Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

Nair, Shalima S.; Luu, Phuc-Loi; Qu, Wenjia; Maddugoda, Madhavi P.; Huschtscha, Lily I.; Reddel, Roger R.; Chenevix-Trench, Georgia; Toso, Martina; Kench, James G.; Horvath, Lisa G.; Hayes, Vanessa M.; Stricker, Phillip D.; Hughes, Timothy P.; White, Deborah L.; Rasko, John E.J.; Wong, Justin; Clark, Susan J.

doi:10.1186/s13072-018-0194-0

Cited by 41 publications

(38 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Whole genome bisulphite sequencing experiments and analysis. Library preparation and indexing were carried out as described in the CEGX TruMethyl WG user guide v2 with minor improvements as described in Nair et al 61 . Sequencing reads from WGBS data were aligned to the human genome using version 1.2 of an internally developed pipeline Meth10X (https://github.com/luuloi/Meth10X 61 ).…”

Section: Methodsmentioning

confidence: 99%

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

et al. 2020

Self Cite

View full text Add to dashboard Cite

Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine-resistant breast cancer cells and that the differential interactions are enriched for resistance-associated genetic variants at CTCFbound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites, and are associated with altered expression of ERregulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. We observe that loss of 3D chromatin interactions often occurs coincidently with hypermethylation and loss of ER binding. Alterations in active A and inactive B chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer.

show abstract

Section: Methodsmentioning

confidence: 99%

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…at 25% amplitude with a microtip using the QSonica (Q55) and stored at -80 o C. (Nair et al, 2018). This is publicly available and can be downloaded from https://github.com/luuloi/Meth10X.…”

Section: Western Blotting For Dnmt Proteinsmentioning

confidence: 99%

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

Smith

Luu

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

DNA replication timing and three-dimensional (3D) genome organisation are associated with distinct epigenome patterns across large domains during differentiation and cancer progression. However, it is unclear if alternations in the epigenome, in particular cancer-associated DNA hypomethylation, can directly promote higher order genome architectural alterations. Here, we use Hi-C and single cell Repli-Seq, in the colorectal cancer DNMT1 and DNMT3B DNA methyltransferases double knockout model, to determine the impact of DNA hypomethylation on replication timing and 3D genome organisation. First, we find that the hypomethylated cells show a striking loss of replication timing precision with gain of intra-population replication timing heterogeneity and loss of 3D genome compartmentalisation. Second, hypomethylated regions that undergo a large change in replication timing also show loss of allelic replication timing, including at cancer-related genes. Finally, we observe the striking formation of ectopic H3K4me3-H3K9me3 domains across hypomethylated regions where late replication is maintained, which we propose serve to prevent aberrant transcription and loss of genome organisation after DNA demethylation. Together, our results highlight a previously underappreciated role for DNA methylation in the maintenance of 3D genome architecture.

show abstract

“…A whole genome bisul te sequencing of Methylomonas sp. DH-1 was carried out according to the manufacturer's instruction [39]. Brie y, genomic DNA of Methylomonas sp.…”

Section: Whole Genome Bisul Te Sequencing and Plasmid Constructionmentioning

confidence: 99%

Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1

Ren

Lee

Thi

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism.Results: We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5 × 103 CFU/μg (124 %). The introduced gene increased the production of carotenoid by 26 %. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70 % as well. The production of carotenoid was decreased by 40 % when the psy gene was translationally repressed by anti-psy sRNA. Conclusions: Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.

show abstract

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

Cited by 41 publications

References 46 publications

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1

Contact Info

Product

Resources

About