DNA methylation methods: Global DNA methylation and methylomic analyses

S Li, TO Tollefsbol - Methods, 2021 - Elsevier
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has
significant involvement for numerous biological processes in health and disease. The …

Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward

CL Richards, C Alonso, C Becker, O Bossdorf… - Ecology …, 2017 - Wiley Online Library
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with
implications across many fields of biology. In plant ecology, recent studies have attempted to …

Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity

B Prinzing, CC Zebley, CT Petersen, Y Fan… - Science translational …, 2021 - science.org
Chimeric antigen receptor (CAR) T cell therapy is revolutionizing cancer immunotherapy for
patients with B cell malignancies and is now being developed for solid tumors and chronic …

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

X Liu, C Wang, W Liu, J Li, C Li, X Kou, J Chen, Y Zhao… - Nature, 2016 - nature.com
Histone modifications have critical roles in regulating the expression of developmental
genes during embryo development in mammals,. However, genome-wide analyses of …

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

C Wang, X Liu, Y Gao, L Yang, C Li, W Liu, C Chen… - Nature cell …, 2018 - nature.com
Abstract H3K9me3-dependent heterochromatin is a major barrier of cell fate changes that
must be reprogrammed after fertilization. However, the molecular details of these events are …

Differential methylation analysis for BS-seq data under general experimental design

Y Park, H Wu - Bioinformatics, 2016 - academic.oup.com
Motivation: DNA methylation is an epigenetic modification with important roles in many
biological processes and diseases. Bisulfite sequencing (BS-seq) has emerged recently as …

[HTML][HTML] Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos

R Xu, S Li, Q Wu, C Li, M Jiang, L Guo, M Chen, L Yang… - Cell Stem Cell, 2022 - cell.com
Summary H3K9me3, as a hallmark of heterochromatin, is important for cell-fate specification.
However, it remains unknown how H3K9me3 is reprogrammed during human early embryo …

Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal

D Sun, M Luo, M Jeong, B Rodriguez, Z Xia, R Hannah… - Cell stem cell, 2014 - cell.com
To investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem
cells during aging, we have conducted a comprehensive integrated genomic analysis of …

Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

F Jühling, H Kretzmer, SH Bernhart, C Otto… - Genome …, 2016 - genome.cshlp.org
The detection of differentially methylated regions (DMRs) is a necessary prerequisite for
characterizing different epigenetic states. We present a novel program, metilene, to identify …

LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

F Kottakis, BN Nicolay, A Roumane, R Karnik, H Gu… - Nature, 2016 - nature.com
Intermediary metabolism generates substrates for chromatin modification, enabling the
potential coupling of metabolic and epigenetic states. Here we identify a network linking …