Detect accessible chromatin using ATAC-sequencing, from principle to applications

Y Sun, N Miao, T Sun - Hereditas, 2019 - Springer
Background Chromatin accessibility is crucial for gene expression regulation in specific cells
and in multiple biological processes. Assay for Transposase Accessible Chromatin with high …

Gene expression in organoids: an expanding horizon

A Smirnov, G Melino, E Candi - Biology Direct, 2023 - Springer
Recent development of human three-dimensional organoid cultures has opened new doors
and opportunities ranging from modelling human development in vitro to personalised …

Integrative approaches based on genomic techniques in the functional studies on enhancers

Q Wang, J Zhang, Z Liu, Y Duan… - Briefings in …, 2024 - academic.oup.com
With the development of sequencing technology and the dramatic drop in sequencing cost,
the functions of noncoding genes are being characterized in a wide variety of fields (eg …

Non-coding variants in cancer: mechanistic insights and clinical potential for personalized medicine

M Lange, R Begolli, A Giakountis - Non-coding RNA, 2021 - mdpi.com
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide
Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) …

Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: implications for environmental epigenetics studies

LK Svoboda, K Neier, K Wang, RG Cavalcante… - Epigenetics, 2021 - Taylor & Francis
Early developmental environment can influence long-term health through reprogramming of
the epigenome. Human environmental epigenetics studies rely on surrogate tissues, such …

CFA: An explainable deep learning model for annotating the transcriptional roles of cis-regulatory modules based on epigenetic codes

TH Yang, YH Yu, SH Wu, FY Zhang - Computers in Biology and Medicine, 2023 - Elsevier
Metazoa gene expression is controlled by modular DNA segments called cis-regulatory
modules (CRMs). CRMs can convey promoter/enhancer/insulator roles, generating …

[HTML][HTML] regCNN: identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns in epigenetic marks and transcription factor binding …

TH Yang, YC Yang, KC Tu - Computational and Structural Biotechnology …, 2022 - Elsevier
Transcription regulation in metazoa is controlled by the binding events of transcription
factors (TFs) or regulatory proteins on specific modular DNA regulatory sequences called cis …

A novel oncogenic enhancer of estrogen receptor-positive breast cancer

C Bao, J Duan, Y Xie, Y Liu, P Li, J Li, H Zhao… - … Therapy-Nucleic Acids, 2022 - cell.com
Estrogen receptor-positive (ER+) breast cancer accounts for the majority of breast cancers
diagnosed, and nearly 20% of patients do not respond to endocrine therapy. The …

Microsatellites used in forensics are in regions enriched for trait-associated variants

V Link, YJA Zavaleta, RJ Reyes, L Ding, J Wang… - Iscience, 2023 - cell.com
The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are the
basis of the vast majority of forensic genetics in the United States. One argument for …

The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors

J Ren, R Finney, K Ni, M Cam, K Muegge - Epigenetics, 2019 - Taylor & Francis
Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation
during embryogenesis, but the precise factors that control access to chromatin remain …