DNA methylation in mammalian development and disease

ZD Smith, S Hetzel, A Meissner - Nature Reviews Genetics, 2024 - nature.com
The DNA methylation field has matured from a phase of discovery and genomic
characterization to one seeking deeper functional understanding of how this modification …

Regulation, functions and transmission of bivalent chromatin during mammalian development

TA Macrae, J Fothergill-Robinson… - … reviews Molecular cell …, 2023 - nature.com
Cells differentiate and progress through development guided by a dynamic chromatin
landscape that mediates gene expression programmes. During development, mammalian …

Integrated spatial genomics reveals global architecture of single nuclei

Y Takei, J Yun, S Zheng, N Ollikainen, N Pierson… - Nature, 2021 - nature.com
Identifying the relationships between chromosome structures, nuclear bodies, chromatin
states and gene expression is an overarching goal of nuclear-organization studies …

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

L Core, K Adelman - Genes & development, 2019 - genesdev.cshlp.org
Precise spatio–temporal control of gene activity is essential for organismal development,
growth, and survival in a changing environment. Decisive steps in gene regulation involve …

Venn diagrams in bioinformatics

A Jia, L Xu, Y Wang - Briefings in bioinformatics, 2021 - academic.oup.com
Venn diagrams are widely used tools for graphical depiction of the unions, intersections and
distinctions among multiple datasets, and a large number of programs have been developed …

The interplay of epigenetic marks during stem cell differentiation and development

Y Atlasi, HG Stunnenberg - Nature Reviews Genetics, 2017 - nature.com
Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly
reshaped during early development and differentiation. Epigenetic modification of chromatin …

Hallmarks of totipotent and pluripotent stem cell states

P Du, J Wu - Cell Stem Cell, 2024 - cell.com
Though totipotency and pluripotency are transient during early embryogenesis, they
establish the foundation for the development of all mammals. Studying these in vivo has …

Translational control of stem cell function

JA Saba, K Liakath-Ali, R Green, FM Watt - Nature reviews Molecular …, 2021 - nature.com
Stem cells are characterized by their ability to self-renew and differentiate into many different
cell types. Research has focused primarily on how these processes are regulated at a …

Classification of low quality cells from single-cell RNA-seq data

T Ilicic, JK Kim, AA Kolodziejczyk, FO Bagger… - Genome biology, 2016 - Springer
Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical
research. One of the key challenges is to ensure that only single, live cells are included in …

Genome-wide map** of G-quadruplex structures with CUT&Tag

J Lyu, R Shao, PY Kwong Yung… - Nucleic acids …, 2022 - academic.oup.com
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA: RNA
hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect …