A census of human RNA-binding proteins.
TL;DR: This work presents a census of 1,542 manually curated RBPs that are analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression, a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
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Abstract: Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
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Expanded encyclopaedias of DNA elements in the human and mouse genomes
Jill Moore,Michael J. Purcaro,Henry Pratt,Charles B. Epstein,Noam Shoresh,Jessika Adrian,Trupti Kawli,Carrie A. Davis,Alexander Dobin,Rajinder Kaul,Jessica Halow,Eric L. Van Nostrand,Peter Freese,David U. Gorkin,David U. Gorkin,Yin Shen,Yin Shen,Yupeng He,Mark Mackiewicz,Florencia Pauli-Behn,Brian A. Williams,Ali Mortazavi,Cheryl A. Keller,Xiao-Ou Zhang,Shaimae I. Elhajjajy,Jack Huey,Diane E. Dickel,Valentina Snetkova,Xintao Wei,Xiaofeng Wang,Xiaofeng Wang,Juan Carlos Rivera-Mulia,Juan Carlos Rivera-Mulia,Joel Rozowsky,Jing Zhang,Surya B. Chhetri,Jialing Zhang,Alec Victorsen,Kevin P. White,Axel Visel,Axel Visel,Gene W. Yeo,Christopher B. Burge,Eric Lécuyer,Eric Lécuyer,David M. Gilbert,Job Dekker,John L. Rinn,Eric M. Mendenhall,Joseph R. Ecker,Manolis Kellis,Manolis Kellis,Robert J. Klein,William Stafford Noble,Anshul Kundaje,Roderic Guigó,Peggy J. Farnham,J. Michael Cherry,Richard M. Myers,Bing Ren,Bing Ren,Brenton R. Graveley,Mark Gerstein,Len A. Pennacchio,Len A. Pennacchio,Michael Snyder,Bradley E. Bernstein,Barbara J. Wold,Ross C. Hardison,Thomas R. Gingeras,John A. Stamatoyannopoulos,Zhiping Weng,Zhiping Weng,Zhiping Weng +73 more
TL;DR: The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development.
A brave new world of RNA-binding proteins
TL;DR: The RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA, are discussed.
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Eric L. Van Nostrand,Gabriel A. Pratt,Alexander A. Shishkin,Chelsea Gelboin-Burkhart,Mark Y. Fang,Balaji Sundararaman,Steven M. Blue,Thai B. Nguyen,Christine Surka,Keri Elkins,Rebecca Stanton,Frank Rigo,Mitchell Guttman,Gene W. Yeo +13 more
TL;DR: An enhanced CLIP (eCLIP) protocol is developed that decreases requisite amplification by ∼1,000-fold, decreasing discarded PCR duplicate reads by ∼60% while maintaining single-nucleotide binding resolution, and improves specificity in the discovery of authentic binding sites.
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A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand,Peter Freese,Gabriel A. Pratt,Xiaofeng Wang,Xintao Wei,Rui Xiao,Rui Xiao,Steven M. Blue,Jia-Yu Chen,Neal A.L. Cody,Daniel Dominguez,Sara Olson,Balaji Sundararaman,Lijun Zhan,Cassandra Bazile,Louis Philip Benoit Bouvrette,Julie Bergalet,Michael O. Duff,Keri E. Garcia,Chelsea Gelboin-Burkhart,Myles Hochman,Nicole J. Lambert,Hairi Li,Michael P. McGurk,Thai B. Nguyen,Tsultrim Palden,Ines Rabano,Shashank Sathe,Rebecca Stanton,Amanda Su,Ruth Wang,Brian A. Yee,Bing Zhou,Ashley L. Louie,Stefan Aigner,Xiang-Dong Fu,Eric Lécuyer,Eric Lécuyer,Christopher B. Burge,Brenton R. Graveley,Gene W. Yeo +40 more
TL;DR: The spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization are described.
RNA-binding proteins in human genetic disease.
TL;DR: The authors review the role of RBPs in human genetic disorders, both Mendelian and somatic, discuss the molecular mechanisms of disease and highlight emerging therapeutic interventions that target RBPs.
References
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TL;DR: This analysis analyzes the structure and phylogenetic distribution of the known exoribonucleases and identifies common motifs that can be used to characterize newly-discovered exorIBonucle enzymes, and correct some previously misassigned proteins.
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Pierre Kerner,Sandie M. Degnan,Lauriane Marchand,Bernhard M. Degnan,Michel Vervoort,Michel Vervoort +5 more
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TL;DR: It is shown that PARalyzer delineates sites with a high signal-to-noise ratio, which identifies the sequence preferences of RNA-binding proteins, as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins.
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