Deciphering the multi-scale, quantitative cis-regulatory code

S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

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 …

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

RJ Schmitz, E Grotewold, M Stam - The plant cell, 2022 - academic.oup.com
The identification and characterization of cis-regulatory DNA sequences and how they
function to coordinate responses to developmental and environmental cues is of paramount …

[HTML][HTML] Chromatin potential identified by shared single-cell profiling of RNA and chromatin

S Ma, B Zhang, LM LaFave, AS Earl, Z Chiang, Y Hu… - Cell, 2020 - cell.com
Cell differentiation and function are regulated across multiple layers of gene regulation,
including modulation of gene expression by changes in chromatin accessibility. However …

Overview of histone modification

Y Zhang, Z Sun, J Jia, T Du, N Zhang, Y Tang… - Histone Mutations and …, 2021 - Springer
Epigenetics is the epi-information beyond the DNA sequence that can be inherited from
parents to offspring. From years of studies, people have found that histone modifications …

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

C Li, MC Virgilio, KL Collins, JD Welch - Nature biotechnology, 2023 - nature.com
Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the
same cell, offer an opportunity to understand the temporal relationship between epigenome …

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells

L Li, S Bowling, SE McGeary, Q Yu, B Lemke, K Alcedo… - Cell, 2023 - cell.com
Cellular lineage histories and their molecular states encode fundamental principles of tissue
development and homeostasis. Current lineage-recording mouse models have insufficient …

H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation

N Kubo, PB Chen, R Hu, Z Ye, H Sasaki, B Ren - Molecular Cell, 2024 - cell.com
Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers.
KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase …

Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Epigenetic modifications of histones in cancer

Z Zhao, A Shilatifard - Genome biology, 2019 - Springer
The epigenetic modifications of histones are versatile marks that are intimately connected to
development and disease pathogenesis including human cancers. In this review, we will …