A protein interaction framework for human mRNA degradation

Genome Res. 2004 Jul;14(7):1315-23. doi: 10.1101/gr.2122004.


The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5'-->3' exonucleases. Moreover, multiple interactions connect 5'-->3' and 3'-->5' decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways.

Publication types

  • Comparative Study

MeSH terms

  • Carrier Proteins / chemistry
  • Carrier Proteins / physiology
  • Conserved Sequence / physiology
  • Evolution, Molecular
  • Exoribonucleases / chemistry*
  • Exoribonucleases / physiology*
  • Exosome Multienzyme Ribonuclease Complex
  • Guanylate Kinases
  • Humans
  • Membrane Proteins
  • Multienzyme Complexes / chemistry
  • Multienzyme Complexes / physiology
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / physiology
  • Protein Interaction Mapping / methods
  • Protein Subunits / chemistry
  • Protein Subunits / physiology
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / physiology
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / physiology
  • Structure-Activity Relationship
  • Two-Hybrid System Techniques


  • Carrier Proteins
  • MPP6 protein, human
  • Membrane Proteins
  • Multienzyme Complexes
  • Nuclear Proteins
  • Protein Subunits
  • RNA, Messenger
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Guanylate Kinases
  • EXOSC4 protein, human
  • EXOSC8 protein, human
  • Exoribonucleases
  • Exosome Multienzyme Ribonuclease Complex
  • EXOSC10 protein, human