bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/237099

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

Erdogan, I.·Cosacak, M. I. I.·Nalbant Aldanmaz, A.·Akgul, B.
View original source ↗Export metadata ↓

Abstract

microRNAs (miRNAs) are small non-coding RNAs of about 19-25 nt that regulate gene expression post-transcriptionally 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 Jurkat T cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of two Jurkat sub-populations: one that is sensitive to camptothecin and the other being rather intrinsically resistant. We sorted apoptotic Jurkat cells from the non-apoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs were dysregulated. Interestingly, apoptotic and non-apoptotic sub-populations exhibited a distinct miRNA expression profile. In particular, 6 miRNAs were inversely expressed in these two sub-populations. 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.

Source connections

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Erdogan, I., Cosacak, M. I. I., Nalbant Aldanmaz, A., Akgul, B.. 2017-12-19. Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis. https://doi.org/10.1101/237099

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

IER3-N-cadherin axis contributes to apoptosis resistance in dermal fibroblasts under profibrotic conditions

Background: Persistent activation and resistance to apoptosis of dermal fibroblasts contribute to pathological skin fibrosis. Immediate early response 3 (IER3) is a stress-responsive protein involved in cell survival, but its role in cutaneous fibrosis remains unclear. We investigated the functional significance of IER3 in dermal fibroblasts and its potential contribution to fibrosis. Methods: IER3 expression was examined in skin samples from patients with systemic sclerosis, keloids, and hypertrophic scars. Primary human dermal fibroblasts were stimulated with transforming growth factor-{beta}1 (TGF-{beta}1). RNA sequencing, siRNA-mediated gene silencing, quantitative PCR, and flow cytometric apoptosis assays were performed to investigate the downstream mechanisms and functional consequences of IER3 expression. Results: IER3 expression was increased in dermal fibroblasts within fibrotic skin lesions and was induced by TGF-{beta}1 independently of SMAD3 and MEK/ERK signaling. Transcriptomic analysis identified CDH2, encoding N-cadherin, as a downstream target of IER3. Moreover, TGF-{beta}1 induced CDH2 expression in a SMAD3 phosphorylation-dependent manner. IER3 knockdown attenuated TGF-{beta}1-induced CDH2 expression, whereas CDH2 knockdown did not affect IER3 expression. Furthermore, CDH2 knockdown enhanced staurosporine-induced apoptosis in TGF-{beta}1-stimulated fibroblasts, accompanied by a shift in apoptosis-related gene expression toward a pro-apoptotic profile. Conclusion: Our findings identify a previously unrecognized IER3-N-cadherin regulatory axis that may promote dermal fibroblast survival by suppressing apoptosis under profibrotic conditions. Targeting this pathway may represent a novel therapeutic strategy for persistent skin fibrosis.

molecular biology↗
bioRxiv2026

Molecular basis of Cyclin B1-CDK1 recruitment by MAD1

The interaction between Cyclin B1-CDK1 and MAD1 recruits kinase activity to the nuclear pore complex and kinetochore corona to sustain spindle assembly checkpoint (SAC) signaling. Here, we characterize a short linear motif (SLiM) within MAD1 that mediates its interaction with Cyclin B1. This SLiM peptide is specific for B-type cyclins and lacks the canonical "RxL" cyclin-binding consensus sequence, suggesting a distinct mode of cyclin recognition. Using a combination of deep mutational scanning, structural analysis by cryogenic electron microscopy, and binding affinity measurements, we define the molecular basis of the Cyclin B1-MAD1 interaction. These approaches reveal that a short MAD1 peptide binds as an -helix to the RxL-binding hydrophobic patch of Cyclin B1. The interaction employs hydrophobic contacts that overlap with those used by canonical RxL motifs, but is distinguished by additional contacts and sequence features that confer preferential recognition by B-type cyclins while excluding other cyclin types. We also show that the MAD1 motif is sufficient to confer B-type cyclin-specific substrate phosphorylation in mitotic cells. Together, these findings reveal a non-canonical, B-type cyclin-specific helical binding mode that ensures selective Cyclin B1-CDK1 recruitment at two critical stages of SAC signaling, and suggest potential strategies for selective therapeutic targeting of this interaction.

molecular biology↗
bioRxiv2026

Characterizing nascent readthrough transcripts in human cells

Termination of transcription by RNA polymerase II (RNAPII) is critical to appropriately define transcriptome and proteome identity; yet mechanisms of termination regulation are incompletely understood. Current models suggest critical roles for the exonuclease XRN2, which is posited to "torpedo" out RNAPII after degrading uncapped and RNAPII-tethered nascent transcripts and posit an allosteric model wherein elongating RNAPII loses its processivity downstream of the transcription end site (TES) via unknown mechanisms. Here, we used nascent RNA Bru-seq to interrogate transcription termination across 16 human cell lines of distinct lineages, as part of the ENCODE 4 project, to identify key regulatory modes. We find that > 75% of protein-coding genes engage in readthrough transcription under homeostatic conditions. Exposing human cells to oxidative stress or hyperosmotic conditions or splicing inhibitors cause an increase in readthrough transcripts globally. Using an auxin-inducible degradation approach we find that depletion of BRD4, MED14 or XRN2 increases the extent and pervasiveness of readthrough transcripts while depletion of SUPT16H results in shorter readthrough transcripts. Our study provides a comprehensive view of homeostatic readthrough transcripts in human cells and delineates key components regulating transcription termination.

molecular biology↗