scholarly journals Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 665 ◽  
Author(s):  
Krzysztof Kowal ◽  
Angelika Tkaczyk ◽  
Tomasz Ząbek ◽  
Mariusz Pierzchała ◽  
Brygida Ślaska
Keyword(s):  
Mitochondrial Genome ◽  
Epigenetic Modification ◽  
Mitochondrial Gene ◽  
Cpg Islands ◽  
Model Organisms ◽  
12S Rrna ◽  
Cpg Sites ◽  
Starting Point ◽  
D Loop ◽  
Taxonomic Groups

The information about mtDNA methylation is still limited, thus epigenetic modification remains unclear. The lack of comprehensive information on the comparative epigenomics of mtDNA prompts comprehensive investigations of the epigenomic modification of mtDNA in different species. This is the first study in which the theoretical CpG localization in the mtDNA reference sequences from various species (12) was compared. The aim of the study was to determine the localization of CpG sites and islands in mtDNA of model organisms and to compare their distribution. The results are suitable for further investigations of mtDNA methylation. The analysis involved both strands of mtDNA sequences of animal model organisms representing different taxonomic groups of invertebrates and vertebrates. For each sequence, such parameters as the number, length, and localization of CpG islands were determined with the use of EMBOSS (European Molecular Biology Open Software Suite) software. The number of CpG sites for each sequence was indicated using the newcpgseek algorithm. The results showed that methylation of mtDNA in the analysed species involved mitochondrial gene expression. Our analyses showed that the CpG sites were commonly present in genomic regions including the D-loop, CYTB, ND6, ND5, ND4, ND3, ND2, ND1, COX3, COX2, COX1, ATP6, 16s rRNA, and 12s rRNA. The CpG distribution in animals from different species was diversified. Generally, the number of observed CpG sites of the mitochondrial genome was higher in the vertebrates than in the invertebrates. However, there was no relationship between the frequency of the CpG sites in the mitochondrial genome and the complexity of the analysed organisms. Interestingly, the distribution of the CpG sites for tRNA coding genes was usually cumulated in a larger CpG region in vertebrates. This paper may be a starting point for further research, since the collected information indicates possible methylation regions localized in mtDNA among different species including invertebrates and vertebrates.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

Abstract 428: DNA Methylation of ASC is Associated with Decreased ASC and IL-1β Expression in Heart Failure

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Brittany Butts ◽  
Javed Butler
Keyword(s):  
Heart Failure ◽  
Dna Methylation ◽  
Inflammatory Cytokines ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Inflammasome Activation ◽  
Cpg Sites ◽  
Exon 1 ◽  
Vital Component ◽  
Intron Region

Introduction: Heart failure (HF) is associated with formation and activation of inflammasome, a complex of intracellular interaction proteins that trigger maturation of inflammatory cytokines to initiate inflammatory response. ASC, a vital component of the inflammasome, is controlled through epigenetic modification via methylation of CpG islands surrounding exon 1. Methods: To assess the relationships between DNA methylation of ASC, ASC expression, and inflammatory cytokines IL-1β and IL-18 in HF, stored samples from 155 chronic HF patients (age 56.9±12.0 yr, 64% male, 47% black, and ejection fraction 29.9±14.9) were analyzed. DNA extracted from PMBCs were analyzed by pyrosequencing for percent methylation of seven CpG sites in the intron region preceding exon 1 of the ASC gene. ASC mRNA was quantified via real-time PCR and analyzed as the ratio ASC:GAPDH. Serum ASC, IL-1β, and IL-18 were measured by ELISA. Results: Higher ASC methylation was associated with lower ASC mRNA (r=0-.328, p<0.001) and protein (r=-.464, p<0.001) expression. Lower ASC mRNA expression was associated with lower ASC protein expression (r=0.494, p<0.001). Decreased IL-1β expression was associated with higher ASC methylation (r=-.424, p=0.005) and lower ASC mRNA (r=.619, p<0.001) and ASC protein (r=.433, p<0.001). IL-18 expression was not significantly associated with ASC methylation or expression. Conclusions: Increased ASC methylation was associated with lower IL-1β, likely via decreased ASC gene expression. As ASC is required for inflammasome activation of IL-1β, this study implicates the inflammasome pathway as a driver of inflammation in HF, proving a potential target for novel interventions.

The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders

Zootaxa ◽  
2017 ◽  
Vol 4329 (6) ◽  
pp. 574
Author(s):  
HYUNG JIK WOO ◽  
ANH D. NGUYEN ◽  
KUEM HEE JANG ◽  
EUN HWA CHOI ◽  
SHI HYUN RYU ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
12S Rrna ◽  
Coding Region ◽  
Protein Coding ◽  
Close Relationship ◽  
Relationship Of ◽  
Rna Genes

The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76.6%) and Sphaerotheriidae sp. (order Sphaerotheriida; 71.2%). In comparison with the mitochondrial gene arrangement of eight other millipede species, the whole mitochondrial gene arrangement of A. koreanus is most similar to the nemasomatid species, Antrokoreana gracilipes Verhoeff, 1938, but differs from those of the other diplopod orders. The absence of tRNACys between the ND2 and COI regions is unique to the order Polydesmida, whereas the translocation of tRNATyr to between ND2 and COI is exclusive to the Sphaerotheriida. It is also shown that the translocation of tRNAThr between ND4L and ND1 may be a synapomorphy to support a close relationship of two orders Spirobolida and Spirostreptida. 

scholarly journals Widespread Mitochondrial DNA Methylation Drift Contributes to Postoperative Delirium in Young and Old Mice

2020 ◽  
Author(s):  
Yue Liu ◽  
Shuai Yang ◽  
Wei Zhang ◽  
Yan Yang ◽  
Ming Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mitochondrial Dna ◽  
Prefrontal Cortex ◽  
Mitochondrial Dysfunction ◽  
Postoperative Delirium ◽  
Mitochondrial Gene ◽  
Mitochondrial Gene Expression ◽  
Cpg Sites ◽  
D Loop ◽  
Old Mice

Abstract Background: Mitochondrial dysfunction is linked to the etiopathogenesis of postoperative delirium (POD), which severely affects the prognosis of elderly patients undergoing surgery. The methylation of mitochondrial DNA (mtDNA), a new and incompletely described phenomenon that regulates the structure and function of mitochondria, is associated with aging. However, the relationship between mtDNA methylation and POD has not been established. Methods: 5-methylcytosine (5-mC) at 5 CpG sites of the displacement loop (D-loop) and at 60 CpG sites of coding gene loci in the mitochondrial genome after surgery of the hippocampus, prefrontal cortex, amygdala, and anterior cingulate cortex in 6- and 18-month-old mice were detected using bisulfite pyrosequencing. Mitochondrial structure, mitochondrial gene expression and mtDNA copy number were also examined using Electron microscopy and real time PCR to find the association with mtDNA methylationResults: The mtDNA methylation drift manifested as a decrease in the methylation levels at the D-loop and an increase or decrease in the methylation levels at several coding gene loci, ultimately resulting in reduced mtDNA copy numbers, altered mitochondrial gene expression, and damaged mitochondrial structures in the hippocampus and prefrontal cortex after surgery. The activation of Silent information regulator-1 (SIRT1) ameliorated anesthesia- and surgery-induced mitochondrial dysfunction and delirium-like behaviors by regulating mtDNA methyltransferase-mediated mtDNA methylation. Conclusions: These data support the existence of epigenetic mtDNA regulation in POD; however, further studies are required to explore the specific mechanisms.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

scholarly journals Reduced Variation in Drosophila simulans Mitochondrial DNA

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1519-1528
Author(s):  
J William O Ballad ◽  
Joy Hatzidakis ◽  
Timothy L Karr ◽  
Martin Kreitman
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Evolutionary Dynamics ◽  
Selective Sweep ◽  
Mitochondrial Gene ◽  
Drosophila Simulans ◽  
Dramatic Reduction ◽  
Nucleotide Variability ◽  
Pooled Samples ◽  
Mitochondrial Gene Mutation

We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.

An International Campaign for Agricultural and Livestock Genomics (CALG)

2002 ◽  
Vol 06 (24) ◽  
pp. 958-965
Author(s):  
Jun Yu ◽  
Jian Wang ◽  
Huanming Yang
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Model Organisms ◽  
Environmental Biology ◽  
Cdna Sequences ◽  
Governmental Agencies ◽  
Technology Innovations ◽  
A Genome ◽  
Starting Point ◽  
The Cost

A coordinated international effort to sequence agricultural and livestock genomes has come to its time. While human genome and genomes of many model organisms (related to human health and basic biological interests) have been sequenced or plugged in the sequencing pipelines, agronomically important crop and livestock genomes have not been given high enough priority. Although we are facing many challenges in policy-making, grant funding, regional task emphasis, research community consensus and technology innovations, many initiatives are being announced and formulated based on the cost-effective and large-scale sequencing procedure, known as whole genome shotgun (WGS) sequencing that produces draft sequences covering a genome from 95 percent to 99 percent. Identified genes from such draft sequences, coupled with other resources, such as molecular markers, large-insert clones and cDNA sequences, provide ample information and tools to further our knowledge in agricultural and environmental biology in the genome era that just comes to its accelerated period. If the campaign succeeds, molecular biologists, geneticists and field biologists from all countries, rich or poor, would be brought to the same starting point and expect another astronomical increase of basic genomic information, ready to convert effectively into knowledge that will ultimately change our lives and environment into a greater and better future. We call upon national and international governmental agencies and organizations as well as research foundations to support this unprecedented movement.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals The dynamics of mitochondrial-linked gene expression among tissues and life stages in two contrasting strains of laying hens

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262613
Author(s):  
Clara Dreyling ◽  
Martin Hasselmann
Keyword(s):  
Gene Expression ◽  
Energy Metabolism ◽  
Life Span ◽  
Laying Hens ◽  
Mitochondrial Gene ◽  
Model Organisms ◽  
Life Stages ◽  
Mitochondrial Gene Expression ◽  
Cellular Energy ◽  
Cellular Energy Metabolism

The cellular energy metabolism is one of the most conserved processes, as it is present in all living organisms. Mitochondria are providing the eukaryotic cell with energy and thus their genome and gene expression has been of broad interest for a long time. Mitochondrial gene expression changes under different conditions and is regulated by genes encoded in the nucleus of the cell. In this context, little is known about non-model organisms and we provide the first large-scaled gene expression analysis of mitochondrial-linked genes in laying hens. We analysed 28 mitochondrial and nuclear genes in 100 individuals in the context of five life-stages and strain differences among five tissues. Our study showed that mitochondrial gene expression increases during the productive life span, and reacts tissue and strain specific. In addition, the strains react different to potential increased oxidative stress, resulting from the increase in mitochondrial gene expression. The results suggest that the cellular energy metabolism as part of a complex regulatory system is strongly affected by the productive life span in laying hens and thus partly comparable to model organisms. This study provides a starting point for further analyses in this field on non-model organisms, especially in laying-hens.

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