Isolation, sequence, and chromosomal localisation of the human IκBR gene (NFKBIL2)
7
Citation
14
Reference
10
Related Paper
Citation Trend
Abstract:
T he inhibitors of NF‐κ B (Iκ B s) play an important role in the regulation of the NF‐κ B pathway. IκBR (for Iκ B ‐Related) is proposed to be a novel member of this family. We report the cloning and characterization of the region of the human gene encoding the previously reported mRNA. This region contains 13 exons, spread over 6550 bp of genomic sequence. The coding sequence is only weakly similar to other IκBs and the exons display a more complicated structure than has been found in other members of the IκB gene family. Moreover, the positions of intron‐exon junctions are different from those found in other IκB genes, even within the otherwise conserved ankyrin‐like repeat region, suggesting that the IκBR gene is not a member of this extended gene family. We report a revised mRNA and protein sequence for IκBR, which predicts that the protein is larger than originally described. We also report the chromosomal localisation of the human IκBR gene (approved gene symbol NFKBIL2 ) to 8q24.3 using PCR‐based somatic cell hybrid panel analysis and fluorescence in situ hybridization (FISH) mapping.Keywords:
Coding region
Ankyrin repeat
Conserved sequence
Pair-rule gene
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.
Conserved sequence
Molecular evolution
Cite
Citations (0)
Functional divergence
Pair-rule gene
Cite
Citations (41)
Drosomycin ( Drs ) encoding an inducible 44‐residue antifungal peptide is clustered with six additional genes, Dro1, Dro2, Dro3, Dro4, Dro5, and Dro6 , forming a multigene family on the 3L chromosome arm in Drosophila melanogaster . To get further insight into the regulation of each member of the drosomycin gene family, here we investigated gene expression patterns of this family by either microbe‐free injury or microbial challenges using real time RT‐PCR. The results indicated that among the seven drosomycin genes, Drs, Dro2, Dro3, Dro4, and Dro5 showed constitutive expressions. Three out of five, Dro2, Dro3, and Dro5 , were able to be upregulated by simple injury. Interestingly, Drs is an only gene strongly upregulated when Drosophila was infected with microbes. In contrast to these five genes, Dro1 and Dro6 were not transcribed at all in either noninfected or infected flies. Furthermore, by 5 ′ rapid amplification of cDNA ends, two transcription start sites were identified in Drs and Dro2 , and one in Dro3, Dro4, and Dro5 . In addition, NF‐ κ B binding sites were found in promoter regions of Drs, Dro2, Dro3, and Dro5 , indicating the importance of NF‐ κ B binding sites for the inducibility of drosomycin genes. Based on the analyses of flanking sequences of each gene in D. melanogaster and phylogenetic relationship of drosomycins in D. melanogaster species‐group, we concluded that gene duplications were involved in the formation of the drosomycin gene family. The possible evolutionary fates of drosomycin genes were discussed according to the combining analysis of gene expression pattern, gene structure, and functional divergence of these genes.
Pair-rule gene
Melanogaster
TBX1
Functional divergence
Cite
Citations (14)
Cite
Citations (37)
Sequencing of multiple, nearly complete eukaryotic genomes creates opportunities for detecting previously unnoticed, subtle functional signals in non‐coding regions. A genome‐wide comparative analysis of orthologous sets of mammalian and yeast mRNAs revealed distinct patterns of evolutionary conservation at the boundaries of the untranslated regions (UTRs) and the coding region (CDS). Elevated sequence conservation was detected in ∼30 nt regions around the start codon. There seems to be a complementary relationship between sequence conservation in the ∼30 nt regions of the 5′‐UTR immediately upstream of the start codon and that in the synonymous positions of the 5′‐terminal 30 nt of the CDS: in mammalian mRNAs, the 5′‐UTR shows a greater conservation than the CDS, whereas the opposite trend holds for yeast mRNAs. Unexpectedly, a ∼30 nt region downstream of the stop codon shows a substantially lower level of sequence conservation than the downstream portions of the 3′‐UTRs. However, the sequence in this poorly conserved 30 nt portion of the 3′‐UTR is non‐random in that it has a higher GC content than the rest of the UTR. It is hypothesized that the elevated sequence conservation in the region immediately upstream of the start codon is related to the requirement for initiation factor binding during pre‐initiation ribosomal scanning. In contrast, the poorly conserved region downstream of the stop codon could be involved in the post‐ termination scanning and dissociation of the ribosomes from the mRNA, which requires only the mRNA–ribosome interaction. Additionally, it was found that the choice of the stop codon in mammals, but not in yeasts, and the context in the immediate vicinity of the stop codons in both mammals and yeasts are subject to strong selection. Thus, genome‐wide analysis of orthologous gene sets allows detection of previously unrecognized patterns of sequence conservation, which are likely to reflect hidden functional signals, such as ribosomal filters that could regulate translation by modulating the interaction between the mRNA and ribosomes.
Coding region
Conserved sequence
Shine-Dalgarno sequence
Stop codon
Eukaryotic translation
Ribosomal binding site
Cite
Citations (95)
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.
Conserved sequence
Molecular evolution
Cite
Citations (34)
To identify evolutionary conserved domains and facilitate the recognition of potentially significant mutations in NF1 patients or tumors, we have determined the complete approximately 12 kb sequence of mouse neurofibromatosis type 1 mRNA. The sequence predicts a 2841 amino acid protein that is more than 98% identical to human neurofibromin. All but 9 of the 45 amino acid differences between mouse and human neurofibromin occur in the N-terminal half of the protein, with 16 changes clustered just upstream of the IRA-related segment. Given the high degree of sequence identity, virtually any sequence alteration in NF1 patients or tumors is potentially significant. We have also found that the 3' untranslated segment of NF1 mRNA is highly conserved, suggesting that this region may also be a target for mutations in NF1 patients.
Neurofibromin 1
Coding region
Conserved sequence
Sequence (biology)
Cite
Citations (68)
Synteny
Functional divergence
Conserved sequence
Protein family
Cite
Citations (4)
The internal NAD(P)H dehydrogenase (NDA) gene family was a member of the NAD(P)H dehydrogenase (ND) gene family, mainly involved in the non-phosphorylated respiratory pathways in mitochondria and played crucial roles in response to abiotic stress.The whole genome identification, structure analysis and expression pattern of NDA gene family were conducted to analyze the NDA gene family.There were 51, 52, 26, and 24 NDA genes identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. According to the structural characteristics of genes and traits of phylogenetic tree, we divided the NDA gene family into 8 clades. Gene structure analysis showed that the NDA gene family was relatively conservative. The four Gossypium species had good collinearity, and segmental duplication played an important role in the evolution of the NDA gene family. Analysis of cis-elements showed that most GhNDA genes contained cis-elements related to light response and plant hormones (ABA, MeJA and GA). The analysis of the expression patterns of GhNDA genes under different alkaline stress showed that GhNDA genes were actively involved in the response to alkaline stress, possibly through different molecular mechanisms. By analyzing the existing RNA-Seq data after alkaline stress, it was found that an NDA family gene GhNDA32 was expressed, and then theGhNDA32 was silenced by virus-induced gene silencing (VIGS). By observing the phenotype, we found that the wilting degree of silenced plants was much higher than that of the control plant after alkaline treatment, suggesting that GhNDA32 gene was involved in the response to alkaline stress.In this study, GhNDAs participated in response to alkaline stress, especially NaHCO3 stress. It was of great significance for the future research on the molecular mechanism of NDA gene family in responding to abiotic stresses.
Pair-rule gene
Neofunctionalization
Gossypium barbadense
Cite
Citations (7)
Coding region
Conserved sequence
Heterologous
Cite
Citations (0)