Deep learning and ensemble deep learning for circRNA-RBP interaction prediction in the last decade: A review

D Lasantha, S Vidanagamachchi… - … Applications of Artificial …, 2023 - Elsevier
Circular ribonucleic acids (circRNAs) are widely expressed in cells and tissues and play vital
roles in cellular physiological processes. Their expressions are associated with …

Satellite RNAs: emerging players in subnuclear architecture and gene regulation

K Ninomiya, T Yamazaki, T Hirose - The EMBO journal, 2023 - embopress.org
Satellite DNA is characterized by long, tandemly repeated sequences mainly found in
centromeres and pericentromeric chromosomal regions. The recent advent of telomere‐to …

A central chaperone-like role for 14-3-3 proteins in human cells

D Segal, S Maier, GJ Mastromarco, WW Qian… - Molecular cell, 2023 - cell.com
3-3 proteins are highly conserved regulatory proteins that interact with hundreds of
structurally diverse clients and act as central hubs of signaling networks. However, how 14-3 …

Multiomics analyses reveal DARS1-AS1/YBX1–controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance

C Zheng, Y Wei, Q Zhang, M Sun, Y Wang, J Hou… - Science …, 2023 - science.org
The glioblastoma (GBM) stem cell–like cells (GSCs) are critical for tumorigenesis/therapeutic
resistance of GBM. Mounting evidence supports tumor-promoting function of long noncoding …

Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

J Klughammer, D Romanovskaia, A Nemc… - Nature …, 2023 - nature.com
Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been
implicated in various regulatory mechanisms across the animal kingdom and particularly in …

Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition

OJ Ziff, J Harley, Y Wang, J Neeves, G Tyzack… - Neuron, 2023 - cell.com
Amyotrophic lateral sclerosis (ALS) is characterized by nucleocytoplasmic mislocalization of
the RNA-binding protein (RBP) TDP-43. However, emerging evidence suggests more …

[HTML][HTML] Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3′ untranslated region mutations

SL Schuster, S Arora, CL Wladyka, P Itagi, L Corey… - Cell reports, 2023 - cell.com
Summary 3′ untranslated region (3′ UTR) somatic mutations represent a largely
unexplored avenue of alternative oncogenic gene dysregulation. To determine the …

Mechanism of U6 snRNA oligouridylation by human TUT1

S Yamashita, K Tomita - Nature Communications, 2023 - nature.com
U6 snRNA is a catalytic RNA responsible for pre-mRNA splicing reactions and undergoes
various post-transcriptional modifications during its maturation process. The 3' …

MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer

J Bhin, J Yemelyanenko, X Chao… - Journal of Experimental …, 2023 - rupress.org
Targeting the PI3K–AKT–mTOR pathway is a promising therapeutic strategy for breast
cancer treatment. However, low response rates and development of resistance to PI3K–AKT …

Deciphering RNA splicing logic with interpretable machine learning

SE Liao, M Sudarshan… - Proceedings of the …, 2023 - National Acad Sciences
Machine learning methods, particularly neural networks trained on large datasets, are
transforming how scientists approach scientific discovery and experimental design …