A large-scale screening of the normalized mammalian mitochondrial gene expression profiles

Anisimov, S. V.

doi:10.1017/s0016672305007718

Cited by 10 publications

(6 citation statements)

References 45 publications

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“…Among the most abundant transcripts in our study were those encoded in mitochondrial DNA. This is in accordance with results from SAGE analysis of the adult mouse heart transcriptome, which indicate that the cardiac tissue contains the highest percentage of mitochondrial-genome derived transcripts [37,38]. The estimate of the number of unique transcripts in the adult mouse heart derived from the extrapolation of the results of SAGE experiments exceeds 23,000 [37], and a similar order of magnitude has been suggested for human heart [39].…”

Section: Discussionsupporting

confidence: 86%

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Babik

Stuglik

Qi³

et al. 2010

BMC Genomics

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BackgroundUnderstanding the genetic basis of adaptive changes has been a major goal of evolutionary biology. In complex organisms without sequenced genomes, de novo transcriptome assembly using a longer read sequencing technology followed by expression profiling using short reads is likely to provide comprehensive identification of adaptive variation at the expression level and sequence polymorphisms in coding regions. We performed sequencing and de novo assembly of the bank vole heart transcriptome in lines selected for high metabolism and unselected controls.ResultsA single 454 Titanium run produced over million reads, which were assembled into 63,581 contigs. Searches against the SwissProt protein database and the ENSEMBL collection of mouse transcripts detected similarity to 11,181 and 14,051 genes, respectively. As judged by the representation of genes from the heart-related Gene Ontology categories and UniGenes detected in the mouse heart, our detection of the genes expressed in the heart was nearly complete (> 95% and almost 90% respectively). On average, 38.7% of the transcript length was covered by our sequences, with notably higher (45.0%) coverage of coding regions than of untranslated regions (24.5% of 5' and 32.7% of 3'UTRs). Lower sequence conservation between mouse and bank vole in untranslated regions was found to be partially responsible for poorer UTR representation. Our data might suggest a widespread transcription from noncoding genomic regions, a finding not reported in previous studies regarding transcriptomes in non-model organisms. We also identified over 19 thousand putative single nucleotide polymorphisms (SNPs). A much higher fraction of the SNPs than expected by chance exhibited variant frequency differences between selection regimes.ConclusionLonger reads and higher sequence yield per run provided by the 454 Titanium technology in comparison to earlier generations of pyrosequencing proved beneficial for the quality of assembly. An almost full representation of genes known to be expressed in the mouse heart was identified. Usage of the extensive genomic resources available for the house mouse, a moderately (20-40 mln years) divergent relative of the voles, enabled a comprehensive assessment of the transcript completeness. Transcript sequences generated in the present study allowed the identification of candidate SNPs associated with divergence of selection lines and constitute a valuable permanent resource forming a foundation for RNAseq experiments aiming at detection of adaptive changes both at the level of gene expression and sequence variants, that would facilitate studies of the genetic basis of evolutionary divergence.

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Section: Discussionsupporting

confidence: 86%

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Babik

Stuglik

Qi³

et al. 2010

BMC Genomics

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“…Of the candidate imprinted genes identified in the latter, high-confidence gene candidates (predicted via Equbits Foresight and SMLR means [6]) were selected. Following exclusion of the redundant entries, appropriate short (10 bp) SAGE tags matching NlaIII anchoring enzyme were annotated to gene targets using CGAP (Cancer Genome Anatomy Project, NCI, NIH) SAGE Anatomic Viewer (SAV) applet or manually, as described earlier [18]. For a number of the candidate imprinted genes, a complete sequence was unavailable via GenBank or alternative databases (e.g., GenBank ID: NM_016158, NM_024547, NM_181648, etc.…”

Section: Resultsmentioning

confidence: 99%

“…In the current study, expression of established and candidate imprinted genes was evaluated in a wide array of cell and tissue samples using a comprehensive set of currently available SAGE data for Homo sapiens . Five hundred eighty-one SAGE catalogues based on the libraries generated with most commonly used NlaIII anchoring enzyme were screened using a conservative set of criteria, and in 492 of these (accounting for nearly 36 million SAGE tags) gene expression profiles of the imprinted genes were analyzed, using a proved algorithm [18]. It was therefore possible to estimate a prevalence of imprinted genes within the total human transcriptome.…”

Section: Introductionmentioning

confidence: 99%

A Prevalence of Imprinted Genes within the Total Transcriptomes of Human Tissues and Cells

Anisimov

2012

Molecular Biology International

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Genomic imprinting is an epigenetic phenomenon that causes a differential expression of paternally and maternally inherited alleles of a subset of genes (the so-called imprinted genes). Imprinted genes are distributed throughout the genome and it is predicted that about 1% of the human genes may be imprinted. It is recognized that the allelic expression of imprinted genes varies between tissues and developmental stages. The current study represents the first attempt to estimate a prevalence of imprinted genes within the total human transcriptome. In silico analysis of the normalized expression profiles of a comprehensive panel of 173 established and candidate human imprinted genes was performed, in 492 publicly available SAGE libraries. The latter represent human cell and tissue samples in a variety of physiological and pathological conditions. Variations in the prevalence of imprinted genes within the total transcriptomes (ranging from 0.08% to 4.36%) and expression profiles of the individual imprinted genes are assessed. This paper thus provides a useful reference on the size of the imprinted transcriptome and expression of the individual imprinted genes.

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“…SAGE libraries were annotated using SAGEmap (http://www.ncbi.nlm.nih.gov/projects/SAGE/). Mitochondrial tags were identified using previously described annotation[16]. Genespring was used to perform hierarchical clustering, and to graphically represent the SAGE data.…”

Section: Methodsmentioning

confidence: 99%

Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors

et al. 2010

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BackgroundChondrosarcomas are malignant cartilage tumors that do not respond to traditional chemotherapy or radiation. The 5-year survival rate of histologic grade III chondrosarcoma is less than 30%. An animal model of chondrosarcoma has been established - namely, the Swarm Rat Chondrosarcoma (SRC) - and shown to resemble the human disease. Previous studies with this model revealed that tumor microenvironment could significantly influence chondrosarcoma malignancy.MethodsTo examine the effect of the microenvironment, SRC tumors were initiated at different transplantation sites. Pyrosequencing assays were utilized to assess the DNA methylation of the tumors, and SAGE libraries were constructed and sequenced to determine the gene expression profiles of the tumors. Based on the gene expression analysis, subsequent functional assays were designed to determine the relevancy of the specific genes in the development and progression of the SRC.ResultsThe site of transplantation had a significant impact on the epigenetic and gene expression profiles of SRC tumors. Our analyses revealed that SRC tumors were hypomethylated compared to control tissue, and that tumors at each transplantation site had a unique expression profile. Subsequent functional analysis of differentially expressed genes, albeit preliminary, provided some insight into the role that thymosin-β4, c-fos, and CTGF may play in chondrosarcoma development and progression.ConclusionThis report describes the first global molecular characterization of the SRC model, and it demonstrates that the tumor microenvironment can induce epigenetic alterations and changes in gene expression in the SRC tumors. We documented changes in gene expression that accompany changes in tumor phenotype, and these gene expression changes provide insight into the pathways that may play a role in the development and progression of chondrosarcoma. Furthermore, specific functional analysis indicates that thymosin-β4 may have a role in chondrosarcoma metastasis.

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A large-scale screening of the normalized mammalian mitochondrial gene expression profiles

Cited by 10 publications

References 45 publications

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

A Prevalence of Imprinted Genes within the Total Transcriptomes of Human Tissues and Cells

Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors

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