The zebrafish klf gene family

Blood ◽  
2001 ◽  
Vol 98 (6) ◽  
pp. 1792-1801 ◽  
Author(s):  
Andrew C. Oates ◽  
Stephen J. Pratt ◽  
Brenda Vail ◽  
Yi-lin Yan ◽  
Robert K. Ho ◽  
...  
Keyword(s):  
Blood Vessel ◽  
Gene Family ◽  
Danio Rerio ◽  
Expression Patterns ◽  
Regulatory Proteins ◽  
Developmental Expression ◽  
Vertebrate Development ◽  
Functional Conservation ◽  
Transcriptional Regulatory ◽  
High Degree

Abstract The Krüppel-like factor(KLF) family of genes encodes transcriptional regulatory proteins that play roles in differentiation of a diverse set of cells in mammals. For instance, the founding memberKLF1 (also known as EKLF) is required for normal globin production in mammals. Five new KLF genes have been isolated from the zebrafish, Danio rerio, and the structure of their products, their genetic map positions, and their expression during development of the zebrafish have been characterized. Three genes closely related to mammalian KLF2 andKLF4 were found, as was an ortholog of mammalianKLF12. A fifth gene, apparently missing from the genome of mammals and closely related to KLF1 and KLF2,was also identified. Analysis demonstrated the existence of novel conserved domains in the N-termini of these proteins. Developmental expression patterns suggest potential roles for these zebrafish genes in diverse processes, including hematopoiesis, blood vessel function, and fin and epidermal development. The studies imply a high degree of functional conservation of the zebrafish genes with their mammalian homologs. These findings further the understanding of theKLF genes in vertebrate development and indicate an ancient role in hematopoiesis for the Krüppel-like factorgene family.

Developmental Expression Patterns of FTZ-F1 Homologues in Zebrafish (Danio rerio)

2001 ◽  
Vol 121 (2) ◽  
pp. 146-155 ◽  
Author(s):  
Jonas von Hofsten ◽  
Iwan Jones ◽  
Johnny Karlsson ◽  
Per-Erik Olsson
Keyword(s):  
Danio Rerio ◽  
Expression Patterns ◽  
Developmental Expression

scholarly journals Genome-Wide Identification and Analysis of Chitinase-Like Gene Family in Bemisia tabaci (Hemiptera: Aleyrodidae)

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 254
Author(s):  
Zhengke Peng ◽  
Jun Ren ◽  
Qi Su ◽  
Yang Zeng ◽  
Lixia Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Wide Distribution ◽  
Developmental Expression ◽  
Glycoside Hydrolase Family ◽  
Genome Wide ◽  
And Function ◽  
Disk Growth ◽  
Hydrolase Family

Chitinases are of great importance in chitin degradation and remodeling in insects. However, the genome-wide distribution of chitinase-like gene family in Bemsia tabaci, a destructive pest worldwide, is still elusive. With the help of bioinformatics, we annotated 14 genes that encode putative chitinase-like proteins, including ten chitinases (Cht), three imaginal disk growth factors (IDGF), and one endo-β-N-acetylglucosaminidase (ENGase) in the genome of the whitefly, B. tabaci. These genes were phylogenetically grouped into eight clades, among which 13 genes were classified in the glycoside hydrolase family 18 groups and one in the ENGase group. Afterwards, developmental expression analysis suggested that BtCht10, BtCht5, and BtCht7 were highly expressed in nymphal stages and exhibit similar expression patterns, implying their underlying role in nymph ecdysis. Notably, nymphs exhibited a lower rate of survival when challenged by dsRNA targeting these three genes via a nanomaterial-promoted RNAi method. In addition, silencing of BtCht10 significantly resulted in a longer duration of development compared to control nymphs. These results indicate a key role of BtCht10, BtCht5, and BtCht7 in B. tabaci nymph molting. Our research depicts the differences of chitinase-like family genes in structure and function and identified potential targets for RNAi-based whitefly management.

scholarly journals Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression

2022 ◽  
pp. gr.275655.121
Author(s):  
Ni-Chen Chang ◽  
Quirze Rovira ◽  
Jonathan N Wells ◽  
Cedric Feschotte ◽  
Juan M Vaquerizas
Keyword(s):  
Transposable Elements ◽  
Single Cell ◽  
Expression Patterns ◽  
Developmental Expression ◽  
Gene Promoters ◽  
Vertebrate Development ◽  
Genomic Distribution ◽  
Dna Transposons ◽  
Wide Range ◽  
The Impact

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

Phylogenetic and evolutionary relationships and developmental expression patterns of the zebrafish twist gene family

2009 ◽  
Vol 219 (6) ◽  
pp. 289-300 ◽  
Author(s):  
Gare Hoon Yeo ◽  
Felicia S. H. Cheah ◽  
Christoph Winkler ◽  
Ethylin Wang Jabs ◽  
Byrappa Venkatesh ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Developmental Expression ◽  
Evolutionary Relationships ◽  
Twist Gene

scholarly journals The Pyrus bretschneideri invertase gene family: identification, phylogeny and expression patterns

2020 ◽  
Vol 34 (1) ◽  
pp. 319-329
Author(s):  
Tao Wu ◽  
Zheng Liu ◽  
Li Yang ◽  
Yinsheng Cheng ◽  
Junfan Tu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Invertase Gene

scholarly journals Tissue-specific developmental expression of the kallikrein gene family in the rat.

1990 ◽  
Vol 265 (2) ◽  
pp. 1077-1081
Author(s):  
J A Clements ◽  
B A Matheson ◽  
J W Funder
Keyword(s):  
Gene Family ◽  
Developmental Expression ◽  
Tissue Specific

scholarly journals Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

scholarly journals Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Heather S. Deter ◽  
Tahmina Hossain ◽  
Nicholas C. Butzin
Keyword(s):  
Transcriptional Regulatory Network ◽  
Transcriptional Response ◽  
Regulatory Proteins ◽  
Health Concern ◽  
Transcriptional Networks ◽  
Antibiotic Tolerance ◽  
Multiple Gene ◽  
E Coli ◽  
Transcriptional Regulatory ◽  
Antibiotic Efficacy

AbstractAntibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a population gains antibiotic resistance, a growing health concern. We examined how E. coli transcriptional networks changed in response to lethal ampicillin concentrations. We are the first to apply transcriptional regulatory network (TRN) analysis to antibiotic tolerance by leveraging existing knowledge and our transcriptional data. TRN analysis shows that gene expression changes specific to ampicillin treatment are likely caused by specific sigma and transcription factors typically regulated by proteolysis. These results demonstrate that to survive lethal concentration of ampicillin specific regulatory proteins change activity and cause a coordinated transcriptional response that leverages multiple gene systems.

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