Stem–loop RNA labeling can affect nuclear and cytoplasmic mRNA processing

S Heinrich, CL Sidler, CM Azzalin, K Weis - Rna, 2017 - rnajournal.cshlp.org
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2
or PP7 coat proteins, to their corresponding target sequences has been extremely useful …

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

EW Yang, JH Bahn, EYH Hsiao, BX Tan, Y Sun… - Nature …, 2019 - nature.com
Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic
variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of …

Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast

G Kudla, S Granneman, D Hahn… - Proceedings of the …, 2011 - National Acad Sciences
Many protein–protein and protein–nucleic acid interactions have been experimentally
characterized, whereas RNA–RNA interactions have generally only been predicted …

Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins

AG Cridge, LM Castelli, JB Smirnova… - Nucleic acids …, 2010 - academic.oup.com
Abstract eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes.
However the extent to which specific mRNA targets are regulated by 4E-BPs remains …

Coding region: the neglected post-transcriptional code

EK Lee, M Gorospe - RNA biology, 2011 - Taylor & Francis
The control of mammalian mRNA turnover and translation has been linked almost
exclusively to specific cis-elements within the 5'-and 3'-untranslated regions (UTRs) of the …

A genomic integration method for the simultaneous visualization of endogenous mRNAs and their translation products in living yeast

L Haim-Vilmovsky, N Gadir, RH Herbst, JE Gerst - Rna, 2011 - rnajournal.cshlp.org
Protein localization within cells can be achieved by the targeting and localized translation of
mRNA. Yet, our understanding of the dynamics of mRNA targeting and protein localization …

Functional interchangeability of the structurally similar tetranucleotide loops GAAA and UUCG in fission yeast signal recognition particle RNA.

D Selinger, X Liao, JA Wise - Proceedings of the National …, 1993 - National Acad Sciences
Signal recognition particle (SRP) RNA exhibits significant primary sequence conservation
only in domain IV, a bulged hairpin capped by a GNRA (N, any nucleotide; R, purine) …

Probing RNA–protein networks: biochemistry meets genomics

ZT Campbell, M Wickens - Trends in biochemical sciences, 2015 - cell.com
RNA–protein interactions are pervasive. The specificity of these interactions dictates which
RNAs are controlled by what protein. Here we describe a class of revolutionary new …

Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression

C Fagre, W Gilbert - Wiley Interdisciplinary Reviews: RNA, 2024 - Wiley Online Library
Post‐transcriptional mRNA modifications play diverse roles in gene expression and RNA
function. In many cases, RNA modifications function by altering how cellular machinery such …

Deciphering the mRNP code: RNA-bound determinants of post-transcriptional gene regulation

NH Gehring, E Wahle, U Fischer - Trends in biochemical sciences, 2017 - cell.com
Eukaryotic cells determine the final protein output of their genetic program not only by
controlling transcription but also by regulating the localization, translation and turnover rates …