Nucleosome patterns in circulating tumor DNA reveal transcriptional regulation of advanced prostate cancer phenotypes

N De Sarkar, RD Patton, AL Doebley, B Hanratty… - Cancer discovery, 2023 - AACR
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains
clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor …

Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts

BJ Patty, SJ Hainer - Nature protocols, 2021 - nature.com
Determining chromatin-associated protein localization across the genome has provided
insight into the functions of DNA-binding proteins and their connections to disease …

Dam assisted fluorescent tagging of chromatin accessibility (dafca) for optical genome mapping in nanochannel arrays

G Nifker, A Grunwald, S Margalit, Z Tulpova… - ACS …, 2023 - ACS Publications
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in
order to perform genomic tasks such as gene activation and transcription. Hence, chromatin …

Genomic enhancers in cardiac development and disease

CG Anene-Nzelu, MCJ Lee, WLW Tan… - Nature Reviews …, 2022 - nature.com
Abstract The Human Genome Project marked a major milestone in the scientific community
as it unravelled the~ 3 billion bases that are central to crucial aspects of human life. Despite …

ATF3 drives senescence by reconstructing accessible chromatin profiles

C Zhang, X Zhang, L Huang, Y Guan, X Huang… - Aging …, 2021 - Wiley Online Library
Chromatin organization and transcriptional profiles undergo tremendous reordering during
senescence. However, uncovering the regulatory mechanisms between chromatin …

[HTML][HTML] Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin

K Li, Y Li, F Nakamura - Scientific Reports, 2023 - nature.com
The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of
growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by …

[HTML][HTML] Centromeric RNA and its function at and beyond centromeric chromatin

S Corless, S Höcker, S Erhardt - Journal of molecular biology, 2020 - Elsevier
The most fundamental region of the chromosome for maintaining accurate genome
segregation and stability is the centromeric chromatin [1, 2]. In this review, we will focus on …

[HTML][HTML] Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

S Varotto, T Krugman, R Aiese Cigliano… - Theoretical and Applied …, 2022 - Springer
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop
improvement. However, successful crop improvement using CWR relies on identifying …

Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq

N Petryk, N Reveron-Gomez, C Gonzalez-Aguilera… - Nature …, 2021 - nature.com
Elucidating the mechanisms underlying chromatin maintenance upon genome replication is
critical for the understanding of how gene expression programs and cell identity are …

Functional genomics in Spiralia

FM Martín-Zamora, BE Davies… - Briefings in …, 2023 - academic.oup.com
Our understanding of the mechanisms that modulate gene expression in animals is strongly
biased by studying a handful of model species that mainly belong to three groups: Insecta …