[HTML][HTML] CLIP and complementary methods

M Hafner, M Katsantoni, T Köster, J Marks… - Nature Reviews …, 2021 - nature.com
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …

RNA-binding proteins in cancer: old players and new actors

B Pereira, M Billaud, R Almeida - Trends in cancer, 2017 - cell.com
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The
combination of versatility of their RNA-binding domains with structural flexibility enables …

starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

JH Li, S Liu, H Zhou, LH Qu, JH Yang - Nucleic acids research, 2014 - academic.oup.com
Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs)(eg lncRNAs,
pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been …

Advances in CLIP technologies for studies of protein-RNA interactions

FCY Lee, J Ule - Molecular cell, 2018 - cell.com
RNA binding proteins (RBPs) regulate all aspects in the life cycle of RNA molecules. To
elucidate the elements that guide RNA specificity, regulatory mechanisms, and functions of …

Systematic transcriptome wide analysis of lncRNA-miRNA interactions

S Jalali, D Bhartiya, MK Lalwani, S Sivasubbu… - PloS one, 2013 - journals.plos.org
Background Long noncoding RNAs (lncRNAs) are a recently discovered class of non-
protein coding RNAs, which have now increasingly been shown to be involved in a wide …

Computational solutions for omics data

B Berger, J Peng, M Singh - Nature reviews genetics, 2013 - nature.com
High-throughput experimental technologies are generating increasingly massive and
complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to …

Unambiguous identification of miRNA: target site interactions by different types of ligation reactions

S Grosswendt, A Filipchyk, M Manzano, F Klironomos… - Molecular cell, 2014 - cell.com
To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially
complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays …

Competition between target sites of regulators shapes post-transcriptional gene regulation

M Jens, N Rajewsky - Nature Reviews Genetics, 2015 - nature.com
Post-transcriptional gene regulation (PTGR) of mRNA turnover, localization and translation
is mediated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). These regulators …

Computational models for lncRNA function prediction and functional similarity calculation

X Chen, YZ Sun, NN Guan, J Qu… - Briefings in …, 2019 - academic.oup.com
From transcriptional noise to dark matter of biology, the rapidly changing view of long non-
coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by …

System-wide identification of RNA-binding proteins by interactome capture

A Castello, R Horos, C Strein, B Fischer… - Nature protocols, 2013 - nature.com
Owing to their preeminent biological functions, the repertoire of expressed RNA-binding
proteins (RBPs) and their activity states are highly informative about cellular systems. We …