Project description:We present results of RNA-Seq, Ribo-Seq, and RIP-Seq (YB-1, YB-3) experiments performed in HEK293T cells, as well as in HEK293T cells with YB-1 knockout and overexpression. The data shows YB-1 function as a global translation inhibitor and YB-3 ability to substitute YB-1 in its function in YB-1 knockout mutant.
Project description:To understand the mechanistic basis of YB-1’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. (RIP) and sequencing of YB-1-bound RNAs was performed in the JJN3 line (two biological replicates/condition).
Project description:Total RNAs were isolated from WT_CON, KO_CON, WT_LPS and KO_LPS Raw 264.7 cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to Sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat , and gene expression levels were measured by Cufflinks.
Project description:To assess the direct association of the nucleic acid binding protein yb-1 with mature microRNAs in breast cancer. To do this we performed immunoprecipitation (IP) of YB-1 protein to pull-down linked RNAs Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. An input control represents the RNA present in the lysate used for the IP, prior to treatment.
Project description:CD4+ T cells were isolated by StemCell CD4+ T cell isolation kit of spleen and lymph nodes WT mice. Total RNAs were isolated from the pure CD4+ T cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat, and gene expression levels were measured by Cufflinks.
Project description:To assess the direct association of the nucleic acid binding protein yb-1 with mature microRNAs in breast cancer. To do this we performed immunoprecipitation (IP) of YB-1 protein to pull-down linked RNAs Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. An input control represents the RNA present in the lysate used for the IP, prior to treatment. IPs were performed in triplicates on different cell-lysates with one input control used as a representative of the RNA added to the IP reaction.
Project description:Armitage (Armi) is a component of Yb bodies and functions in the primary piRNA processing pathway. Armi interaction with Piwi does not require Yb expression; however, without Yb, the Armi-Piwi complex does not localize at Yb bodies and contains few piR-ILs (small RNAs associated with Armitage complex). These results suggest that only upon its localization at Yb bodies does the Armi-Piwi-Yb complex gain an opportunity to interact with piR-ILs. Currently, however, it remains unclear how piR-ILs are loaded onto the Piwi complex at Yb bodies and which protein(s) within the complex is directly bound to them.
Project description:PfNF-YB is a transcription factor of Plasmodium falciparum and is known as a CCAAT-box-binding subunit B. PfNF-YB belongs to NF-Y complex family that is conserved from yeast to human. PfNF-YB is highly expressed in schizont stage and co-localized at the nucleus in mature form during intraerythrocytic stage. We found that melatonin and cAMP second messenger can modulate the PfNF-YB expression in P. falciparum. To better understand the function of PfNF-YB in P. falciparum we proposed to perform chromatin immunoprecipitation (ChIP) of PfNF-YB together with chromatin profiling by ChIP-on-chip analysis. The results showed that PfNF-YB binds to CCAAT of several genes in schizont stage.
