From compartments to loops: understanding the unique chromatin organization in neuronal cells

D Zagirova, A Kononkova, N Vaulin… - Epigenetics & Chromatin, 2024 - Springer
The three-dimensional organization of the genome plays a central role in the regulation of
cellular functions, particularly in the human brain. This review explores the intricacies of …

A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome

LT Phan, C Oh, T He, B Manavalan - Proteomics, 2023 - Wiley Online Library
Enhancers are non‐coding DNA elements that play a crucial role in enhancing the
transcription rate of a specific gene in the genome. Experiments for identifying enhancers …

Integrative machine learning framework for the identification of cell-specific enhancers from the human genome

S Basith, MM Hasan, G Lee, L Wei… - Briefings in …, 2021 - academic.oup.com
Enhancers are deoxyribonucleic acid (DNA) fragments which when bound by transcription
factors enhance the transcription of related genes. Due to its sporadic distribution and …

In vivo dissection of chamber-selective enhancers reveals estrogen-related receptor as a regulator of ventricular cardiomyocyte identity

Y Cao, X Zhang, BN Akerberg, H Yuan, T Sakamoto… - Circulation, 2023 - ahajournals.org
Background: Cardiac chamber-selective transcriptional programs underpin the structural
and functional differences between atrial and ventricular cardiomyocytes (aCMs and vCMs) …

Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture

HJ Cha, Ö Uyan, Y Kai, T Liu, Q Zhu, Z Tothova… - Nature …, 2021 - nature.com
Precise control of gene expression during differentiation relies on the interplay of chromatin
and nuclear structure. Despite an established contribution of nuclear membrane proteins to …

Map** the evolving landscape of super-enhancers during cell differentiation

Y Kai, BE Li, M Zhu, GY Li, F Chen, Y Han, HJ Cha… - Genome Biology, 2021 - Springer
Background Super-enhancers are clusters of enhancer elements that play critical roles in
the maintenance of cell identity. Current investigations on super-enhancers are centered on …

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekee** gene regulation

I Abnizova, C Stapel, R Boekhorst, JTH Lee… - BMC biology, 2024 - Springer
Background Regulation of transcription is central to the emergence of new cell types during
development, and it often involves activation of genes via proximal and distal regulatory …

ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease

P Azad, AB Caldwell, S Ramachandran… - … & molecular medicine, 2022 - nature.com
At high altitude Andean region, hypoxia-induced excessive erythrocytosis (EE) is the
defining feature of Monge's disease or chronic mountain sickness (CMS). At the same …

Enhancers regulate 3′ end processing activity to control expression of alternative 3′ UTR isoforms

B Kwon, MM Fansler, ND Patel, J Lee, W Ma… - Nature …, 2022 - nature.com
Multi-UTR genes are widely transcribed and express their alternative 3′ UTR isoforms in a
cell type-specific manner. As transcriptional enhancers regulate mRNA expression, we …

Three‐dimensional chromatin re‐organization during muscle stem cell aging

BA Yang, JA Larouche, KM Sabin, PM Fraczek… - Aging …, 2023 - Wiley Online Library
Age‐related skeletal muscle atrophy or sarcopenia is a significant societal problem that is
becoming amplified as the world's population continues to increase. The regeneration of …