Conserved and divergent roles for members of the Snail family of transcription factors in the chick and mouse embryo

Development ◽  
1998 ◽  
Vol 125 (16) ◽  
pp. 3111-3121 ◽  
Author(s):  
M. Sefton ◽  
S. Sanchez ◽  
M.A. Nieto
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Chick Embryo ◽  
Neural Crest ◽  
Family Member ◽  
Zinc Finger ◽  
Mouse Embryo ◽  
Amino Acid Sequences ◽  
Mouse Homologue ◽  
Snail Family

The members of the Snail family of zinc-finger transcription factors have been implicated in the formation of distinct tissues within the developing vertebrate and invertebrate embryo. Two members of this family have been described in higher vertebrates, Snail (Sna) and Slug (Slu), where they have been implicated in the formation of tissues such as the mesoderm and the neural crest. We have isolated the mouse homologue of the Slu gene enabling us to analyse and compare the amino acid sequences and the patterns of expression of both Sna and Slu in the chick and mouse. We have detected features in the sequences that allow the unequivocal ascription of any family member to the Sna or Slu subfamilies and we have observed that, during early stages of development, many of the sites of Slu and Sna expression in the mouse and chick embryo are swapped. Later in development, the sites of expression of Slu and Sna are conserved between these two species. These data, together with the data available in other species, lead us to propose that Slu and Sna arose as a duplication of an ancestor gene and that an extra duplication in the fish lineage has given rise to two Sna genes. Furthermore, several early sites of Slu and Sna expression have been swapped in the avian lineage. Our analysis of the Snail family may also shed new light on the origin of the neural crest.

Overexpression of Snail family members highlights their ability to promote chick neural crest formation

Development ◽  
2002 ◽  
Vol 129 (7) ◽  
pp. 1583-1593 ◽  
Author(s):  
Marta G. del Barrio ◽  
M. Angela Nieto
Keyword(s):  
Chick Embryo ◽  
Neural Crest ◽  
Neural Tube ◽  
Family Members ◽  
Ectopic Expression ◽  
Endogenous Gene ◽  
The Family ◽  
Snail Family ◽  
Migratory Cells ◽  
Snail Gene

The Snail gene family of transcription factors plays crucial roles in different morphogenetic processes during the development of vertebrate and invertebrate embryos. In previous studies of function interference for one of the family members, Slug, we showed its involvement and neural crest formation in the chick embryo. Now we have carried out a series of gain-of-function experiments in which we show that Slug overexpression in the neural tube of the chick embryo induces an increase in neural crest production. The analysis of electroporated embryos shows that Slug can induce the expression of rhoB and an increase in the number of HNK-1-positive migratory cells, indicating that it lies upstream of them in the genetic cascade of neural crest development. The increase in neural crest production after Slug overexpression was confined to the cranial region, indicating that the mechanisms of crest induction somehow differ between head and trunk. The expression of the two vertebrate family members, Slug and Snail, is peculiar with respect to the neural crest. Slug is not expressed in the premigratory crest in the mouse, whereas it is expressed in this cell population in the chick and the opposite is true for Snail(Sefton, M., Sánchez, S. and Nieto M. A. (1998) Development125, 3111-3121). This raises the question of whether they can be functionally equivalent. To test this hypothesis both intra- and interspecies, we have performed a series of ectopic expression experiments by electroporating chick and mouse Snail in the chick embryo hindbrain. We observe that both genes elicit the same responses in the neural tube. Our results indicate that they can be functionally equivalent, although the embryos show a higher response to the endogenous gene, chick Slug.

Activation domains of gene-specific transcription factors: are histones among their targets?

2004 ◽  
Vol 82 (4) ◽  
pp. 453-459 ◽  
Author(s):  
Alexandre M Erkine
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Chromatin Remodeling ◽  
Transcription Initiation ◽  
Protein Complexes ◽  
Amino Acid Sequences ◽  
Gene Promoters ◽  
Activation Domain ◽  
Activation Domains ◽  
Multiple Protein

Activation domains of promoter-specific transcription factors are critical entities involved in recruitment of multiple protein complexes to gene promoters. The activation domains often retain functionality when transferred between very diverse eukaryotic phyla, yet the amino acid sequences of activation domains do not bear any specific consensus or secondary structure. Activation domains function in the context of chromatin structure and are critical for chromatin remodeling, which is associated with transcription initiation. The mechanisms of direct and indirect recruitment of chromatin-remodeling and histone-modifying complexes, including mechanisms involving direct interactions between activation domains and histones, are discussed.Key words: activation domain, transcription, chromatin, nucleosome.

scholarly journals Acheron, an novel LA antigen family member, binds to cask and forms a complex with id transcription factors

2009 ◽  
Vol 14 (2) ◽  
Author(s):  
Haifeng Weng ◽  
Chul Kim ◽  
Christos Valavanis ◽  
Zhaohui Wang ◽  
Lawrence Schwartz
Keyword(s):  
Transcription Factors ◽  
Family Member ◽  
Cdna Library ◽  
Mouse Embryo ◽  
Yeast Two Hybrid ◽  
Binding Partner ◽  
C Terminus ◽  
La Antigen ◽  
Two Hybrid

AbstractAcheron, a Lupus antigen ortholog, was identified as a novel death-associated transcript from the intersegmental muscles of the mothManduca sexta. Acheron is phylogenetically-conserved and represents a new sub-family of Lupus antigen proteins. Acheron is expressed predominantly in neurons and muscle in vertebrates, and regulates several developmental events including myogenesis, neurogenesis and possibly metastasis. Using Acheron as bait, we performed a yeast two-hybrid screen with a mouse embryo cDNA library and identified CASK-C, a novel CASK/Lin-2 isoform, as an Acheron binding partner. Acheron and CASK-C bind via the C-terminus of Acheron and the CaMKII-like domain of CASK-C. Co-immunoprecipitation assays verify this interaction and demonstrate that Acheron also forms a complex with all members of the Id (inhibitor of differentiation) proteins. Taken together, these data suggest a mechanism by which Acheron may regulate development and pathology.

Characterization of the isoforms of MOVO zinc finger protein, a mouse homologue of Drosophila Ovo, as transcription factors

Gene ◽  
2004 ◽  
Vol 336 (1) ◽  
pp. 47-58 ◽  
Author(s):  
Sawako Unezaki ◽  
Mikio Nishizawa ◽  
Emiko Okuda-Ashitaka ◽  
Yasuo Masu ◽  
Masanori Mukai ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Protein A ◽  
Mouse Homologue ◽  
Finger Protein

scholarly journals Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Indeok Hwang ◽  
Ranjith Kumar Manoharan ◽  
Jong-Goo Kang ◽  
Mi-Young Chung ◽  
Young-Wook Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Cold Stress ◽  
Stress Responses ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Cold Response ◽  
Bzip Transcription Factors

Cabbages (Brassica oleraceaL.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsiveBolbZIPgenes were screened in inbred lines,BN106andBN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes,Bol008071,Bol033132, andBol042729, was significantly increased inBN107under cold conditions and was unchanged inBN106. The upregulation of these genes inBN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes,Bol033132has 97% sequence similarity toBra020735, which was identified in a screen for cold-related genes inB. rapaand a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.

cDNA cloning of transcription factor E4TF1 subunits with Ets and notch motifs

1993 ◽  
Vol 13 (3) ◽  
pp. 1385-1391
Author(s):  
H Watanabe ◽  
J Sawada ◽  
K Yano ◽  
K Yamaguchi ◽  
M Goto ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Sequence ◽  
Binding Activity ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Cdna Clones ◽  
Dna Binding Activity

E4TF1 was originally identified as one of the transcription factors responsible for adenovirus E4 gene transcription. It is composed of two subunits, a DNA binding protein with a molecular mass of 60 kDa and a 53-kDa transcription-activating protein. Heterodimerization of these two subunits is essential for the protein to function as a transcription factor. In this study, we identified a new E4TF1 subunit, designated E4TF1-47, which has no DNA binding activity but can associate with E4TF1-60. We then cloned the cDNAs for each of the E4TF1 subunits. E4TF1 was purified, and the partial amino acid sequence of each subunit was determined. The predicted amino acid sequence of each cDNA clone revealed that E4TF1-60 had an ETS domain, which is a DNA binding domain common to ets-related transcription factors. E4TF1-53 had four tandemly repeated notch-ankyrin motifs. The putative cDNA of E4TF1-47 coded almost the same amino acid sequences as E4TF1-53. Three hundred and thirty-two amino acids of the N termini of E4TF1-47 and -53 were identical except for one amino acid insertion in E4TF1-53, and they differ from each other at the C terminus. These three recombinant cDNA clones were expressed in Escherichia coli, and the proteins behaved in the same manner as purified proteins in a gel retardation assay. Nucleotide and predicted amino acid sequences were highly homologous to GABP-alpha and -beta, which is further supported by the observation that GABP-specific antibody can recognize human E4TF1.

scholarly journals miR-1322 Binding Sites in Paralogous and Orthologous Genes

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Raigul Niyazova ◽  
Olga Berillo ◽  
Shara Atambayeva ◽  
Anna Pyrkova ◽  
Aigul Alybayeva ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factors ◽  
Amino Acid ◽  
Binding Site ◽  
Binding Sites ◽  
Target Genes ◽  
Amino Acid Sequences ◽  
Orthologous Genes ◽  
Start Position ◽  
Human Genes

We searched for 2,563 microRNA (miRNA) binding sites in 17,494 mRNA sequences of human genes. miR-1322 has more than 2,000 binding sites in 1,058 genes withΔG/ΔGmratio of 85% and more. miR-1322 has 1,889 binding sites in CDSs, 215 binding sites in 5′ UTRs, and 160 binding sites in 3′ UTRs. From two to 28 binding sites have arranged localization with the start position through three nucleotides of each following binding site. The nucleotide sequences of these sites in CDSs encode oligopeptides with the same and/or different amino acid sequences. We found that 33% of the target genes encoded transcription factors. miR-1322 has arranged binding sites in the CDSs of orthologousMAMLD1,MAML2, andMAML3genes. These sites encode a polyglutamine oligopeptide ranging from six to 47 amino acids in length. The properties of miR-1322 binding sites in orthologous and paralogous target genes are discussed.

scholarly journals Growth factor-induced tyrosine phosphorylation of Hrs, a novel 115-kilodalton protein with a structurally conserved putative zinc finger domain.

1995 ◽  
Vol 15 (11) ◽  
pp. 6213-6221 ◽  
Author(s):  
M Komada ◽  
N Kitamura
Keyword(s):  
Amino Acid ◽  
Growth Factor ◽  
Hepatocyte Growth Factor ◽  
Tyrosine Phosphorylation ◽  
Zinc Finger ◽  
Amino Acid Sequences ◽  
Zinc Finger Domain ◽  
Rich Region ◽  
Putative Zinc Finger ◽  
Hepatocyte Growth

The activation of growth factor receptor tyrosine kinases leads to tyrosine phosphorylation of many intracellular proteins which are thought to play crucial roles in growth factor signaling pathways. We previously showed that tyrosine phosphorylation of a 115-kDa protein is rapidly induced in cells treated with hepatocyte growth factor. To clarify the structure and possible function of the 115-kDa protein (designated Hrs for hepatocyte growth factor-regulated tyrosine kinase substrate), we purified this protein from B16-F1 mouse melanoma cells by anti-phosphotyrosine immunoaffinity chromatography and determined its partial amino acid sequences. On the basis of the amino acid sequences, we molecularly cloned the cDNA for mouse Hrs. The nucleotide sequence of the cDNA revealed that Hrs is a novel 775-amino-acid protein with a putative zinc finger domain that is structurally conserved in several other proteins. This protein also contained a proline-rich region and a proline- and glutamine-rich region. The expression of Hrs mRNA was detected in all adult mouse tissues tested and also in embryos. To analyze the Hrs cDNA product, we prepared a polyclonal antibody against bacterially expressed Hrs. Using this antibody, we showed by subcellular fractionation that Hrs is localized to the cytoplasm; we also showed that that tyrosine phosphorylation of Hrs is induced in cells treated with epidermal growth factor or platelet-derived growth factor. These results suggest that Hrs plays a unique and important role in the signaling pathway of growth factors.

scholarly journals Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0252181
Author(s):  
Mangi Kim ◽  
Hong Xi ◽  
Jongsun Park
Keyword(s):  
Amino Acids ◽  
Transcription Factors ◽  
Amino Acid ◽  
Phylogenetic Trees ◽  
Low Cost ◽  
Amino Acid Sequences ◽  
Plant Genome ◽  
Genome Database ◽  
Link Type ◽  
Gata Transcription Factors

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

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