A protein that binds RNA. Binding specificity can depend on nucleotide sequence, RNA secondary structure, chemical modification and other partners; recovery in an RNA pull-down alone does not establish direct recognition.
Recognition and positioning of a primary hairpin help the Drosha complex generate a shorter precursor. Later export and Dicer processing are additional stages, so loss of a mature microRNA can arise from defects at several different steps. [ref]
NCBI Gene by the National Library of Medicine. Homo sapiens, DGCR8 record, Summary: primary microRNA processing
An RNA-binding protein that collaborates with Nanos and other factors in sequence-specific repression of target messenger RNAs.
G3BP2 is an RNA-binding protein involved in the organization of stress granules. Together with related components, it helps couple RNA-protein interactions to formation of a condensed cytoplasmic assembly. The granule state depends on concentration, binding partners and stress context. Presence of G3BP2 in a granule supports participation, while testing a requirement for assembly needs depletion or a defined functional perturbation. [ref]
G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits by Nancy Kedersha and others. 2016, G3BP-family interactions and stress-granule assembly
An RNA-associated regulator of stress-granule assembly. Requirements for assembly depend on stress and partner context.
Like G3BP2, it can organize interactions among RNA and proteins during stress-granule formation. Perturbing those interactions distinguishes a direct assembly requirement from mere co-localization in an already formed granule. [ref]
A Drosophila regulator whose RNA recognition supports sex-specific and autoregulatory splicing. It can act through competition at early recognition or through substrate-specific later spliceosomal interactions.
A common structured RNA-binding domain. Multiple motifs in a protein can recognize separated RNA segments and support geometry-dependent regulation.
A budding-yeast regulator that targets selected AU-rich transcripts for degradation during iron deficiency, reallocating resources away from iron-consuming processes.[ref]
Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation by Sergi Puig and others. Iron-deficiency-dependent target turnover
A family of microRNA-silencing effectors linking Argonaute-associated recognition to downstream repression and RNA-deadenylation machinery.[ref]
GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets by Joerg E. Braun and others. Direct recruitment interactions
A bacteriophage RNA-recognition module used as a complement to MS2 coat protein for experimental RNA recruitment and imaging.
A bacteriophage protein recognizing a defined RNA hairpin, used as a fusion partner in RNA tethering assays and RNA imaging. Hairpin arrays and bound fusion proteins can themselves perturb RNA behaviour.
A member of a repeat-containing protein family with major roles in organellar RNA recognition and regulation. Different members can support distinct processing, editing, stability or translational functions.
A plastid RNA-binding protein that can protect a bound region against exonucleolytic decay from either direction, helping define stable transcript termini.[ref]
Zipcode-binding protein 1, also known as IGF2BP1. It recognizes a localization element in beta-actin messenger RNA and can repress its biological translation during transport.[ref]
An insulin-like growth factor 2 messenger RNA-binding protein family member. Stabilization and enhanced biological translation of modified targets have been reported; this does not identify every modification-dependent stabilizer as an IGF2BP protein.[ref]
A protein that binds a poly(A) tail and can influence messenger RNA stability and biological translation.
A protein family that binds small guide RNAs and participates in sequence-directed regulation. Guide complementarity can identify targets, but cleavage activity varies among family members and pathways.
A germline nuclear Caenorhabditis elegans Argonaute required for maintenance of some inherited small-RNA-dependent silencing states.
Endonucleolytic target cleavage directed by a small-RNA guide and a catalytically competent Argonaute. Cleavage typically falls opposite guide positions 10 and 11; not all Argonautes can slice.
An Argonaute-family branch binding piRNAs. Cytoplasmic cleavage and nuclear transcriptional silencing protect the germline in many animals, with important species and tissue differences.
The Caenorhabditis elegans Piwi-family protein associated with 21U piRNAs and germline surveillance of RNA expression.
Recognition by its associated small RNAs helps distinguish transcripts for germline surveillance. Establishing a persistent silenced state additionally involves downstream pathways, so initial recognition and long-term maintenance are different stages. [ref]
piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans by Alyson Ashe and others. 2012, recognition and inherited silencing
A mouse Piwi-family protein associated with fetal male germ-cell transposon repression and de novo DNA methylation.
Its associated guide RNAs contribute sequence information for recognition of transposon-related material. Repression can involve both RNA-level and chromatin-associated outputs, depending on developmental stage and partner factors. [ref]
A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice by Alexei A. Aravin and others. 2008, germline piRNA pathway and methylation
Complementary cleavage relationships between small-RNA molecular populations can reinforce production of transposon-targeting guides. The resulting signature links sequence recognition to amplification rather than simply accumulating every small RNA indiscriminately. [ref]
A Drosophila Piwi-family protein participating in germline piRNA-mediated regulation, including ping-pong amplification.
It binds selected small RNAs and participates in transcript recognition and cleavage within a germline defence network. Its relationship with AGO3 helps amplify appropriate guide molecular populations, linking molecular specificity to transposon control. [ref]
An epigenetic role for maternally inherited piRNAs in transposon silencing by Julius Brennecke and others. 2008, inherited piRNAs and transposon repression
In Arabidopsis thaliana, it associates with small interfering RNAs that help target RNA-directed DNA methylation. Sequence complementarity supplies specificity while partner proteins connect recognition to a chromatin modification rather than cleavage of every matching transcript. [ref]
ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation by Daniel Zilberman and others. 2003, AGO4-dependent methylation and silencing
A heterogeneous nuclear ribonucleoprotein involved in RNA processing. Its binding can respond to modification-dependent accessibility of an RNA motif.[ref]
A polypyrimidine-tract-binding RNA-binding protein family member involved in precursor-RNA processing and other aspects of gene expression.
A polypyrimidine-tract-binding protein with four RNA recognition motifs. Its splicing effects depend on site position, RNA geometry and other proteins; it is not exclusively a repressor.
A member of a family of sequence-selective RNA-binding proteins involved in regulating alternative splicing.
Sequence-selective binding near an alternative exon can change recruitment or activity of the splicing machinery. The same binding motif can be associated with different outcomes depending on position and the surrounding regulatory context. [ref]
Molecular Biology of the Cell, 4th edition by Bruce Alberts and others. Chapter 7, RNA Processing and Alternative Splicing
A member of a neural RNA-binding protein family with position-dependent effects on alternative splicing. Binding-site position helps predict activation or repression of exon inclusion.[ref]
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