Dincaslan, F. B. | Search bioRxiv

bioRxiv2024

Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq

Detecting the complete portrait of the transcriptome is essential to understanding the roles of both polyadenylated and non-polyadenylated RNA species. However, current efforts to investigate the heterogeneity of the total cellular transcriptome in single cells are limited by the lack of an automated, high-throughput assay that can be carried out on existing platforms. To address this issue, we developed scComplete-seq, a method that can easily augment existing high-throughput droplet-based single-cell mRNA sequencing to provide additional information on the non-polyadenylated transcriptome. Using scComplete-seq, we have successfully detected long and short non-polyadenylated RNAs at single-cell resolution, including cell-cycle-specific histone RNAs, cell-type-specific short non-coding RNA, as well as enhancer RNAs in cancer cells and PBMCs. By applying scComplete-seq, we have identified changes in both coding and non-coding transcriptome in PBMCs during different stimulations. Measuring the enhancer RNA expression also revealed the activation of specific biological processes and the transcription factors regulating such changes.

genomics↗

bioRxiv2020

ace2 expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafish

Human Angiotensin I Converting Enzyme 2 (ACE2) that acts as a receptor for SARS-CoV-2 entry is highly expressed in human type II pneumocytes and enterocytes and similarly in other mammals and zebrafish (Danio rerio). The zebrafish genome has a highly conserved, one-to-one ortholog of ACE2, i.e., ace2, whose expression profile however has not yet been studied during development or in pathologies relevant to COVID-19. Herein, we identified significant development-, tissue- and gender-specific modulations in ace2 expression based on meta-analysis of zebrafish Affymetrix transcriptomics datasets (ndatasets=107, GPL1319 in GEO database). Co-expression network analysis of ace2 revealed distinct positively correlated (carboxypeptidase activity and fibrin clot formation), and negatively correlated (cilia biogenesis/transport and chromatin modifications) STRING network modules. Using additional transcriptomics datasets, we showed zebrafish embryos before 3 days post fertilization (dpf) exhibited low levels of ace2 that increased significantly until 4 dpf implicating a role for ace2 in organogenesis. Re-analysis of RNA-seq datasets from zebrafish adult tissues demonstrated ace2 was expressed highly in intestines, variably in liver, and at lower levels in other organs. In addition, zebrafish females and males showed significant dimorphism in their age-dependent expression of ace2, and between ovary and testis where the latter had higher levels. Moreover, we demonstrated ace2 expression was significantly modulated under different physiological and pathological conditions associated with development, diet, infection, and inflammation. Our findings implicate a novel translational role for zebrafish ace2 in differentiation and pathologies predominantly found in intestines and liver, in which the effects of SARS-CoV-2 could be detrimental.

molecular biology↗