Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases.
RNA-protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA-protein networks. Extensive efforts have been made to purify in vivo-assembled RNA-protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA-protein interactions that result in the development of many neurological diseases.
Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Magdalena
M
Jazurek
Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Adam
A
Ciesiolka
Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Julia
J
Starega-Roslan
Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Katarzyna
K
Bilinska
Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland wlodkrzy@ibch.poznan.pl.
Wlodzimierz J
WJ
Krzyzosiak
D000818:Animals; D052157:Aptamers, Nucleotide; D001426:Bacterial Proteins; D064130:CRISPR-Associated Proteins; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D042622:DNA Repeat Expansion; D004722:Endoribonucleases; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D040901:Proteomics / Q000379:methods*; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D016372:RNA, Antisense; D016601:RNA-Binding Proteins / Q000378:metabolism*; D015203:Reproducibility of Results; D052156:SELEX Aptamer Technique
D052157:Aptamers, Nucleotide; D001426:Bacterial Proteins; D064130:CRISPR-Associated Proteins; D016372:RNA, Antisense; D016601:RNA-Binding Proteins; D012313:RNA; C552242:Csy4 endoribonuclease, Pseudomonas aeruginosa; D004722:Endoribonucleases