Resources

Here the authors apply low-input methyl RNA immunoprecipitation and sequencing to map the N⁶-methyladenosine landscape during mouse oocyte and early embryo development. They show that RNAs derived from retrotransposons are often N⁶-methyladenosine marked and so are many genes important for the maternal-to-zygotic transition.

High-throughput chemical screening identifies retinoic acid signaling as a regulatory pathway of 2-cell-like cell reprogramming and early mouse development.

A survey of human RNA-binding proteins based on luciferase-based 3ʹ-untranslated-region tethered function assays and identification of their target mRNAs provides insights into their role in RNA metabolism.

NEDD8-ubiquitin substrate profiling (sNUSP) identifies neddylation sites in many non-cullin proteins. Among the candidates, neddylation of cofilin regulates actin dynamics and neurite growth and outgrowth in developing neurons.

Deep mutational scanning data for multiple kinases reveal generalizable residues that mediate activity and drug resistance across the mammalian kinome.

A quantitative atlas of RNA m⁵C sites in human and mouse tissues based on a new discovery pipeline allows the identification of sequence motifs and structural features associated with the modification and provides a resource for future studies.

Structure maps of RNAs localized to chromatin, nucleoplasm and cytoplasm provide a rich resource with which to investigate the interplay of RNA structure, RNA–protein interactions and RNA modifications.

Using UbiSite, an antibody-based approach that specifically detects protein lysine and N-terminal ubiquitination, Blagoev and colleagues uncover lack of correlation between changes in protein ubiquitination and abundance upon proteasome inhibition.

A comprehensive proteomics screen for ‘reader’ proteins that recognize m⁶A-modified RNA reveals that the modification both promotes and prevents the binding of factors that control mRNA homeostasis in mammalian cells.

A comprehensive analysis of the human SUMO proteome, in HeLa and U2OS cell lines and under different conditions, identifies new SUMOylated sites and reveals cross-talk between SUMO and other post-translational modifications, such as phosphorylation.

Quantitative assessment of transcription, splicing, degradation, localization and translation of coding and noncoding genes allows classification of RNAs on the basis of their metabolism and may aid in inference of lncRNA function.

Proteomic and genomic analysis of Polycomb group complexes in embryonic stem cells and neural progenitor cells identifies new PRC1 and PRC2 interaction partners and targets during neural lineage commitment.

Analysis of changes in the EGFR interactome, ubiquitinome, phosphoproteome and proteome in response to EGF or TGF-α identifies RAB7 phosphorylation and RCP recruitment to EGFR as ligand-specific switches controlling receptor trafficking, signal duration and cellular responses.

Comprehensive identification of mRNA-binding proteins in S. cerevisiae and C. elegans reveals their evolutionary conservation; strikingly, most components of the glycolytic pathway and proteasome are detected, thus possibly indicating an ancient mechanism for metabolic control.

High-resolution MS identifies >4,300 SUMOylation sites in >1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications.

A randomized RNA library is used to determine the specificities of RNA recognition by PUF repeats. The code is then used to design a protein that targets endogenous human cyclin B1 mRNA and activates its translation.

A transcription activator–like effector nuclease (TALEN)-mediated knockout approach to delete human microRNA (miRNA) genes was used to generate a library of 540 TALEN pairs for 274 miRNA loci. As a case study, single and double knockouts for two related miRNAs, miR-141 and miR-200c, revealed intriguing functional differences.

Analysis of data from The Cancer Genome Atlas generates a pan-cancer network of 143 recurrent miRNA-target relationships. The identified miRNAs were frequently regulated by genetic and epigenetic alterations in cancer. The work also reveals that some miRNAs might coordinately regulate cancer pathways, such as miR-29 regulation of TET1 and TDG mRNAs, encoding components from the active DNA demethylation pathway.

The accurate and thorough genome-wide detection of A-to-I editing has proven technically challenging. Using a combination of computational prediction and experimental validation, the authors report ~3,500 high-probability editing sites with sufficient accuracy to reveal the global patterns underlying biological functions of RNA editing in adult male Drosophila melanogaster.

Individual microRNAs (miRNAs) can target many mRNAs that form networks of presumably cooperating genes. A new study now tests this idea by screening miRNAs and their targets in the context of dedifferentiation, or reprogramming, of mouse fibroblasts to induced pluripotent stem cells. These data establish two networks of miRNA-mRNA interactions that act together to suppress early stages of reprogramming.