title: Global target mRNA specification and regulation by the RNA-binding protein ZFP36.
abstract: BACKGROUND
  ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embryonic kidney cells, and examined the combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1.
  
  
  RESULTS
  Targets bound and negatively regulated by ZFP36 include transcripts encoding proteins necessary for immune function and cancer, and transcripts encoding other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance upon ZFP36 overexpression independent of effects from confounding features. Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes, and found that ZFP36 degrades transcripts through specific AU-rich sequences, representing a subset of the U-rich sequences ELAVL1 interacts with to stabilize transcripts.
  
  
  CONCLUSIONS
  ZFP36-RNA target specificities in vivo are quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to unravel in vivo combinatorial regulation by RNA-binding proteins.
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Jacobs
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kennington
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Nusbaum
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Perry J
authors.initials: PJ
authors.lastname: Blackshear
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
mesh_terms: D019295:Computational Biology; D000067780:ELAV-Like Protein 1 / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D047468:Immunoprecipitation; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software; D051816:Tristetraprolin / Q000235:genetics / Q000378:metabolism*
chemical_list: D000067780:ELAV-Like Protein 1; C098770:ELAVL1 protein, human; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D051816:Tristetraprolin; C497552:ZFP36 protein, human