Post-transcriptional control of miRNA biogenesis

Abstract

MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.

Keywords: DGCR8; DICER; DROSHA; Microprocessor; RNA-binding proteins (RBPs); microRNAs (miRNAs); terminal loop.

FIGURE 1.

(A) The canonical pathway of miRNA biogenesis, including the Microprocessor-mediated (DROSHA/DGCR8) step in the nucleus followed by DICER processing in the cytoplasm. Structural and sequence features important for miRNA processing are highlighted in both the pri-mir and pre-miR molecules. (B) Positive regulators of miRNA biogenesis bind to the terminal loop (TL) or other elements within miRNA precursors (pri-mir and pre-mir) and stimulate Drosha and/or Dicer processing, leading to increased levels of mature miRNAs (miR). The TL, also known as apical loop, is depicted in red. (C) Negative regulators of miRNA biogenesis bind to TL or other elements within miRNA precursors (pri-mir and pre-mir) and abrogate Drosha and/or Dicer processing, leading to decreased levels of mature miRNAs (miRs). The TL, also known as apical loop, is depicted in red.

FIGURE 2.

HnRNP A1 as a paradigm for RBP-mediated regulation of miRNA biogenesis in the nucleus. (A) Binding of hnRNP A1 to the TL of pri-mir-18a induces a structural rearrangement that results in enhanced Drosha processing. (B) Each RRM of hnRNP A1 recognizes an UAG motif in the TL of pri-mir-18a. (C) Binding of hnRNP A1 to the TL of pri-let-7 in differentiated cells outcompetes binding of the stimulatory factor, KSRP, resulting in decreased Drosha processing.

FIGURE 3.

Influence of genetic variation on miRNA biogenesis. (A) Schematic structure of pri-mir-30c-1 with the CNNC motif (CAUC) occluded by the RNA secondary structure in the G₂₇ (wild-type) variant (indicated by a G in the TL). (B) A single G to A substitution (A₂₇) present in the TL of pri-mir-30c-1 in breast and gastric cancer patients leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 to the CAUC sequence determinant, causing increased Microprocessor-mediated processing and elevated miR-30c levels.