Current Status of Regulatory Non-Coding RNAs Research in the Tritryp

Abstract

Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.

Nanopore-Based Direct RNA Sequencing of the Trypanosoma brucei Transcriptome Identifies Novel lncRNAs

“…For some mRNAs, >50% of the mature sequence are the result of the processing reaction. The sequence information for editing is provided by a trypanosome-specific class of small (40–60 nt long), ncRNAs, termed guide RNAs (gRNAs) [ 12 , 13 ]. In T. brucei , gRNAs are mostly minicircle encoded.…”

“…The panel of small ncRNAs (RNAs < 200 nucleotides (nt) in length) includes the small nuclear (sn)RNA of the trans -spliceosome [ 6 ], the small nucleolar (sno)RNAs of the ribosomal RNA modification machinery [ 7 , 8 ], as well as transfer (t)RNAs and ribosomal 5S and 5.8S rRNA. Further included are cytosolic Vault (vt)RNA [ 9 ], 7SL RNA [ 10 ], and telomerase RNA [ 11 ] as well as hundreds of guide (g)RNAs, which are a mitochondria-specific class of snRNAs required to edit sequence-deficient mitochondrial transcripts [ 12 , 13 ]. Small interfering (si)RNAs are present in some but not all trypanosomatids and recent experiments identified a new class of anti-sense translational regulators, the so-called TBsRNAs [ 8 ].…”

Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells

“…Our exhaustive analysis of the expression of small RNAs under DENV infection led us to detect candidates of sfd-RNAs related to other sfd-RNAs that were validated to be products of ncRNAs ( Fort et al, 2022 ) or specifically of tRNAs ( Cole et al, 2009 ) in viral infection conditions ( Zhou et al, 2017 ; Taxis et al, 2018 ; Cho et al, 2019 ; Chen and Bao, 2020 ) or under other biological conditions that affect their cleavage and processing ( Christoph et al, 2008 ; Kawaji et al, 2008 ; Hoogstrate et al, 2014 )). Furthermore, our work proposes new candidates whose differential expression must be experimentally tested, particularly those suited to investigate whether our candidates indeed are regulated under dengue virus infection.…”

Life in plastic, it’s fantastic! How Leishmania exploit genome instability to shape gene expression

“…Although ncRNAs do not encode proteins, they are key regulators of cellular metabolism ( Cech and Steitz, 2014 ). In Leishmania , the ‘RNAome’ may contain upwards of 12,000 ncRNAs per species but limited studies have functionally characterised their activities ( Ruy et al., 2019 ; Fort et al., 2022 ). Now, links between ncRNAs and parasite development suggest these elements do directly regulate key parasite processes, for example the recent description of a long ncRNA required for differentiation to the quiescent, transmissible form (the ‘stumpy’ form) of T. brucei ( Guegan et al., 2022 ) or the variable expression of ncRNAs across the Leishmania lifecycle ( Ruy et al., 2019 ).…”