Shulamit Michaeli

trans and cis Splicing in Trypanosomatids: Mechanism, Factors, and Regulation

mRNA maturation in trypanosomes differs from the process in most eukaryotes mainly because protein-coding genes are transcribed into polycistronic RNAs in this organism ([78][1]). Studies from the ongoing genome project suggest that the entire chromosome may be transcribed as large transcripts, but

The spliced leader-associated RNA is a trypanosome-specific sn(o) RNA that has the potential to guide pseudouridine formation on the SL RNA.

The spliced leader-associated (SLA1) RNA is a trypanosome-specific small RNA with unknown function. SLA1 carries a Sm-like site, and is associated with core Sm proteins. Here we found that SLA1 belongs to a family of hairpin-containing RNAs that are implicated in directing pseudouridylation. A potential for base-pair interaction between SLA1 and spliced leader (SL) RNA agrees with the canonical rules for guiding pseudouridylation on SL RNA. Direct RNA analysis showed that this uridine is indeed pseudouridylated in the SL RNA of Leptomonas collosoma, Leishmania major, and Trypanosoma brucei. This position is conserved in all trypanosomatid SL RNAs. Mutations introduced in the SL RNA to disrupt the interaction domain of SLA1/SL RNA abolished the formation of the pseudouridine. SLA1 is localized both to the nucleolus and nucleoplasm. This study solves a long-standing question regarding the function of this novel RNA and describes the first H/ACA RNA, which, unlike all other pseudouridine guides, is also a bona fide snRNA.

Trans-splicing in trypanosomes: machinery and its impact on the parasite transcriptome

In trypanosomes, all RNAs are processed by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common spliced leader (SL) is donated to all mRNAs from a small RNA molecule, the SL RNA. This article summarizes recent findings in the field focusing on SL RNA transcription, cap modifications and pseudouridylation. The role(s) of these modifications for splicing and gene expression are discussed. The recruitment of SL RNA to the spliceosome depends on splicing factors and recent progress in identifying such factors is described. A recent major advance in understanding the role of trans-splicing in the trypanosome transcriptome was obtained by whole-genome mapping of the SL and polyadenylation sites, revealing surprising heterogeneity and suggesting that gene regulation, especially during cycling between the two hosts of the parasite, involves alternative trans-splicing. Finally, the SL silencing mechanism, which is harnessed by the parasite to control gene expression under stress, is discussed.

Persistent ER Stress Induces the Spliced Leader RNA Silencing Pathway (SLS), Leading to Programmed Cell Death in Trypanosoma brucei

Trypanosomes are parasites that cycle between the insect host (procyclic form) and mammalian host (bloodstream form). These parasites lack conventional transcription regulation, including factors that induce the unfolded protein response (UPR). However, they possess a stress response mechanism, the spliced leader RNA silencing (SLS) pathway. SLS elicits shut-off of spliced leader RNA (SL RNA) transcription by perturbing the binding of the transcription factor tSNAP42 to its cognate promoter, thus eliminating trans-splicing of all mRNAs. Induction of endoplasmic reticulum (ER) stress in procyclic trypanosomes elicits changes in the transcriptome similar to those induced by conventional UPR found in other eukaryotes. The mechanism of up-regulation under ER stress is dependent on differential stabilization of mRNAs. The transcriptome changes are accompanied by ER dilation and elevation in the ER chaperone, BiP. Prolonged ER stress induces SLS pathway. RNAi silencing of SEC63, a factor that participates in protein translocation across the ER membrane, or SEC61, the translocation channel, also induces SLS. Silencing of these genes or prolonged ER stress led to programmed cell death (PCD), evident by exposure of phosphatidyl serine, DNA laddering, increase in reactive oxygen species (ROS) production, increase in cytoplasmic Ca2+, and decrease in mitochondrial membrane potential, as well as typical morphological changes observed by transmission electron microscopy (TEM). ER stress response is also induced in the bloodstream form and if the stress persists it leads to SLS. We propose that prolonged ER stress induces SLS, which serves as a unique death pathway, replacing the conventional caspase-mediated PCD observed in higher eukaryotes.

Silencing of Sm proteins in Trypanosoma brucei by RNA interference captured a novel cytoplasmic intermediate in spliced leader RNA biogenesis.

In Trypanosoma brucei the small nuclear (sn) RNAs U1, U2, U4, and U5, as well as the spliced leader (SL) RNA, bind the seven Sm canonical proteins carrying the consensus Sm motif. To determine the function of these proteins in snRNA and SL RNA biogenesis, two of the Sm core proteins, SmE and SmD1, were silenced by RNAi. Surprisingly, whereas the level of all snRNAs, including U1, U2, U4, and U5 was reduced during silencing, the level of SL RNA was dramatically elevated, but the levels of U6 and spliced leader-associated RNA (SLA1) remained unchanged. The SL RNA that had accumulated in silenced cells lacked modification at the cap4 nucleotide but harbored modifications at the cap1 and cap2 nucleotides and carried the characteristic ψ. This SL RNA possessed a longer tail and had accumulated in the cytoplasm in 10 and 50 S particles that were found by in situ hybridization to be present in “speckles.” We propose a model for SL RNA biogenesis involving a cytoplasmic phase and suggest that the trypanosome-specific “cap4” nucleotides function as a signal for export and import of SL RNA out and into the nucleus. The SL RNA biogenesis pathway differs from that of U sn ribonucleoproteins (RNPs) in that it is the only RNA that binds Sm proteins that were stabilized under Sm depletion in a novel RNP, which we termed SL RNP-C.

Small nucleolar RNA interference induced by antisense or double-stranded RNA in trypanosomatids.

In trypanosomes the C/D- and H/ACA-like small nucleolar RNAs (snoRNAs) are clustered and repeated in the genome. The snoRNAs studied to date are transcribed as polycistronic transcripts by RNA polymerase II and then processed, resulting in mature snoRNAs. In this study we demonstrated that snoRNA genes can be silenced in three trypanosomatid species: Leptomonas collosoma, Leishmania major, and Trypanosoma brucei. Silencing was achieved in L. collosoma and L. major by the expressing of an antisense transcript complementary to the snoRNA gene and was accompanied by the accumulation of small interfering RNA. Silencing eliminated the mature snoRNA but not its precursor and abolished the specific 2′-O-methylation guided by the snoRNA. In T. brucei, silencing was achieved by using the inducible synthesis of double-stranded RNA from T7 opposing promoters. Silencing varied between the different snoRNA genes, which may reflect the accessibility of small interfering RNA to the target RNAs. This study suggests that RNA interference can degrade snoRNAs. This study has further implications in elucidating the function of nucleolar RNAs and specific modifications guided by these RNAs in trypanosomatids and perhaps in other eukaryotes as well.

Spliced‐leader RNA silencing: a novel stress‐induced mechanism in Trypanosoma brucei

The signal‐recognition particle (SRP) mediates the translocation of membrane and secretory proteins across the endoplasmic reticulum upon interaction with the SRP receptor. In trypanosomes, the main RNA molecule is the spliced‐leader (SL) RNA, which donates the SL sequence to all messenger RNA through trans‐splicing. Here, we show that RNA interference silencing of the SRP receptor (SRα) in Trypanosoma brucei caused the accumulation of SRP on ribosomes and triggered silencing of SL RNA (SLS). SLS was elicited due to the failure of the SL RNA‐specific transcription factor tSNAP42 to bind to its promoter. SL RNA reduction, in turn, eliminated mRNA processing and resulted in a significant reduction of all mRNA tested. SLS was also induced under pH stress and might function as a master regulator in trypanosomes. SLS is reminiscent of, but distinct from, the unfolded protein response and can potentially act as a new target for parasite eradication.

Silica Nanoparticles and Polyethyleneimine (PEI)-Mediated Functionalization: A New Method of PEI Covalent Attachment for siRNA Delivery Applications

Small-interfering RNA (siRNA) is a synthetic double-stranded RNA that consists of approximately 21 nucleotides (nts). It induces degradation of target mRNAs in a sequence-specific manner by the RNA interference (RNAi) mechanism. Thus, siRNAs offer a potential strategy for silencing mutated or defective genes that cause a variety of human diseases. The main obstacles of harnessing siRNAs as drugs are their inefficient delivery to cells and off-target effect making clinical applications very challenging. To address these issues, researchers have studied a variety of nanocarrier systems for siRNA delivery. This study presents the design, fabrication, and full characterization of innovative polyethyleneimine (PEI)-decorated polycationic 34.2 ± 4.2 nm silica (SiO2) NPs for siRNA-mediated gene silencing. More specifically, a new means of introduction (covalent mode of attachment) of the polycationic 25 kDa PEI polymer onto the SiO2 NP surface has been developed that makes use of an effective electrophilic double Michäel acceptor, divinyl sulfone (DVS). The resulting novel SiO2-PEI nanoparticles (SPEI NPs) have been fully characterized using a wide range of analytical, spectroscopic, and microscopic methods (TEM, DLS, ζ potential, elemental analysis (EA), XPS, TGA, and FTIR). Disclosing quite low cytotoxicity due to this unique mode of PEI covalent grafting, SPEI NPs/siRNA polyplexes have been successfully tested for the induction of gene silencing using dual-reporter luciferase transfected human osteosarcoma U2OS cells. The corresponding gene silencing data showed a clear correlation between PEI/siRNA ratios, siRNA concentration(s), and the level of gene silencing. Moreover, these SPEI NPs have been demonstrated to be thermodynamically stable with an ability to efficiently bind siRNAs and induce silencing for at least a one-year-long storage.

On the role of exon and intron sequences in trans-splicing utilization and cap 4 modification of the trypanosomatid Leptomonas collosoma SL RNA.

In trypanosomatid protozoa the biogenesis of mature mRNA involves addition of the spliced leader (SL) sequence from the SL RNA to polycistronic pre-mRNA viatrans-splicing. Here we present a mutational analysis of the trypanosomatid Leptomonas collosoma SL RNA to further our understanding of its functional domains important fortrans-splicing utilization. Mutant SL RNAs were analyzed for defects in modification of the hypermethylated cap structure (cap 4) characteristic of trypanosomatid SL RNAs, for defects in the first step of the reaction and overall utilization intrans-splicing. Single substitution of the cap 4 nucleotides led to undermethylation of the cap 4 structure, and these mutants were all impaired in their utilization intrans-splicing. Abrogation of the sequence of the Sm-like site and sequences downstream to it also showed cap modification andtrans-splicing defects, thus providing further support for a functional linkage between cap modifications andtrans-splicing. Further, we report that in L. collosoma both the exon and intron of the SL RNA contribute information for efficient function of the SL RNA intrans-splicing. This study, however, did not provide support for the putative SL RNA-U6 small nuclear RNA (snRNA) interaction at the Sm site like in the nematodes, suggesting differences in the bridging role of U6 in the twotrans-splicing systems.

miR-142 orchestrates a network of actin cytoskeleton regulators during megakaryopoiesis

Genome-encoded microRNAs (miRNAs) provide a posttranscriptional regulatory layer that controls the differentiation and function of various cellular systems, including hematopoietic cells. miR-142 is one of the most prevalently expressed miRNAs within the hematopoietic lineage. To address the in vivo functions of miR-142, we utilized a novel reporter and a loss-of-function mouse allele that we have recently generated. In this study, we show that miR-142 is broadly expressed in the adult hematopoietic system. Our data further reveal that miR-142 is critical for megakaryopoiesis. Genetic ablation of miR-142 caused impaired megakaryocyte maturation, inhibition of polyploidization, abnormal proplatelet formation, and thrombocytopenia. Finally, we characterized a network of miR-142-3p targets which collectively control actin filament homeostasis, thereby ensuring proper execution of actin-dependent proplatelet formation. Our study reveals a pivotal role for miR-142 activity in megakaryocyte maturation and function, and demonstrates a critical contribution of a single miRNA in orchestrating cytoskeletal dynamics and normal hemostasis. DOI: http://dx.doi.org/10.7554/eLife.01964.001