High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks

Abstract

From synthesis to decay, mRNA associates with RNA-binding proteins (RBPs) establishing dynamic ribonucleoprotein particles (RNPs). Understanding the composition and function of RNPs is fundamental to understanding how eukaryotic mRNAs are controlled. This is especially relevant for trypanosomes and related kinetoplastid parasites, which mostly rely on post-transcriptional mechanisms to control gene expression. Crucial for trypanosome differentiation, development, or even response to heat shock, RBPs are known to be essential modulators of diverse molecular processes. The recent application of large-scale quantitative methods, such as Next-Generation Sequencing (NGS) and quantitative mass spectrometry, has revealed new exciting features about the parasite RNA-related metabolism. Novel proteins carrying RNA-binding activity, including many proteins without RNA-related ontology were discovered setting a necessary groundwork to get in insights into RNA biology.

Conclusion: This review aims to give the reader an understanding of current trypanosome RNP research, highlighting the progress made using high-throughput approaches.

Keywords: Gene expression regulation; High-throughput; Post-transcriptional control; RNA biology; RNA-binding proteins; mRNA-fate.

Fig. (1)

Proteins found to bind poly(A) mRNA in T. brucei [, -, , 104] affecting reporter expression upon tethering [4] are colored in green for up-regulators and red for repressors. Others RBPs that not fulfill these criteria are not shown. Under starvation, several of these proteins migrate to stress granules (grey box) [6]. RBP42 and DRBD3 are associated with abundant mRNAs, indicating a stabilizing function [46, 47]. RBP33 interacts with region usually not detected which would be consistent with a destabilizing function [38]. Arginine methylation status regulates DRBD18 functions [8]. In T. cruzi, ZC3H39 sequesters highly expressed transcripts to stress granules [39].