Conservation of gene order in human microRNA-neighboring regions

Genome ◽  
2012 ◽  
Vol 55 (09) ◽  
pp. 701-704 ◽  
Author(s):  
Jianshu Chen ◽  
Wei Chen ◽  
Yudong Li
Keyword(s):  
Gene Order ◽  
Biological Function ◽  
Noncoding Rnas ◽  
Genomic Analysis ◽  
Unique Characteristic ◽  
Important Class ◽  
Human Mirnas ◽  
Genomic Architecture ◽  
Conserved Gene ◽  
Mouse Genomic

The biological function and evolution of microRNAs (miRNAs), an important class of noncoding regulatory genes, have attracted wide interest. However, their evolutionary impact on gene order rearrangements remains unknown. We examined the gene-order stability of miRNA-neighboring regions by a comparative human–mouse genomic analysis and found that the neighboring genes of human miRNAs tend to have a conserved gene order. This observation cannot be attributed to the functional bias of neighboring genes, and is a unique characteristic of miRNAs but not other noncoding RNAs. Our findings suggest that mammalian miRNAs stabilize the genomic architecture in evolution.

scholarly journals MicroRNA-143 Regulates Adipocyte Differentiation

2004 ◽  
Vol 279 (50) ◽  
pp. 52361-52365 ◽  
Author(s):  
Christine Esau ◽  
Xiaolin Kang ◽  
Eigen Peralta ◽  
Elaine Hanson ◽  
Eric G. Marcusson ◽  
...  
Keyword(s):  
Antisense Oligonucleotides ◽  
Target Gene ◽  
Adipocyte Differentiation ◽  
Biological Function ◽  
Protein Translation ◽  
Functional Assay ◽  
Expression Data ◽  
Mirna Microarray ◽  
Protein Levels ◽  
Human Mirnas

MicroRNAs (miRNAs) are endogenously expressed 20-24 nucleotide RNAs thought to repress protein translation through binding to a target mRNA (1-3). Only a few of the more than 250 predicted human miRNAs have been assigned any biological function. In an effort to uncover miRNAs important during adipocyte differentiation, antisense oligonucleotides (ASOs) targeting 86 human miRNAs were transfected into cultured human pre-adipocytes, and their ability to modulate adipocyte differentiation was evaluated. Expression of 254 miRNAs in differentiating adipocytes was also examined on a miRNA microarray. Here we report that the combination of expression data and functional assay results identified a role for miR-143 in adipocyte differentiation. miR-143 levels increased in differentiating adipocytes, and inhibition of miR-143 effectively inhibited adipocyte differentiation. In addition, protein levels of the proposed miR-143 target ERK5 (4) were higher in ASO-treated adipocytes. These results demonstrate that miR-143 is involved in adipocyte differentiation and may act through target gene ERK5.

scholarly journals BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Limin Jiang ◽  
Jingjun Zhang ◽  
Ping Xuan ◽  
Quan Zou
Keyword(s):  
Neural Network ◽  
Bp Neural Network ◽  
Regulatory Network ◽  
Bioinformatics Analysis ◽  
Biological Function ◽  
State Of The Art ◽  
Biological Evolution ◽  
Noncoding Rnas ◽  
The Past ◽  
Mirna Identification

MicroRNAs (miRNAs) are a set of short (21–24 nt) noncoding RNAs that play significant regulatory roles in cells. In the past few years, research on miRNA-related problems has become a hot field of bioinformatics because of miRNAs’ essential biological function. miRNA-related bioinformatics analysis is beneficial in several aspects, including the functions of miRNAs and other genes, the regulatory network between miRNAs and their target mRNAs, and even biological evolution. Distinguishing miRNA precursors from other hairpin-like sequences is important and is an essential procedure in detecting novel microRNAs. In this study, we employed backpropagation (BP) neural network together with 98-dimensional novel features for microRNA precursor identification. Results show that the precision and recall of our method are 95.53% and 96.67%, respectively. Results further demonstrate that the total prediction accuracy of our method is nearly 13.17% greater than the state-of-the-art microRNA precursor prediction software tools.

scholarly journals An Evolutionary Perspective of Animal MicroRNAs and Their Targets

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Noam Shomron ◽  
David Golan ◽  
Eran Hornstein
Keyword(s):  
Gene Expression ◽  
Posttranscriptional Regulation ◽  
Noncoding Rnas ◽  
Mrna Degradation ◽  
Evolutionary Perspective ◽  
Mirna Regulation ◽  
Regulate Gene Expression ◽  
Mirna Genes ◽  
Genomic Architecture ◽  
Regulate Gene

MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs. Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

scholarly journals GeneSyn: a tool for detecting conserved gene order across genomes

2004 ◽  
Vol 20 (9) ◽  
pp. 1472-1474 ◽  
Author(s):  
G. Pavesi ◽  
G. Mauri ◽  
F. Iannelli ◽  
C. Gissi ◽  
G. Pesole
Keyword(s):  
Gene Order ◽  
Conserved Gene

scholarly journals Tight association of genome rearrangements with gene expression in conifer plastomes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chung-Shien Wu ◽  
Edi Sudianto ◽  
Shu-Miaw Chaw
Keyword(s):  
Gene Expression ◽  
Gene Order ◽  
Genomic Rearrangements ◽  
First Line ◽  
Conifer Species ◽  
Antisense Transcripts ◽  
Plastid Genomes ◽  
Rnaseq Data ◽  
Tight Association ◽  
Conserved Gene

Abstract Background Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Conclusions Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

scholarly journals Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

Abstract Background: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.

Finding Conserved Gene Order Across Multiple Genomes

2007 ◽  
pp. 111-120
Author(s):  
Giulio Pavesi ◽  
Graziano Pesole
Keyword(s):  
Gene Order ◽  
Multiple Genomes ◽  
Conserved Gene
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