Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Lakshmanan, Vairavan; Sujith, T N; Bansal, Dhiru; Shivaprasad, P. V.; Palakodeti, Dasaradhi; Krishna, Srikar

doi:10.1261/rna.077701.120

Cited by 12 publications

(6 citation statements)

References 88 publications

(140 reference statements)

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“…Around 80% of the tRFs originated from just four tRNAs-tRNA Ala_AGC , tRNA Ala_TGC , tRNA Asp_GTC , and tRNA Arg_TCT . This has been reported in other systems as well (41)(42)(43).…”

Section: Discussionsupporting

confidence: 83%

Stress response inEntamoeba histolyticais associated with robust processing of tRNA to tRNA-halves

Sharma

Zhang

Ehrenkaufer

et al. 2021

Preprint

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tRNA-derived fragments have been reported in many different organisms and have diverse cellular roles such as regulating gene expression, inhibiting protein translation, silencing transposable elements and modulating cell proliferation. In particular tRNA halves, a class of tRNA fragments produced by the cleavage of tRNAs in the anti-codon loop, have been widely reported to accumulate under stress and regulate translation in cells. Here we report the presence of tRNA-derived fragments in Entamoeba with tRNA halves being the most abundant. We further established that tRNA halves accumulate in the parasites upon different stress stimuli such as oxidative stress, heat shock, and serum starvation. We also observed differential expression of tRNA halves during developmental changes of trophozoite to cyst conversion with various tRNA halves accumulating during early encystation. In contrast to other systems, the stress response does not appear to be mediated by a few specific tRNA halves as multiple tRNAs appear to be processed during the various stresses. Furthermore, we identified some tRNA-derived fragments are associated with Entamoeba Argonaute proteins, EhAgo2-2, and EhAgo2-3, which have a preference for different tRNA-derived fragment species. Finally, we show that tRNA halves are packaged inside extracellular vesicles secreted by amoeba. The ubiquitous presence of tRNA-derived fragments, their association with the Argonaute proteins, and the accumulation of tRNA halves during multiple different stresses including encystation suggest a nuanced level of gene expression regulation mediated by different tRNA-derived fragments in Entamoeba.

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“…Around 80% of the tRFs originated from just four tRNAs-tRNA Ala_AGC , tRNA Ala_TGC , tRNA Asp_GTC , and tRNA Arg_TCT . This has been reported in other systems as well (41)(42)(43).…”

Section: Discussionsupporting

confidence: 83%

Stress response inEntamoeba histolyticais associated with robust processing of tRNA to tRNA-halves

Sharma

Zhang

Ehrenkaufer

et al. 2021

Preprint

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“…The roles of tRDFs are still poorly understood in platyhelminthes, however it was recently reported that they may be involved in the regeneration of planaria (Cao et al, 2020). Interestingly, in these organisms, Piwi proteins and Ago1, but not Dicer or Ago2, were associated with the generation and/ or function of 5'tHFs and 5'tRFs, respectively (Lakshmanan et al, 2021). However, the absence of Piwi genes in all Neodermatans implies that, at least the biogenesis of 5'tHFs could be different in trematodes and cestodes (Fontenla et al, 2017;Fontenla et al, 2021) to those described in free-living flatworms.…”

Section: Evs Pack Homodimeric Trdfs That Could Resist Exonuclease Degradationmentioning

confidence: 99%

Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host

Fontenla

Langleib

Torre-Escudero

et al. 2022

Front. Cell. Infect. Microbiol.

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MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression being involved in many different biological processes and play a key role in developmental timing. Additionally, recent studies have shown that miRNAs released from parasites are capable of regulating the expression of host genes. In the present work, we studied the expression patterns of ncRNAs of various intra-mammalian life-cycle stages of the liver fluke, Fasciola hepatica, as well as those packaged into extracellular vesicles and shed by the adult fluke. The miRNA expression profile of the intra-mammalian stages shows important variations, despite a set of predominant miRNAs that are highly expressed across all stages. No substantial variations in miRNA expression between dormant and activated metacercariae were detected, suggesting that they might not be central players in regulating fluke gene expression during this crucial step in the invasion of the definitive host. We generated a curated pipeline for the prediction of putative target genes that reports only sites conserved between three different prediction approaches. This pipeline was tested against an iso-seq curated database of the 3’ UTR regions of F. hepatica genes to detect miRNA regulation networks within liver fluke. Several functions related to the host immune response or modulation were enriched among the targets of the most highly expressed parasite miRNAs, stressing that they might be key players during the establishment and maintenance of infection. Additionally, we detected fragments derived from the processing of tRNAs, in all developmental stages analyzed, and documented the presence of novel long tRNA fragments enriched in vesicles. We confirmed the presence of at least 5 putative vault RNAs (vtRNAs), that are expressed across different stages and enriched in vesicles. The presence of tRNA fragments and vtRNAs in vesicles raise the possibility that they could be involved in the host-parasite interaction.

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“…piRNAs were not detected in Protozoa but were detected in C. elegans and Halichondria panicea , belonging to Nematoda and Porifera [ 14 , 21 ]. In Platyhelminthes, piRNAs were detected in planarians ( Schmidtea mediterranea ) [ 20 ] but were absent in flukes and tapeworms [ 94 ]. Ubiquitously expressed piRNAs were discovered in the soma and germ lines of Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca.…”

Section: Discovery Of Pirnas By Srna-seqmentioning

confidence: 99%

“…Next-generation sequencing (NGS) has been widely used for high-throughput characterization of sncRNAs. Increasingly, piRNAs have been discovered in the soma and germ lines of non-model organisms, including Platyhelminthes [ 20 ], Annelida [ 21 ], Cnidaria [ 22 , 23 , 24 , 25 ], Echinodermata [ 26 ], Mollusca [ 27 ], Crustacea [ 28 ], Arthropoda [ 29 ], Reptilia [ 30 ], and Mammals [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans

Huang

Yoshitake

Asakawa

2021

IJMS

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PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.

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Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Cited by 12 publications

References 88 publications

Stress response inEntamoeba histolyticais associated with robust processing of tRNA to tRNA-halves

Stress response inEntamoeba histolyticais associated with robust processing of tRNA to tRNA-halves

Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host

A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans

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