Analysis of the Consensus Binding Sequence and the DNA-Binding Domain of ZF5

Obata, Takuya; Yanagidani, Akifumi; Yokoro, Kenjiro; Numoto, Michitaka; Yamamoto, Shoso

doi:10.1006/bbrc.1998.9970

Cited by 17 publications

(10 citation statements)

References 40 publications

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“…We used the Transcriptional Element Search System (TESS) (31) to determine whether any of the ribosomal motif groups were similar to TFBSs beyond those that were already annotated. Motif group 12-1 was found to be significantly similar to the binding site for mouse ZF5, whose consensus binding sequence is GSGCGCGR (32) (Table 4). Motif group 12-3 had significant similarities to the binding sites for both EBP-45 [binding sequence TGTTTGC (33)] and HNF3-family TFs [binding consensus sequence described as YGTTTRT in rat (34) and TRTTTGY in the frog Xenopus laevi s (35)].…”

Section: Resultsmentioning

confidence: 98%

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Sleumer

Mah

Baillie

et al. 2010

Nucleic Acids Research

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The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans genome. We used the word-counting motif discovery algorithm DME to form the motifs into groups based on sequence similarity. We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources. Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms. Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites. Additionally, seven motif groups were extensions of the canonical C. elegans trans-splice acceptor site. One motif group was tested for regulatory function in a series of green fluorescent protein expression experiments and was shown to be involved in pharyngeal expression.

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Section: Resultsmentioning

confidence: 98%

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Sleumer

Mah

Baillie

et al. 2010

Nucleic Acids Research

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“…The DNA‐binding domain of ZF5 consists of the third and forth Zn‐fingers [28]. Cyclic amplification and selection of targets (CAST) assays performed independently by two groups confirmed the GC‐rich content of ZF5 binding sites with a common core sequence 5′‐GCGCG‐3′[28,29]. Interestingly, none of the ZF5 sequences isolated by CAST assays contained (GCC) n triplet repeats.…”

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confidence: 99%

Novel repressor of the human FMR1 gene − identification of p56 human (GCC)_n‐binding protein as a Krüppel‐like transcription factor ZF5

Orlov¹,

Kuteykin-Teplyakov²,

Ignatovich³

et al. 2007

The FEBS Journal

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A series of relatively short (GCC)n triplet repeats (n = 3–30) located within regulatory regions of many mammalian genes may be considered as putative cis‐acting transcriptional elements (GCC‐elements). Fragile X‐mental retardation syndrome is caused by an expansion of (GCC)n triplet repeats within the 5′‐untranslated region of the human fragile X‐mental retardation 1 (FMR1) gene. The present study aimed to characterize a novel human (GCC)n‐binding protein and investigate its possible role in the regulation of the FMR1 gene. A novel human (GCC)n‐binding protein, p56, was isolated and identified as a Krüppel‐like transcription factor, ZF5, by MALDI‐TOF analysis. The capacity of ZF5 to specifically interact with (GCC)n triplet repeats was confirmed by the electrophoretic mobility shift assay with purified recombinant ZF5 protein. In cotransfection experiments, ZF5 overexpression repressed activity of the GCC‐element containing mouse ribosomal protein L32 gene promoter. Moreover, RNA interference assay results showed that endogenous ZF5 acts as a repressor of the human FMR1 gene. Thus, these data identify a new class of ZF5 targets, a subset of genes containing GCC‐elements in their regulatory regions, and raise the question of whether transcription factor ZF5 is implicated in the pathogenesis of fragile X syndrome.

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“…Although ETF is abundant in the uterus relative to other tissues [37], its role in embryo implantation is unknown. ZF5 contains five Krüppel-like zinc-fingers at its C-terminus [38]. E2F-1 (E2F transcription factor 1) is an upstream regulator of cell proliferation and decidualization in mouse uterus [39].…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats

Zhang¹,

Zhao²,

Huang³

et al. 2018

Cell Physiol Biochem

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Background/Aims: Embryo implantation is an essential process for eutherian pregnancy, but this process varies across eutherians. The genomic mechanisms that led to the emergence and diversification of embryo implantation are largely unknown. Methods: In this study, we analyzed transcriptomic changes during embryo implantation in mice and rats by using RNA-seq. Bioinformatics and evolutionary analyses were performed to characterize implantation-associated genes in these two species. Results: We identified a total of 518 differentially expressed genes in mouse uterus during implantation, of which 253 genes were up-regulated and 265 genes were down-regulated at the implantation sites compared with the inter-implantation sites. In rat uterus, there were 374 differentially expressed genes, of which 284 genes were up-regulated and 90 genes were down-regulated. A cross-species comparison revealed that 92 up-regulated genes and 20 down-regulated genes were shared. The differences and similarities between mice and rats were investigated further at the gene ontology, pathway, network, and causal transcription factor levels. Additionally, we found that embryo implantation might have evolved through the recruitment of ancient genes into uterine expression. The evolutionary rates of the differentially expressed genes in mouse and rat uterus were significantly lower than those of the non-changed genes, indicating that implantation-related genes are evolutionary conserved due to high selection pressure. Conclusion: Our study provides insights into the molecular mechanisms involved in the evolution of embryo implantation.

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Analysis of the Consensus Binding Sequence and the DNA-Binding Domain of ZF5

Cited by 17 publications

References 40 publications

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Novel repressor of the human FMR1 gene − identification of p56 human (GCC)_n‐binding protein as a Krüppel‐like transcription factor ZF5

Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats

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Analysis of the Consensus Binding Sequence and the DNA-Binding Domain of ZF5

Cited by 17 publications

References 40 publications

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans

Novel repressor of the human FMR1 gene − identification of p56 human (GCC)n‐binding protein as a Krüppel‐like transcription factor ZF5

Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats

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Novel repressor of the human FMR1 gene − identification of p56 human (GCC)_n‐binding protein as a Krüppel‐like transcription factor ZF5