Deadenylation
Methods and Protocols
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Article
Open AccessDeadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution
Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression. The incorporation of non-adenosines in poly(A) tails, or ‘mixe...
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Article
Open AccessRegulation by the RNA-binding protein Unkempt at its effector interface
How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here, we document the existence and functions of a multivalent RBP–effector interface. We show...
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Book
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Protocol
Reconstitution of Human CCR4-NOT Complex from Purified Proteins and an Assay of Its Deadenylation Activity
We describe protocols to produce and reconstitute an active human CCR4-NOT complex. Individual recombinant subunits are expressed in E. coli or baculovirus-infected insect cells, purified using column chromatogra...
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Article
Open AccessStructure and assembly of the NOT10:11 module of the CCR4-NOT complex
NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poor...
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Article
The nexus between RNA-binding proteins and their effectors
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general...
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Article
Open AccessDAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5′ leaders
Half of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events r...
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Article
Open AccessRNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation
The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of...
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Article
Open AccessReconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation
CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombin...
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Article
Structure of the Dcp2–Dcp1 mRNA-decap** complex in the activated conformation
Crystal structures, along with biochemistry data, capture the active form of the Dcp2 decap** enzyme in complex with Dcp1 and a peptide from Edc1, thus revealing the mechanism of activation by Dcp1 and Edc1 ...
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Chapter
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery
Protein–protein interactions (PPI) are integral to the majority of biological functions. Targeting these interactions with small molecule inhibitors is of increased interest both in academia as well as in the ...
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Article
Improved molecular replacement by density- and energy-guided protein structure optimization
With more than 60,000 structures now available in the Protein Data Bank, it is frequently possible to create homology-based models to help solve the X-ray crystal structure of a protein with an unknown three-d...
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Article
Retroviral intasome assembly and inhibition of DNA strand transfer
Integrase is an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The structure of full-length retroviral integrase, either separately or in ...
