E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells

Genes Dev. 2013 Aug 15;27(16):1821-33. doi: 10.1101/gad.210211.112.


Programmed mutagenesis of the immunoglobulin locus of B lymphocytes during class switch recombination (CSR) and somatic hypermutation requires RNA polymerase II (polII) transcription complex-dependent targeting of the DNA mutator activation-induced cytidine deaminase (AID). AID deaminates cytidine residues on substrate sequences in the immunoglobulin (Ig) locus via a transcription-dependent mechanism, and this activity is stimulated by the RNA polII stalling cofactor Spt5 and the 11-subunit cellular noncoding RNA 3'-5' exonucleolytic processing complex RNA exosome. The mechanism by which the RNA exosome recognizes immunoglobulin locus RNA substrates to stimulate AID DNA deamination activity on its in vivo substrate sequences is an important question. Here we report that E3-ubiquitin ligase Nedd4 destabilizes AID-associated RNA polII by a ubiquitination event, leading to generation of 3' end free RNA exosome RNA substrates at the Ig locus and other AID target sequences genome-wide. We found that lack of Nedd4 activity in B cells leads to accumulation of RNA exosome substrates at AID target genes and defective CSR. Taken together, our study links noncoding RNA processing following RNA polII pausing with regulation of the mutator AID protein. Our study also identifies Nedd4 as a regulator of noncoding RNAs that are generated by stalled RNA polII genome-wide.

Keywords: Nedd4; RNA polymerase II stalling; RNA polymerase II ubiquitination; activation-induced deaminase; immunoglobulin locus transcription; noncoding RNA.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • B-Lymphocytes / enzymology*
  • Cell Line, Tumor
  • Cells, Cultured
  • Cytidine Deaminase / metabolism*
  • Endosomal Sorting Complexes Required for Transport / genetics
  • Endosomal Sorting Complexes Required for Transport / metabolism*
  • Exosome Multienzyme Ribonuclease Complex / metabolism
  • Gene Knockdown Techniques
  • HEK293 Cells
  • Humans
  • Immunoglobulin Switch Region / genetics
  • Mice
  • Nedd4 Ubiquitin Protein Ligases
  • Nuclear Proteins / metabolism
  • Protein Binding
  • RNA Polymerase II / metabolism*
  • Transcriptional Elongation Factors / metabolism
  • Ubiquitin-Protein Ligases / genetics
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitination


  • Endosomal Sorting Complexes Required for Transport
  • Nuclear Proteins
  • SUPT5H protein, human
  • Transcriptional Elongation Factors
  • Nedd4 Ubiquitin Protein Ligases
  • Nedd4 protein, human
  • Nedd4l protein, mouse
  • Ubiquitin-Protein Ligases
  • RNA Polymerase II
  • Exosome Multienzyme Ribonuclease Complex
  • AICDA (activation-induced cytidine deaminase)
  • Cytidine Deaminase