[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 …

A brave new world of RNA-binding proteins

MW Hentze, A Castello, T Schwarzl… - Nature reviews Molecular …, 2018 - nature.com
RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one
or multiple globular RNA-binding domains (RBDs) and change the fate or function of the …

[HTML][HTML] TDP-43 condensation properties specify its RNA-binding and regulatory repertoire

M Hallegger, AM Chakrabarti, FCY Lee, BL Lee… - Cell, 2021 - cell.com
Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation
properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the …

[HTML][HTML] The human RNA-binding proteome and its dynamics during translational arrest

J Trendel, T Schwarzl, R Horos, A Prakash, A Bateman… - Cell, 2019 - cell.com
Proteins and RNA functionally and physically intersect in multiple biological processes,
however, currently no universal method is available to purify protein-RNA complexes. Here …

[HTML][HTML] RNA 5-methylcytosine facilitates the maternal-to-zygotic transition by preventing maternal mRNA decay

Y Yang, L Wang, X Han, WL Yang, M Zhang, HL Ma… - Molecular cell, 2019 - cell.com
The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during
which the maternal environment is converted to an environment of embryonic-driven …

[HTML][HTML] 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 …

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq

SM Blue, BA Yee, GA Pratt, JR Mueller, SS Park… - Nature protocols, 2022 - nature.com
Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets
plays a critical role in enabling our understanding of how these RBPs control RNA …

[HTML][HTML] A short tandem repeat-enriched RNA assembles a nuclear compartment to control alternative splicing and promote cell survival

K Yap, S Mukhina, G Zhang, JSC Tan, HS Ong… - Molecular cell, 2018 - cell.com
Functions of many long noncoding RNAs (lncRNAs) depend on their ability to interact with
multiple copies of specific RNA-binding proteins (RBPs). Here, we devised a workflow …

[HTML][HTML] Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing

J Attig, F Agostini, C Gooding, AM Chakrabarti, A Singh… - Cell, 2018 - cell.com
Long mammalian introns make it challenging for the RNA processing machinery to identify
exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection …

[HTML][HTML] PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

S Krakau, H Richard, A Marsico - Genome biology, 2017 - Springer
The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at
high resolution, based on diagnostic events at crosslink sites. However, previous methods …