A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Hasegawa, K.; Nakabayashi, Kazuhiko; Ishiwata, Keisuke; Kasuga, Yoshifumi; Hata, Kenichiro; Tanaka, Mamoru

doi:10.1186/s13104-023-06401-3

Cited by 2 publications

(3 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To gain DNA methylation information at a higher resolution and assess the methylation status of CpG islands at promoters of escapees that are either reversibly or irreversibly silenced, we also performed targeted capture methylation sequencing (EM-Cap) 65 [Fig. 5c,d].…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

Hauth,

Panten,

Kneuss

et al. 2024

Preprint

View full text Add to dashboard Cite

In placental females, one copy of the two X chromosomes is largely silenced during a narrow developmental time window, in a process mediated by the non-coding RNA Xist1. Here, we demonstrate that Xist can initiate X-chromosome inactivation (XCI) well beyond early embryogenesis. By modifying its endogenous level, we show that Xist has the capacity to actively silence genes that escape XCI both in neuronal progenitor cells (NPCs) andin vivo, in mouse embryos. We also show that Xist plays a direct role in eliminating TAD-like structures associated with clusters of escapee genes on the inactive X chromosome, and that this is dependent on Xist’s XCI initiation partner, SPEN2. We further demonstrate that Xist’s function in suppressing gene expression of escapees and topological domain formation is reversible for up to seven days post-induction, but that sustained Xist up-regulation leads to progressively irreversible silencing and CpG island DNA methylation of facultative escapees. Thus, the distinctive transcriptional and regulatory topologies of the silenced X chromosome is actively, directly - and reversibly - controlled by Xist RNA throughout life.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Genomic gDNA samples used for EM-Seq were used for EM-Cap as previously described 65 with minor adjustments. For the final library amplification the cycle number was increased to 14.…”

Section: Methodsmentioning

confidence: 99%

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

Hauth,

Panten,

Kneuss

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…A limitation of whole genome epigenetic approaches is that the cost to achieve high sequencing coverage 14 is currently too expensive to be routinely applicable in clinical settings. 2,15 High sequencing coverage, however, is needed since certain cfDNA fragments may only be present in low quantities, which could be missed by shallow sequencing. 16 Furthermore, many methylation sites are not variable, 17 limiting their value in biomarker development.…”

Section: Introductionmentioning

confidence: 99%

Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis

Caggiano,

Morselli,

Qian

et al. 2024

Preprint

View full text Add to dashboard Cite

Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.

show abstract

A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Cited by 2 publications

References 11 publications

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis

Contact Info

Product

Resources

About