Big data and deep learning for RNA biology

H Hwang, H Jeon, N Yeo, D Baek - Experimental & Molecular Medicine, 2024 - nature.com
The exponential growth of big data in RNA biology (RB) has led to the development of deep
learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL …

New insights into the interaction between m6A modification and lncRNA in cancer drug resistance

Y Jin, Z Fan - Cell Proliferation, 2024 - Wiley Online Library
Drug resistance is perhaps the greatest obstacle in improving outcomes for cancer patients,
leading to recurrence, progression and metastasis of various cancers. Exploring the …

Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

W Huang, T Xiong, Y Zhao, J Heng, G Han, P Wang… - Nature Genetics, 2024 - nature.com
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of
methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME) …

Discovering consensus regions for interpretable identification of rna n6-methyladenosine modification sites via graph contrastive clustering

G Li, B Zhao, X Su, Y Yang, P Hu… - IEEE Journal of …, 2024 - ieeexplore.ieee.org
As a pivotal post-transcriptional modification of RNA, N6-methyladenosine (m6A) has a
substantial influence on gene expression modulation and cellular fate determination …

[HTML][HTML] Control of poly (A)-tail length and translation in vertebrate oocytes and early embryos

K Xiang, J Ly, DP Bartel - Developmental Cell, 2024 - cell.com
During oocyte maturation and early embryogenesis, changes in mRNA poly (A)-tail lengths
strongly influence translation, but how these tail-length changes are orchestrated has been …

Nuclear aggregates of NONO/SFPQ and A-to-I-edited RNA in Parkinson's disease and dementia with Lewy bodies

NR Belur, BI Bustos, SJ Lubbe, JR Mazzulli - Neuron, 2024 - cell.com
Neurodegenerative diseases are commonly classified as proteinopathies that are defined by
the aggregation of a specific protein. Parkinson's disease (PD) and dementia with Lewy …

The splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin

A Damianov, CH Lin, J Huang, L Zhou… - Molecular Cell, 2024 - cell.com
Understanding the mechanisms of pre-mRNA splicing is limited by the technical challenges
to examining spliceosomes in vivo. Here, we report the isolation of RNP complexes derived …

The specificity landscape of bacterial ribonuclease P

AR Chamberlain, L Huynh, W Huang, DJ Taylor… - Journal of Biological …, 2024 - ASBMB
Developing quantitative models of substrate specificity for RNA processing enzymes is a key
step toward understanding their biology and guiding applications in biotechnology and …

[HTML][HTML] An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition

K Lee, K Cho, R Morey, H Cook-Andersen - Cell reports, 2024 - cell.com
Without new transcription, gene expression across the oocyte-to-embryo transition (OET)
relies instead on regulation of mRNA poly (A) tails to control translation. However, how tail …

Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing

K Gupta, C Yang, K McCue, O Bastani, PA Sharp… - Genome Biology, 2024 - Springer
Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions.
Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity …