Protocol to identify the RNA-binding domains of RBPs in a global scale

RBDmap employs UV crosslinking, oligo(dT) selection, partial proteolysis and quantitative proteomics to identify the protein regions engaged in RNA binding in a system-wide scale. Applied to HeLa cells it reported 1,174 RNA-binding sites mapping to 529 RBPs, many of which lacking known RNA-binding domains. A detail RBDmap protocol has now been released for the community in Nature protocols

The use of RBDmap can now be extended to other cell lines or organisms and can be used to profile in a global scale the behaviour of RNA-binding domains in response to different physiological conditions and stresses.”

Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap. Castello A, Frese CK, Fischer B, Järvelin AI, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW. Nat Protoc. 2017 Dec;12(12):2447-2464. doi: 10.1038/nprot.2017.106. Epub 2017 Nov 2. PMID:  29095441

A Molecular View of HIV Therapy

After HIV enters a T-cell, three enzymes play essential roles in the life cycle of the virus. Reverse transcriptase copies the viral RNA genome and makes a DNA copy. Integrase inserts this viral DNA into the cell’s DNA. In the last steps of the viral life cycle, HIV protease cuts HIV proteins into their functional parts.

This animation was created based on atomic structures from the Protein Data Bank: Reverse Transcriptase: 3hvt, 3dlk, 3v6d, 3v4i, 3klg, 3v81 Integrase: 3os1, 3os0, 3oya Protease: 3pj6, 1kj4, 1hxb, 2az9, 2azc HIV Polyprotein, Capsid Protein, Matrix Protein: 1l6n, 2m8l, 1tam

Story: David S. Goodsell

Animation and Video Editing: Maria Voigt

Narration: Brian Hudson

Music: Gosta Berling

The RBPome of yeast (S. cerevisiae) and worms (C. elegans) uncovered

Recently, two independents works published in Nature Com and NSMB have shown the unexpected complexity of the repertoire of RNA-binding proteins in both S. cerevisiae and C. Elegans. Strikingly, metabolic enzymes and other enzymatic cores arise as enigmatic RNA-binders from yeast to human, suggesting either surprising and conserved roles of these proteins in post-transcriptional control of gene expression or a widespread function of RNA as regulator of enzymatic activities.

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The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs.

Benedikt M. Beckmann, Rastislav Horos, Bernd Fischer, Alfredo Castello, Katrin Eichelbaum, Anne-Marie Alleaume, Thomas Schwarzl, Tomaž Curk, Sophia Foehr, Wolfgang Huber, Jeroen Krijgsveld & Matthias W. Hentze

Conserved mRNA-binding proteomes in eukaryotic organisms

Ana M Matia-González, Emma E Laing & André P Gerber


Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins

In the past century, few areas of biology advanced as much as our understanding of the pathways of intermediary metabolism. Initially considered unimportant in terms of gene regulation, crucial cellular fate changes, cell differentiation, or malignant transformation are now known to involve ‘metabolic remodeling’ with profound changes in the expression of many metabolic enzyme genes. This review focuses on the recent identification of RNA-binding activity of numerous metabolic enzymes. We discuss possible roles of this unexpected second activity in feedback gene regulation (‘moonlighting’) and/or in the control of enzymatic function. We also consider how metabolism-driven post-translational modifications could regulate enzyme-RNA interactions. Thus, RNA emerges as a new partner of metabolic enzymes with far-reaching possible consequences to be unraveled in the future.

New angles in the RNA field

In the last issue of the Biochemist (the journal of the Biochemical society) is focus on RNA.  The different reviews, written by leading RNA scientists, give an overview of the function of ribozymes, novel initiation codons and RNA modifications in RNA biology. In addition, this issue provides an comprehensive description of the mechanisms of RNA silencing in plants, the emergent roles of mitochondrial RNAs and chromosome silencing by Xist non-coding RNA. We have contributed to it with a snapshot in our current knowledge in RNA-binding proteins and the news avenues of research that aroused from the HeLa and HEK293 mRNA interactomes (Castello et al., Cell 2012 and Baltz et al., Mol Cell, 2012).

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