Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
Project description:Salt stress leads to devastating effects to agriculture. Presently, the key regulators that control transcriptional dynamics of salt-responsive genes remain poorly understood in plants. Here, we revealed that salt stress can substantially induce the kinase activity of Mediator subunit cyclin-dependent kinase 8 (CDK8), which is essential for its positive role in regulating salt tolerance. We subsequently uncovered that CDK8 phosphorylates the AT-hook motif nuclear-localized protein 10 (AHL10) at serine 314 through direct interaction, thereby promoting its protein degradation under salt stress. In addition, we created ahl10 mutants by CRISPR-Cas9 and showed the negative role of AHL10 in salt tolerance. Moreover, transcriptome analysis revealed that CDK8 regulates more than 20% of salt-responsive genes, about half of which are co-regulated by AHL10. Chromatin immunoprecipitation sequencing (ChIP-seq) further demonstrated that AHL10 binds to the AT-rich DNA sequence related to the nuclear matrix-attachment regions (MARs) in the salt-responsive gene promoters to repress their transcription. Importantly, we further found that AHL10 physically interacts with SU(VAR)3-9 homologs SUVH2/9, thereby repressing transcription of salt-responsive genes in a H3K9me2-dependent epigenetic regulatory manner. Overall, our study identified the CDK8-AHL10-SUVH2/9 module as a key molecular switch controlling plant transcriptional dynamics in response to salt stress.
Project description:Chronic myeloid leukemia (CML) epitomizes successful targeted therapy, with 86% of patients in the chronic phase treated with tyrosine kinase inhibitors (TKIs) attaining remission. However, resistance to TKIs occurs during treatment, and patients with resistance to TKIs progress to the acute phase called Blast Crisis (BC), wherein the survival is restricted to 7-11 months. About 80 % of patients in BC are unresponsive to TKIs. This issue can be addressed by identifying a molecular signature which can predict resistance in CML-CP prior to treatment as well as by delineating the molecular mechanism underlying resistance. Herein, we report genomic analysis of CML patients and imatinib-resistant K562 cell line to achieve the same. WGS was performed on imatinib-sensitive and -resistant K562 cells. Library preparation was done by 30x WGS KAPA PCR-Free v2.1 kit, and Illumina HiSeq X sequencer was used for 2 x 150 bp paired-end sequencing. Our study identified accumulation of aberrations on chromosomes 1, 3, 7, 16 and 22 as predictive of occurrence of resistance. Further, recurrent amplification in chromosomal region 8q11.2-12.1 was detected in highly resistant K562 cells as well as CML patients. The genes present in this region were analyzed to understand molecular mechanism of imatinib resistance.