scholarly journals Comparison of Whole-Genome DNA Methylation Patterns in Whole Blood, Saliva, and Lymphoblastoid Cell Lines

2012 ◽  
Vol 43 (2) ◽  
pp. 168-176 ◽  
Author(s):  
Tara M. Thompson ◽  
Duaa Sharfi ◽  
Maria Lee ◽  
Carolyn M. Yrigollen ◽  
Oksana Yu Naumova ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Whole Blood ◽  
Lymphoblastoid Cell Lines ◽  
Whole Genome ◽  
Methylation Patterns

scholarly journals Lymphoblastoid cell lines reveal associations of adult DNA methylation with childhood and current adversity that are distinct from whole blood associations

2015 ◽  
Vol 44 (4) ◽  
pp. 1331-1340 ◽  
Author(s):  
Matthew Suderman ◽  
Jane J Pappas ◽  
Nada Borghol ◽  
Jessica L Buxton ◽  
Wendy L McArdle ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Whole Blood ◽  
Lymphoblastoid Cell Lines

scholarly journals Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

2011 ◽  
Vol 22 (3) ◽  
pp. 456-466 ◽  
Author(s):  
J. E. Powell ◽  
A. K. Henders ◽  
A. F. McRae ◽  
M. J. Wright ◽  
N. G. Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Control ◽  
Cell Lines ◽  
Whole Blood ◽  
Lymphoblastoid Cell Lines ◽  
Control Of Gene Expression

scholarly journals Insertion of Foreign DNA into an Established Mammalian Genome Can Alter the Methylation of Cellular DNA Sequences

1999 ◽  
Vol 73 (2) ◽  
pp. 1010-1022 ◽  
Author(s):  
Ralph Remus ◽  
Christina Kämmer ◽  
Hilde Heller ◽  
Birgit Schmitz ◽  
Gudrun Schell ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Mammalian Genome ◽  
Dna Integration ◽  
Bhk21 Cell ◽  
Cellular Genes ◽  
Cell Clones ◽  
Dna Insertion ◽  
Foreign Dna ◽  
Methylation Patterns

ABSTRACT The insertion of adenovirus type 12 (Ad12) DNA into the hamster genome and the transformation of these cells by Ad12 can lead to marked alterations in the levels of DNA methylation in several cellular genes and DNA segments. Since such alterations in DNA methylation patterns are likely to affect the transcription patterns of cellular genes, it is conceivable that these changes have played a role in the generation or the maintenance of the Ad12-transformed phenotype. We have now isolated clonal BHK21 hamster cell lines that carry in their genomes bacteriophage λ and plasmid pSV2neo DNAs in an integrated state. Most of these cell lines contain one or multiple copies of integrated λ DNA, which often colocalize with the pSV2neo DNA, usually in a single chromosomal site as determined by the fluorescent in situ hybridization technique. In different cell lines, the loci of foreign DNA insertion are different. The inserted bacteriophage λ DNA frequently becomes de novo methylated. In some of the thus-generated hamster cell lines, the levels of DNA methylation in the retrotransposon genomes of the endogenous intracisternal A particles (IAP) are increased in comparison to those in the non-λ-DNA-transgenic BHK21 cell lines. These changes in the methylation patterns of the IAP subclone I (IAPI) segment have been documented by restriction analyses with methylation-sensitive restriction endonucleases followed by Southern transfer hybridization and phosphorimager quantitation. The results of genomic sequencing experiments using the bisulfite protocol yielded additional evidence for alterations in the patterns of DNA methylation in selected segments of the IAPI sequences. In these experiments, the nucleotide sequences in >330 PCR-generated cloned DNA molecules were determined. Upon prolonged cultivation of cell lines with altered cellular methylation patterns, these differences became less apparent, perhaps due to counterselection of the transgenic cells. The possibility existed that the hamster BHK21 cell genomes represent mosaics with respect to DNA methylation in the IAPI segment. Hence, some of the cells with the patterns observed after λ DNA integration might have existed prior to λ DNA integration and been selected by chance. A total of 66 individual BHK21 cell clones from the BHK21 cell stock have been recloned up to three times, and the DNAs of these cell populations have been analyzed for differences in IAPI methylation patterns. None have been found. These patterns are identical among the individual BHK21 cell clones and identical to the patterns of the originally used BHK21 cell line. Similar results have been obtained with nine clones isolated from BHK21 cells mock transfected by the Ca2+-phosphate precipitation procedure with DNA omitted from the transfection mixture. In four clonal sublines of nontransgenic control BHK21 cells, genomic sequencing of 335 PCR-generated clones by the bisulfite protocol revealed 5′-CG-3′ methylation levels in the IAPI segment that were comparable to those in the uncloned BHK21 cell line. We conclude that the observed changes in the DNA methylation patterns in BHK21 cells with integrated λ DNA are unlikely to preexist or to be caused by the transfection procedure. Our data support the interpretation that the insertion of foreign DNA into a preexisting mammalian genome can alter the cellular patterns of DNA methylation, perhaps via changes in chromatin structure. The cellular sites affected by and the extent of these changes could depend on the site and size of foreign DNA insertion.

scholarly journals Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird

2020 ◽  
Vol 60 (6) ◽  
pp. 1517-1530 ◽  
Author(s):  
Kees van Oers ◽  
Bernice Sepers ◽  
William Sies ◽  
Fleur Gawehns ◽  
Koen J F Verhoeven ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Exploratory Behavior ◽  
Parus Major ◽  
Phenotypic Selection ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Behavioral Differences ◽  
Heritable Variation ◽  
Genome Wide ◽  
Methylation Patterns

Synopsis The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.

Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

2014 ◽  
Vol 81 (2) ◽  
pp. 268-281 ◽  
Author(s):  
Hongxing Yang ◽  
Fang Chang ◽  
Chenjiang You ◽  
Jie Cui ◽  
Genfeng Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Structure ◽  
Flower Development ◽  
Whole Genome ◽  
Gene Structure And Expression ◽  
Methylation Patterns

scholarly journals Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Shuxia Li ◽  
Jesper B. Lund ◽  
Kaare Christensen ◽  
Jan Baumbach ◽  
Jonas Mengel-From ◽  
...  
Keyword(s):  
Dna Methylation ◽  
X Chromosome ◽  
Whole Blood ◽  
Exploratory Analysis ◽  
Blood Samples ◽  
Whole Blood Samples ◽  
Methylation Patterns ◽  
Age And Sex

scholarly journals Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines

2017 ◽  
Vol 11 (1) ◽  
Author(s):  
Itsuki Taniguchi ◽  
Chihiro Iwaya ◽  
Keizo Ohnaka ◽  
Hiroki Shibata ◽  
Ken Yamamoto
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Lymphoblastoid Cell Lines ◽  
Methylation Analysis ◽  
Promoter Regions ◽  
Genome Wide ◽  
Dna Methylation Analysis

scholarly journals Comprehensive DNA methylation analysis of human peripheral blood leukocytes and lymphoblastoid cell lines

Epigenetics ◽  
2011 ◽  
Vol 6 (4) ◽  
pp. 508-515 ◽  
Author(s):  
Hiroko Sugawara ◽  
Kazuya Iwamoto ◽  
Miki Bundo ◽  
Junko Ueda ◽  
Jun Ishigooka ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Peripheral Blood ◽  
Human Peripheral Blood ◽  
Lymphoblastoid Cell Lines ◽  
Peripheral Blood Leukocytes ◽  
Methylation Analysis ◽  
Blood Leukocytes ◽  
Dna Methylation Analysis
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