Untitled

Franz, Henriette; Ullmann, Claudia; Becker, Albert; Ryan, Margaret M.; Bahn, Sabine; Arendt, Thomas; Simon, Matthias; Pääbo, Svante; Khaitovich, Philipp

doi:10.1186/gb-2005-6-13-r112

Cited by 32 publications

(10 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We were motivated to exploit publicly available gene expression data because the tissue samples were obtained from autopsy patients, which inevitably led to delay in tissue collection and 4–8 h autolysis time. Although the gene expression patterns before death and postmortem are largely comparable, death may still induce significant changes in a relatively large number of genes [ 24 , 25 ]. Consequently, we compared our DNA methylome data with that of gene expression from public databases, and observed a clear inverse correlation between promoter methylation within CpG islands and gene expression [ 23 ].…”

Section: Discussionmentioning

confidence: 99%

Imprinted Genes and Imprinting Control Regions Show Predominant Intermediate Methylation in Adult Somatic Tissues

et al. 2016

View full text Add to dashboard Cite

Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200–1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.

show abstract

Section: Discussionmentioning

confidence: 99%

Imprinted Genes and Imprinting Control Regions Show Predominant Intermediate Methylation in Adult Somatic Tissues

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Since spleen samples obtained from the same individuals, displayed far less variation, these findings cannot be attributed to post-mortem or nucleic acid purification artifacts. Indeed, Franz and coworkers [ 36 ] reported that death caused exaggerated homogeneity in expression profiles of coding transcripts in human brain. Human fibroblasts lines from different individuals were maintained for 3-5 passages under identical conditions, yet differences between individuals remained, regardless of treatment.…”

Section: Discussionmentioning

confidence: 99%

Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues

Nellåker

Uhrzander³

et al. 2009

BMC Genomics

View full text Add to dashboard Cite

BackgroundHuman endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcription of genomic regions harboring such elements.ResultsApplying a recently developed technique for obtaining high resolution melting temperature data, we examined the frequency distributions of HERV-W gag element into 13 Tm categories in human tissues. Transcripts containing HERV-W gag sequences were expressed in non-random patterns with extensive variations in the expression between both tissues, including different brain regions, and individuals. Furthermore, the patterns of such transcripts varied more between individuals in brain regions than other tissues.ConclusionThus, regulated expression of non-coding regions of the human genome appears to include the HERV-W family of repetitive elements. Although it remains to be established whether such expression patterns represent leakage from transcription of functional regions or specific transcription, the current approach proves itself useful for studying detailed expression patterns of repetitive regions.

show abstract

“…Furthermore, the two sample sets were collected in distinct ways (i.e. obtained from corrective surgery vs cadavers), which has been recognized to cause difficulty in the interpretation of gene expression studies 50 , 51 .…”

Section: Gene Expression Studiesmentioning

confidence: 99%

Strabismus genetics across a spectrum of eye misalignment disorders

Patel

Wasserman

2014

Clinical Genetics

View full text Add to dashboard Cite

Eye misalignment, called strabismus, is amongst the most common phenotypes observed, occurring in up to 5% of individuals in a studied population. While misalignment is frequently observed in rare complex syndromes, the majority of strabismus cases are non-syndromic. Over the past decade, genes and pathways associated with syndromic forms of strabismus have emerged, but the genes contributing to non-syndromic strabismus remain elusive. Genetic testing for strabismus risk may allow for earlier diagnosis and treatment, as well as decreased frequency of surgery. We review human and model organism literature describing non-syndromic strabismus, including family, twin, linkage, and gene expression studies. Recent advances in the genetics of Duane retraction syndrome are considered, as relatives of those impacted show elevated familial rates of non-syndromic strabismus. As whole genome sequencing efforts are advancing for the discovery of the elusive strabismus genes, this overview is intended to support the interpretation of the new findings.

show abstract

Untitled

Abstract: Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.

Cited by 32 publications

References 24 publications

Imprinted Genes and Imprinting Control Regions Show Predominant Intermediate Methylation in Adult Somatic Tissues

Imprinted Genes and Imprinting Control Regions Show Predominant Intermediate Methylation in Adult Somatic Tissues

Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues

Strabismus genetics across a spectrum of eye misalignment disorders

Contact Info

Product

Resources

About