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Regulation of gene expression by miR-144/451 during mouse erythropoiesis

Peng Xu, Lance E Palmer, Christophe Lechauve, Guowei Zhao, Yu Yao, Jing Luan, Anastasios Vourekas, Haiyan Tan, Junmin Peng, John Scheutz, Zissimos Mourelatos, Gang Wu, Mitchell J Weiss and Vikram R Paralkar

Key Points

  • miR-144/451 represses only a small subset of bound mRNAs in mouse erythroblasts

  • miR-451 represses mitochondrial respiration during erythropoiesis

Abstract

The microRNA (miRNA) locus miR-144/451 is abundantly expressed in erythrocyte precursors, facilitates their terminal maturation and protects against oxidant stress. However, the full repertoire of erythroid miR-144/451 target mRNAs and associated cellular pathways is unknown. In general, the numbers of mRNAs predicted to be targeted by a miRNA vary greatly from hundreds to thousands, and are dependent on experimental approaches. To comprehensively and accurately identify erythroid miR-144/451 target mRNAs, we compared gene knockout (KO) and wild-type fetal liver erythroblasts by RNA-sequencing, quantitative proteomics and RNA immunoprecipitation of Argonaute (Ago), a component of the RNA induced silencing complex (RISC) that binds miRNAs complexed to their target mRNAs. Argonaute bound approximately 1400 erythroblast mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs were stabilized after miR-144/451 loss. Thus, miR-144 and miR-451 deregulate <10% of mRNAs that they bind, a characteristic that likely applies generally to other miRNAs. Using stringent selection criteria, we identified 53 novel miR-144/451 target mRNAs. One of these, Cox10, facilitates the assembly of mitochondrial electron transport complex IV. Loss of miR-144/451 caused increased Cox10 mRNA and protein, accumulation of Complex IV, and increased mitochondrial membrane potential with no change in mitochondrial mass. Thus, miR-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting the production of Cox10.

  • Submitted May 31, 2018.
  • Revision received March 29, 2019.
  • Accepted March 29, 2019.