Korea Advanced Institute of Science and Technology · Biochemistry, Genetics and Molecular Biology
Professor Daeyoup Lee's research lab focuses on chromatin biology and gene regulation, with a central emphasis on epigenetic mechanisms controlling transcription. The lab investigates how post-translational modifications of histones—such as acetylation, methylation, and phosphorylation—coordinate gene expression during development and disease. Key research directions include the regulation of RNA polymerase II elongation, the role of chromatin remodeling complexes like SWI/SNF in tumor suppression, and the functional crosstalk between histone modifications and transcription factors such as p53 and HPV E2. The lab also develops innovative molecular tools and bioinformatics pipelines, such as the Octopus-toolkit, to enable high-throughput epigenomic and transcriptomic data analysis.
Figures are computed from collected data and may differ slightly.
Nucleosomes must be deacetylated behind elongating RNA polymerase II to prevent cryptic initiation of transcription within the coding region. RNA polymerase II signals for deacetylation through the methylation of histone H3 lysine 36 (H3K36), which provides the recruitment signal for the Rpd3S histone deacetylase complex (HDAC). The recognition of methyl H3K36 by Rpd3S requires the chromodomain of its Eaf3 subunit. Paradoxically, Eaf3 is also a subunit of the NuA4 acetyltransferase complex, yet
The SWI/SNF complex is required for the transcription of several genes and has been shown to alter nucleosome structure in an ATP-dependent manner. The tumor suppressor protein p53 displays growth and transformation suppression functions that are frequently lost in mutant p53 proteins detected in various cancers. Using genetic and biochemical approaches, we show that several subunits of the human SWI/SNF complex bind to the tumor suppressor protein p53 in vivo and in vitro. The transactivation f
Phosphoserine incorporation: A general strategy for producing recombinant histones with site-specific serine phosphorylation is developed by engineering phosphoseryl-tRNA synthetase (SepRS) and elongation factor Tu (EF-Tu; see picture). Serine-phosphorylated nucleosomes provide direct evidence for crosstalk between phosphorylation and acetylation in histones.
cAMP response element-binding protein-binding protein (CBP) is a eucaryotic transcriptional co-activator that contains multiple protein-protein interaction domains for association with various transcription factors, components of the basal transcriptional apparatus, and other co-activator proteins. Here, we report that CBP is also a co-activator of the human papillomavirus (HPV) E2 protein, which is a sequence-specific transcription/replication factor. We provide biochemical, genetic, and functi
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcripto
The transcriptional regulation of the human telomerase reverse transcriptase (hTERT) gene is a critical step in transformation and differentiation. Human papillomavirus E2 protein inhibits cell growth in HPV-infected cells and triggers apoptosis in HeLa cells. Because E2 induces cell growth suppression and senescence, we hypothesize that the protein may modulate cellular gene expression related to these processes. In this report, we demonstrate that E2 inhibits the hTERT promoter. The mapping of
p300/CREB-binding protein-associated factor (p/CAF), a transcriptional co-activator, interacts with co-activator p300/CBP and acidic transcription factors. p/CAF mediates transcriptional activation by acetylating nucleosomal histones and cellular factors. Previously we reported that CBP binds to human papillomavirus E2 and activates E2-dependent transcription (Lee, D., Lee, B., Kim, J., Kim, D. W., and Choe, J. (2000) J. Biol. Chem. 275, 7045-7051). Here we show that p/CAF binds to the human pap
BRG-1, a component of the human SWI/SNF complex, either activates or represses cellular promoters by modulating chromatin structure via the formation of a multiple polypeptide complex. Human papillomavirus E7 binds and destabilizes pRb, resulting in the blockage of G(1) arrest in the cell cycle. We show here that the high-risk human papillomavirus E7 protein group binds BRG-1 and modulates repression of the c-fos promoter mediated by this protein. In addition, both wild-type and Rb binding-defec
Cumulative evidence suggests that non-proteolytic functions of the proteasome are involved in transcriptional regulation, mRNA export, and ubiquitin-dependent histone modification and thereby modulate the intracellular levels of regulatory proteins implicated in controlling key cellular functions. To date, the non-proteolytic roles of the proteasome have been mainly investigated in euchromatin; their effects on heterochromatin are largely unknown. Here, using fission yeast as a model, we randoml
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