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Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain.
Miller, Lucas G; Demny, Madeline; Tamamis, Phanourios; Contreras, Lydia M.
Afiliación
  • Miller LG; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
  • Demny M; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
  • Tamamis P; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
  • Contreras LM; Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA.
Comput Struct Biotechnol J ; 21: 3541-3556, 2023.
Article en En | MEDLINE | ID: mdl-37501707
To date, over 150 chemical modifications to the four canonical RNA bases have been discovered, known collectively as the epitranscriptome. Many of these modifications have been implicated in a variety of cellular processes and disease states. Additional work has been done to identify proteins known as "readers" that selectively interact with RNAs that contain specific chemical modifications. Protein interactomes with N6-methyladenosine (m6A), N1-methyladenosine (m1A), N5-methylcytosine (m5C), and 8-oxo-7,8-dihydroguanosine (8-oxoG) have been determined, mainly through experimental advances in proteomics techniques. However, relatively few proteins have been confirmed to bind directly to RNA containing these modifications. Furthermore, for many of these protein readers, the exact binding mechanisms as well as the exclusivity for recognition of modified RNA species remain elusive, leading to questions regarding their roles within different cellular processes. In the case of the YT-521B homology (YTH) family of proteins, both experimental and in silico techniques have been leveraged to provide valuable biophysical insights into the mechanisms of m6A recognition at atomic resolution. To date, the YTH family is one of the best characterized classes of readers. Here, we review current knowledge about epitranscriptome recognition of the YTH domain proteins from previously published experimental and computational studies. We additionally outline knowledge gaps for proteins beyond the well-studied human YTH domains and the current in silico techniques and resources that can enable investigation of protein interactions with modified RNA outside of the YTH-m6A context.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Comput Struct Biotechnol J Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Países Bajos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Comput Struct Biotechnol J Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Países Bajos