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.
read more
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.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
MicroRNAs: An adaptive mechanism in the pancreatic β-cell…and beyond?
TL;DR: Results indicate miRNAs play an integral role in the fundamental mechanics of how the cell manages the balance between these independent functions and may uncover mechanisms which can be exploited to improve differentiation protocols in producing fully mature β-cells.
9
Sam68 splicing regulation contributes to motor unit establishment in the postnatal skeletal muscle.
Elisa De Paola,Laura Forcina,Laura Pelosi,Simona Pisu,Piergiorgio La Rosa,Eleonora Cesari,Carmine Nicoletti,Luca Madaro,Neri Mercatelli,Filippo Biamonte,Annalisa Nobili,Marcello D'Amelio,Marco De Bardi,Elisabetta Volpe,Daniela Caporossi,Claudio Sette,Antonio Musarò,Maria Paola Paronetto +17 more
- 04 Aug 2020
TL;DR: Analysis of the motor units revealed that Sam68 ablation impairs the establishment of neuromuscular junctions and causes progressive loss of motor neurons in the spinal cord, suggesting that proper establishment of motor units requires timely expression of synaptic splice variants.
9
RNA Binding Protein PTBP1 Promotes the Metastasis of Gastric Cancer by Stabilizing PGK1 mRNA.
TL;DR: It is verified that PTBP1 was upregulated in GC tissues and cell lines, and higher PTBP1 level was associated with poorer prognosis, and discoveries suggest that PTBP1 could be a promising therapeutic target for GC.
9
Exploring the Diverse Functional and Regulatory Consequences of Alternative Splicing in Development and Disease
TL;DR: In this paper, the use of alternative splicing of noncoding exons to regulate the stability and localization of RNA transcripts is discussed, as well as the role of protein-coding spliceforms during development.
9
Structural basis for mRNA recognition by human RBM38.
TL;DR: The crystal structure of the RRM domain of human RBM38 in complex with a single-stranded RNA revealed the RNA-recognition mechanism of human G(U/C/A)GUG sequence single-Stranded RNA in a sequence-specific and structure-specific manner and provided structural information for understanding theRNA-binding property of R BM38.
9
References
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
98.8K
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
36K
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Related Papers (5)
Debashish Ray,Hilal Kazan,Kate B. Cook,Matthew T. Weirauch,Matthew T. Weirauch,Hamed S. Najafabadi,Xiao Li,Serge Gueroussov,Mihai Albu,Hong Zheng,Ally Yang,Hong Na,Manuel Irimia,Leah H. Matzat,Ryan K. Dale,Sarah A. Smith,Christopher A. Yarosh,Seth M. Kelly,Behnam Nabet,D. Mecenas,Weimin Li,Rakesh S. Laishram,Mei Qiao,Howard D. Lipshitz,Fabio Piano,Anita H. Corbett,Russ P. Carstens,Brendan J. Frey,Richard A. Anderson,Kristen W. Lynch,Luiz O. F. Penalva,Elissa P. Lei,Andrew G. Fraser,Benjamin J. Blencowe,Quaid Morris,Timothy P. Hughes +35 more
[...]