Scientific Topics

Publication: “Subtelomeres constitute a safeguard for gene expression and chromosome homeostasis”

Nucleic Acids Research Breakthrough article describes the biological role of subtelomeric sequences in chromosome maintenance and chromatin structure.

Research teams led by Dr. Junko Kanoh at Osaka University and by Kunihiro Ohta at the University of Tokyo (Japan), have described a study of the biological function of subtelomeric homologous (SH) sequences (and of subtelomeres more generally) through phenotypic analysis of a Schizosaccharomyces pombe (fission yeast) mutant in which all SH sequences in the genome were deleted.

 

NAR_Breakthrough.pdf

 

 

A paper by Dr. Gert-Jan Bekker has been published from Journal of Chemical Theory and Computation with its cover picture of the Issue 7, 2017.

A paper”Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and its Inhibitor (http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b01127, DOI: 10.1021/acs.jctc.6b01127) by Dr. Gert-Jan Bekker, who is a Specially Appointed Assistant Professor in IPR, has been published from Journal of Chemical Theory and Computation (JCTC, IF=5.301) with its cover picture of the Issue 7, 2017.

 

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Press Release: Calredoxin, a novel protein for promoting efficient photosynthesis

Outline

A group of researchers reports on the structure and function of a novel protein named “Calredoxin”. Calredoxin binds calcium and catalyzes in dependence of its binding, redox reactions, particularly driving the detoxification of harmful oxygen species. The researchers are exploring how this protein functions at the crossroad of calcium- and redox-dependent reactions to promote efficient oxygenic photosynthesis.

Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing.

A chromosome is composed of structurally and functionally distinct domains. However, the molecular mechanisms underlying the formation of chromatin structure and the function of subtelomeres, the telomere-adjacent regions, remain obscure. Here we report the roles of the conserved centromeric protein Shugoshin 2 (Sgo2) in defining chromatin structure and functions of the subtelomeres in the fission yeast Schizosaccharomyces pombe.

Received the Most-downloaded Publication Award Q3 2015! Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR

・Magic-angle spinning (MAS) NMR probe system with a closed-loop helium recirculation.
・Stable MAS for weeks at sample temperature T = 35 K without consuming helium.
・Multi-dimensional MAS NMR at T = 35 K at a low running cost for electricity 16 kW/h.
・An order of magnitude sensitivity gain at T = 40 K and B0 = 16.4 T.

Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution.

5-Methylcytosine (5mC) is oxidized by ten-eleven translocation (TET) enzymes. This process followed by thymine DNA glycosylase is proposed to be the mechanism for methylcytosine demethylation. 5-Hydroxymethylcytosine (5hmC) is one of the most important key oxidative metabolites in the demethylation process, and therefore, simple and accurate method to determine 5hmC at single base resolution is desired. In the present study, we developed a mild catalytic oxidation of 5-hmC using micelle incarcerated oxidants that enables to determine the position of 5hmC at single base resolution.

The RFTS (replication foci targeting sequence) domain of Dnmt1 is not only necessary for replication-coupled maintenance DNA methylation, but also protects genome from aberrant DNA methylation.

In mammals, DNA methylation plays important roles in embryogenesis and terminal differentiation via regulation of the transcription-competent chromatin state. The methylation patterns are propagated to the next generation during replication by maintenance DNA methyltransferase, Dnmt1, in co-operation with Uhrf1.

Development of a novel method to analyze 5-hydroxymethylcytosine in the CpG sequence of the genome using maintenance DNA methyltransferase, DNMT1.

In mammals, cytosine in the CpG sequence is often methylated by DNA methyltransferase (Dnmt). Methylated cytosine (5mC) plays crucial roles in gene silencing, genomic imprinting, X-chromosome inactivation and the stability of genomic DNA. Aberrant DNA methylation causes embryonic lethality and cancer. Recently, 5-hydoxymethylcytosine (5hmC) was discovered to be a new modification of cytosine, being an intermediate of the demethylation process, and thus is implicated in the pluripotency of stem cells, development, and disease. Therefore, it is quite important to develop the technique to analyze the position of 5hmC in genome. To determine 5hmC at single-base resolution, several techniques have been reported. However, each method has advantages and disadvantages.