Advances in the characterization of RNA‐binding proteins

D Marchese, NS de Groot… - Wiley …, 2016 - Wiley Online Library
From transcription, to transport, storage, and translation, RNA depends on association with
different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and …

A concentration-dependent liquid phase separation can cause toxicity upon increased protein expression

B Bolognesi, NL Gotor, R Dhar, D Cirillo, M Baldrighi… - Cell reports, 2016 - cell.com
Multiple human diseases are associated with a liquid-to-solid phase transition resulting in
the formation of amyloid fibers or protein aggregates. Here, we present an alternative …

RNA structure drives interaction with proteins

N Sanchez de Groot, A Armaos… - Nature …, 2019 - nature.com
The combination of high-throughput sequencing and in vivo crosslinking approaches leads
to the progressive uncovering of the complex interdependence between cellular …

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

E Kelmer Sacramento, JM Kirkpatrick… - Molecular systems …, 2020 - embopress.org
A progressive loss of protein homeostasis is characteristic of aging and a driver of
neurodegeneration. To investigate this process quantitatively, we characterized proteome …

Phase separation drives X-chromosome inactivation: a hypothesis

A Cerase, A Armaos, C Neumayer, P Avner… - Nature structural & …, 2019 - nature.com
The long non-coding RNA Xist induces heterochromatinization of the X chromosome by
recruiting repressive protein complexes to chromatin. Here we gather evidence, from the …

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

AM Mas, E Goñi, I Ruiz de Los Mozos, A Arcas… - Nature …, 2023 - nature.com
Cells must coordinate the activation of thousands of replication origins dispersed throughout
their genome. Active transcription is known to favor the formation of mammalian origins …

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

M Stražar, M Žitnik, B Zupan, J Ule, T Curk - Bioinformatics, 2016 - academic.oup.com
Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control
of gene expression, including splicing, transport, polyadenylation and RNA stability. To …

catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

CM Livi, P Klus, R Delli Ponti, GG Tartaglia - Bioinformatics, 2016 - academic.oup.com
Motivation: Recent technological advances revealed that an unexpected large number of
proteins interact with transcripts even if the RNA-binding domains are not annotated. We …

RNA-binding and prion domains: the Yin and Yang of phase separation

NL Gotor, A Armaos, G Calloni… - Nucleic acids …, 2020 - academic.oup.com
Proteins and RNAs assemble in membrane-less organelles that organize intracellular
spaces and regulate biochemical reactions. The ability of proteins and RNAs to form …

Phase separation of chromatin and small RNA pathways in plants

Z Lei, L Wang, EY Kim, J Cho - The Plant Journal, 2021 - Wiley Online Library
Gene expression can be modulated by epigenetic mechanisms, including chromatin
modifications and small regulatory RNAs. These pathways are unevenly distributed within a …