Chromatin accessibility profiling by ATAC-seq

FC Grandi, H Modi, L Kampman, MR Corces - Nature protocols, 2022 - nature.com
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …

Trained immunity—basic concepts and contributions to immunopathology

J Ochando, WJM Mulder, JC Madsen… - Nature Reviews …, 2023 - nature.com
Trained immunity is a functional state of the innate immune response and is characterized
by long-term epigenetic reprogramming of innate immune cells. This concept originated in …

Autocrine vitamin D signaling switches off pro-inflammatory programs of TH1 cells

D Chauss, T Freiwald, R McGregor, B Yan, L Wang… - Nature …, 2022 - nature.com
The molecular mechanisms governing orderly shutdown and retraction of CD4+ type 1
helper T (TH1) cell responses remain poorly understood. Here we show that complement …

The evolving metabolic landscape of chromatin biology and epigenetics

Z Dai, V Ramesh, JW Locasale - Nature Reviews Genetics, 2020 - nature.com
Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These
inputs—which include both nutrient availability as a result of diet and growth factor signalling …

EZH2 noncanonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis

J Wang, X Yu, W Gong, X Liu, KS Park, A Ma… - Nature cell …, 2022 - nature.com
Canonically, EZH2 serves as the catalytic subunit of PRC2, which mediates H3K27me3
deposition and transcriptional repression. Here, we report that in acute leukaemias, EZH2 …

CUT&Tag for efficient epigenomic profiling of small samples and single cells

HS Kaya-Okur, SJ Wu, CA Codomo, ES Pledger… - Nature …, 2019 - nature.com
Many chromatin features play critical roles in regulating gene expression. A complete
understanding of gene regulation will require the mapping of specific chromatin features in …

Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future

D Akhoundova, MA Rubin - Cancer Cell, 2022 - cell.com
Next-generation DNA sequencing technology has dramatically advanced clinical oncology
through the identification of therapeutic targets and molecular biomarkers, leading to the …

Efficient low-cost chromatin profiling with CUT&Tag

HS Kaya-Okur, DH Janssens, JG Henikoff, K Ahmad… - Nature protocols, 2020 - nature.com
Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …

Stat5 opposes the transcription factor Tox and rewires exhausted CD8+ T cells toward durable effector-like states during chronic antigen exposure

JC Beltra, MS Abdel-Hakeem, S Manne, Z Zhang… - Immunity, 2023 - cell.com
Summary Rewiring exhausted CD8+ T (Tex) cells toward functional states remains a
therapeutic challenge. Tex cells are epigenetically programmed by the transcription factor …

Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells

I Zanin, E Ruggiero, G Nicoletto, S Lago… - Nucleic Acids …, 2023 - academic.oup.com
Abstract i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich
sequences in acidic conditions in vitro. Their formation in cells is still under debate. We …