4172 ◽

2017 ◽

Vol 5 ◽

pp. e4172 ◽

Cited By ~ 9

Author(s):

Bernard Kinuthia Karanja ◽

Liang Xu ◽

Yan Wang ◽

Everlyne M’mbone Muleke ◽

Bashir Mohammed Jabir ◽

...

Keyword(s):

Transcription Factor ◽

Abiotic Stresses ◽

Expression Patterns ◽

Hormone Signaling ◽

Preferential Expression ◽

Genome Wide ◽

Raphanus Sativus L ◽

Transcription Factor Genes ◽

Membrane Bound ◽

Polymerase Chain

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.

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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.

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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.

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Deep conservation of wrist and digit enhancers in fish

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1420208112 ◽

2014 ◽

Vol 112 (3) ◽

pp. 803-808 ◽

Cited By ~ 80

Author(s):

Andrew R. Gehrke ◽

Igor Schneider ◽

Elisa de la Calle-Mustienes ◽

Juan J. Tena ◽

Carlos Gomez-Marin ◽

...

Keyword(s):

Gene Expression ◽

Limb Development ◽

Expression Patterns ◽

Late Phase ◽

Phylogenetic Footprinting ◽

Molecular Data ◽

Distal Portion ◽

Spotted Gar ◽

Mouse Limb ◽

And Function

There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a “late” phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5′ end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of “autopod” enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish “autopod” enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods.

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

PLoS ONE ◽

10.1371/journal.pone.0018661 ◽

2011 ◽

Vol 6 (4) ◽

pp. e18661 ◽

Cited By ~ 14

Author(s):

Malcolm Fisher ◽

Helen Downie ◽

Monique C. M. Welten ◽

Irene Delgado ◽

Andrew Bain ◽

...

Keyword(s):

Transcription Factor ◽

Comparative Analysis ◽

Expression Patterns ◽

Transcription Factor Genes

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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.

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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.

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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.

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