Small RNA data set that includes tRNA-derived fragments from Jurkat cells treated with camptothecin

In this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted two Jurkat subpopulations in treated cells: one that is sensitive to the drug and the other being relatively more resistant. We report new original data that include the frequency of tRNA-derived fragments (tRF) in drug-sensitive and resistant cells. We also present partially analyzed data to show the origin of reads on tRNAs as well as the borders of the fragments. We believe that this data can benefit the science community working in the field of tRF and/or apoptosis.The Scientific and Technical Research Council of Turkey ( 107T475 to BA

Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis

MicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events in T cells are partially known. However, heterogeneity associated with cell lines makes it difficult to interpret gene expression signatures, especially in cancer-related cell lines. Treatment of the Jurkat T-cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of two Jurkat subpopulations: one that is sensitive to camptothecin and another that is rather intrinsically resistant. We sorted apoptotic Jurkat cells from nonapoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs were dysregulated. Interestingly, the apoptotic and nonapoptotic subpopulations exhibited distinct miRNA expression profiles. In particular, 6 miRNAs were inversely expressed in these two subpopulations. The pyrosequencing results were validated by real-time qPCR. Altogether, these results suggest that miRNAs modulate apoptotic events in T cells and that cellular heterogeneity requires careful interpretation of miRNA expression profiles obtained from drug-treated cell lines.İYTE BİYOMER and TUBITAK (grant 107T475

Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos

Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0-1 h and 7-8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0-1 h and 7-8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery. Although most micro RNAs (miRNAs) did not have a specific preference for any state of the translational machinery, we detected fraction-specific enrichment of a few miRNAs such as dme-miR-1-3p, -184-3p, 5-5p and 263-5p. More interestingly, we observed changes in the subcellular location of a subset of miRNAs in fractionated embryos despite no measurable difference in their amount in unfractionated embryos. Transposon-derived endo small interfering RNAs (siRNAs) were over-expressed in 7-8 h embryos and associated mainly with the mRNP fraction. In contrast, transposon-derived PIWI-interacting RNAs (piRNA), which were more abundant in 0-1 h embryos, co-sedimented primarily with the polysome fractions. These results suggest that there appears to be a complex interplay among the small RNAs with respect to their polysome-cosedimentation pattern during early development in Drosophila melanogaster.The Scientific and Technical Research Council of Turkey [104T144 to BA]; Pennsylvania State Universit

Differentially expressed tRNA-derived small RNAs co-sediment primarily with non-polysomal fractions in Drosophila

Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5’ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following thematernal-to-zygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. Differential tRF expression pattern points to developmental significance at the organismal level. These results suggest that tRFs are associated primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.Scientific and Technical Research Council of Turkey (210T006