ABSTRACT: Identification of cyclical expressed coding and non-coding genes during the circadian rhythm in NIH3T3 cells. NIH3T3 cells were synchronized for their circadian rhythm and RNA sequencing were performed at several time points along the rhythm. This data was used to identify cyclical expressed genes as well as long intergenic non-coding RNAs. NIH3T3 cells were synchronized with 100 nM Dexamethasone for 2 hours, then medium was changed to normal culture medium (0h). Every 4 hours cells were harvested, RNA isolated and RNAseq performed.
Project description:Identification of cyclical expressed coding and non-coding genes during the circadian rhythm in NIH3T3 cells. NIH3T3 cells were synchronized for their circadian rhythm and RNA sequencing were performed at several time points along the rhythm. This data was used to identify cyclical expressed genes as well as long intergenic non-coding RNAs.
Project description:Purpose: The purpose of this study is to investigate role of JNK signaling during EMT. Method: Transcriptome of TGF-b treated NmuMG cells along with DMSO and JNKi treated NMuMG was generated using next generation high throughput sequencing in triplicates and duplicates respectively. Reads were mapped using Tophat and transcript abundance and differential expression was calculated using HTSeq-Count and DESeq programs. Results: Using time course RNA-Seq data, we uncover a large number of coding and noncoding RNAs that are modulated during stepwise progression of TGF-?-induced EMT. Concomitant with their activation behavior, Smad and JNK pathway are required for onset and progression of EMT respectively, a finding that was also confirmed in patients. Transcriptome analysis further revealed a progressive dependency of EMT on JNK signaling. Conclusion: We identified several novel transcription factors that require JNK signaling for their enhanced expression upon EMT and show that depletion of these factors during EMT hampers acquisition of transcriptional and phenotypic changes hallmark of this process. These factors are similarly induced during neurogenesis, a process also involving JNK activation and EMT. Transcriptome of TGF-b treated NmuMG cells along with DMSO and JNKi treated NMuMG was generated using next generation high throughput sequencing in triplicates and duplicates respectively.
Project description:Molecular analysis of circadian rhythm in mice. Liver tissue of wildtype, Clock mutant and Cry deficient C57BL/6 8- to 10-week-old male mice examined. Keywords = circadian rhythm Keywords: other
Project description:Topoisomerases are essential for resolving topological problems in the genome, while their function in gene regulation, especially during cellular differentiation, remains unknown. We reveal that the expression of two Topo II isoforms, Top2a and Top2ß, is characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, Top2a preferentially binds to promoters embedded in an active chromatin environment. Inhibition of Top2a activity results in misregulation of target gene expression that accompanies accumulation of double-strand breaks. Common targets of Top2a and Top2ß are housekeeping genes while their unique targets are involved in proliferation/pluripotency and neurogenesis, respectively. Moreover, a subset of Top2a targets exhibit bivalent chromatin state that is resolved upon differentiation concomitant with their activation and occupancy by Top2ß, a feature further observed for long genes. These findings suggest that Top2a not only contributes to stem cell transcriptome regulation but may also prime developmental genes for subsequent activation upon differentiation. mRNA profiles of DMSO and ICRF-193 treated mESCs were generated by deep sequencing in triplicates. ICRF-193 is a well established catalytic inhibitor of Topoisomerase II, hence, we used ICRF-193 to the elucidate role of Top2a catalytic activity on transcription by genome wide transcription profiling.
Project description:We examined the biological difference between H1299 cells with the treatments targeting circadian rhythm in order to better understand circadian rhythm disruption as a feature of cancer. To this end, we knocked down CLOCK using siRNA (siCLOCK) or melatonin pre-treatment and assessed the gene expression pattern by RNA-Seq.