Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.

Katsuhiko Minami, Kako Nakazato, Satoru Ide, Kazunari Kaizu, Koichi Higashi, Sachiko Tamura, Atsushi Toyoda, Koichi Takahashi, Ken Kurokawa, Kazuhiro Maeshima*
*corresponding author

Science Advances (2025) 11, eadu8400 DOI:10.1126/sciadv.adu8400

Press release (In Japanese only)

A string of nucleosomes, where genomic DNA is wrapped around histones, is organized in the cell as chromatin, ranging from euchromatin to heterochromatin, with distinct genome functions. Understanding physical differences between euchromatin and heterochromatin is crucial, yet specific labeling methods in living cells remain limited. Here, we have developed replication-dependent histone (Repli-Histo) labeling to mark nucleosomes in euchromatin and heterochromatin based on DNA replication timing (Fig. 1). Using this approach, we investigated local nucleosome motion in the four known chromatin classes, from euchromatin to heterochromatin, of living human and mouse cells. The more euchromatic (earlier-replicated) and more heterochromatic (later-replicated) regions exhibit greater and lesser nucleosome motions, respectively. Notably, the motion profile in each chromatin class persists throughout interphase. Genome chromatin is essentially replicated from regions with greater nucleosome motions, even though the replication timing is perturbed. Our findings, combined with computational modeling, suggest that earlier-replicated regions have more accessibility, and local chromatin motion can be a major determinant of genome-wide replication timing (Fig. 2).

• The article of “EurekAlert!” is here.

Figure1: (Top) The replication-dependent histone labeling (Repli-Histo labeling) specifically visualizes euchromatin (IA and IB), where gene expression is active, and heterochromatin (II and III), where it is repressed. (Bottom) The fluorescently labeled single-nucleosomes in euchromatin (left) and heterochromatin (right) in living HeLa cells. Each dot represents a single nucleosome.

Figure2: Euchromatic regions (IA and IB) exhibit greater nucleosome motion, whereas heterochromatic regions (II and III) show more restricted motion. The nucleosome motions facilitate chromatin accessibility to large proteins (purple), which can regulate various genomic functions, including DNA replication and transcription.

Minami, Katsuhiko(Genome Dynamics Laboratory, Thesis Advisor: Dr. Maeshima, Kazuhiro)
Thesis Title: Replication-dependent histone (Repli-Histo) labeling dissects the physical properties of euchromatin/heterochromatin in living human cells

Iida, Shiori(Genome Dynamics Laboratory, Thesis Advisor: Dr. Maeshima, Kazuhiro）
Thesis Title: How nuclear environment influences chromatin motion and organization

Hatoyama, Yuki(Molecular Cell Engineering Laboratory, Thesis Advisor: Dr. Kanemaki, Masato)
Thesis Title: A combinational degron system with AID2 and BromoTag uncovers the relationship between DNA replication and the cell cycle

▶ The Morishima Award

▶ — Professor Emeritus — MORISHIMA, Hiroko

The National Institute of Genetics (NIG) invites applications for one full or associate professor position in the field of human genetics. Please see the details below and apply accordingly.
Application Guidelines：PDF  　　Application Materials：Brief summary of career(excel)  

1. Division: Department of Informatics

2. Recruiting: Full /Associate Professor (1 qualified person)

3. Appointment Start Date: On and after August 2025 (negotiable)

4. Term of Appointment:
Indefinite term appointment (until the mandatory retirement age of 65, based on the regulations of the Research Organization of Information and Systems)

5. Qualifications:
The successful candidate should have excellent research achievements in the field of human genetics and possess the expertise and leadership to conduct integrated research utilizing the research infrastructure of related institutions in and outside of Japan including NIG.

6. Responsibilities:
The appointed researcher will lead an independent laboratory as a principal investigator. He or she will also participate in the education of graduate students as a faculty member of the Genetics Program of SOKENDAI.

7. Research environment and support:
・As an Inter-University Research Institute, NIG provides substantial common equipment and research infrastructure and promotes collaborative research worldwide. We expect the appointed researcher to take advantage of this research environment to organize and lead his/her research team.
・One assistant professor and one technical support staff member will be allocated to the laboratory.

8. Application Deadline: Noon (Japan Time) on May 7, 2025

9. Application Materials:
I. Curriculum Vitae (In English. Japanese applicants should also submit a Japanese version. Include your e-mail address.)
II. List of publications (If there are multiple authors, briefly describe your contribution. Indicate your most significant papers.)
III. Summary of past and present research and future directions (In English, max. 1,500 words. Include figures if necessary.)
IV. Names and contacts of references (At least two domestic and two international references.)
V. Summary of career
VI. Your key papers
*All the personal data in the application is handled in strict confidentiality, and used solely for recruitment purposes.

10. Submission:
Submit items I to VI listed above electronically as follows:
(a) The subject line should be “Application for Department of Informatics Full / Associate Professor”, which should be also noted in the e-mail body.
(b) Put items I to IV together in a single file by separating each item by page. E-mail the file as an attachment. The file format should be MS Word or PDF. Also attach item V (form can be downloaded from the NIG homepage) as a separate file.
(c) Send your key papers as PDF attachments. The file format should be PDF. If your key papers are available to access online, include a list of URLs in the e-mail body.

* We will notify you via e-mail upon receipt of your electronic application within two business days.

Based on gender equality National Institute of Genetics has been actively promoting female scientists. In case of equivalent aptitude and achievements in research, education, and social contributions, preference will be given to female candidates.

National Institute of Genetics is promoting safety and healthy working, including preventing passive smoking. (Indoor smoking is banned. / Smoking is allowed only in the designated outdoor areas.)

Send your application and inquiries to:
NIG Personnel Committee (Personnel Team)
E-mail:
Mailing Address:
National Institute of Genetics
Yata 1111, Mishima, Shizuoka 411-8540 JAPAN
TEL: +81-55-981-6716
FAX: +81-55-981-6715
Homepage: https://www.nig.ac.jp/nig/
NIG Organization Chart: https://www.nig.ac.jp/nig/research/organization-top/organization

The National Institute of Genetics (NIG) invites one assistant professor for basic research related to the nervous system, research on neurological diseases, or development of genetic tools. Please see the details below and apply accordingly.
Application Guidelines：PDF  　　Application Materials：Brief summary of career(excel)  

1. Division: Neurobiology and Pathology Laboratory, Department of Gene Function and Phenomics (Asakawa Group)

2. Recruiting: Assistant Professor (1 qualified person)

3. Appointment Start Date: On and after August 2025 (negotiable)

4. Term of Appointment:
5 years
One-time extension of five additional years would be possible based on evaluation.
(For those who are/were employed by The Research Organization of Information and Systems (ROIS) at any time between April 1st, 2013 and the day before the starting date of this advertised position, the aforesaid term(s) of employment will be subtracted from the term of appointment.)

5. Qualifications:
The successful candidate is expected to demonstrate strong motivation for conducting basic research on the nervous system, investigating neurological disorders, or developing genetic tools, using zebrafish as a model, in collaboration with Associate Professor Kazuhide Asakawa.

6. Salary and Allowance: Based on ROIS Regulations

7. Social Insurance:
MEXT Mutual Society of Health Insurance
Worker’s Accident Compensation Insurance
Employment Insurance

8. Work Hours: Discretionary Labor System

9. Holiday: Saturday and Sunday, National Holidays,
From December 29th to January 3rd (New Year’s Break), Summer Break

10. Application Deadline: Noon (Japan Time) on May 7, 2025

11. Application Materials:
I. Curriculum Vitae (In English. Japanese applicants should also submit a Japanese version. Include your e-mail address.)
II. List of publications (If there are multiple authors, briefly describe your contribution. Indicate your most significant papers.)
III. Summary of past and present research and future directions (In English, max. 1,500 words. Include figures if necessary.)
IV. Names and contacts of references (two to four references including at least one international reference is desirable.)
V. Summary of career
VI. Your key papers
*All the personal data in the application is handled in strict confidentiality, and used solely for recruitment purposes.

12. Submission:
Submit items I to VI listed above electronically as follows:
(a) The subject line should be “Application for Neurobiology and Pathology Laboratory Assistant Professor”, which should be also noted in the e-mail body.
(b) Put items I to IV together in a single file by separating each item by page. E-mail the file as an attachment. The file format should be MS Word or PDF. Also attach item V (form can be downloaded from the NIG homepage) as a separate file.
(c) Send your key papers as PDF attachments. The file format should be PDF. If your key papers are available to access online, include a list of URLs in the e-mail body.

* We will notify you via e-mail upon receipt of your electronic application within two business days.

Based on gender equality National Institute of Genetics has been actively promoting female scientists. In case of equivalent aptitude and achievements in research, education, and social contributions, preference will be given to female candidates.

National Institute of Genetics is promoting safety and healthy working, including preventing passive smoking. (Indoor smoking is banned. / Smoking is allowed only in the designated outdoor areas.)

Send your application and inquiries to:
NIG Personnel Committee (Personnel Team)
E-mail:
Mailing Address:
National Institute of Genetics
Yata 1111, Mishima, Shizuoka 411-8540 JAPAN
TEL: +81-55-981-6716
FAX: +81-55-981-6715
Homepage: https://www.nig.ac.jp/nig/
NIG Organization Chart: https://www.nig.ac.jp/nig/research/organization-top/organization

The National Institute of Genetics (NIG) invites applications for one assistant professor position in the field of Biophysics or Molecular and Cellular Biology. Please see the details below and apply accordingly.
Application Guidelines：PDF  　　Application Materials：Brief summary of career(excel)  

1. Division: Genome Dynamics Laboratory, Department of Chromosome Science (Maeshima Group)

2. Recruiting: Assistant Professor (1 qualified person)

3. Appointment Start Date: On and after August 2025 (negotiable)

4. Term of Appointment:
5 years
One-time extension of five additional years would be possible based on evaluation.
(For those who are/were employed by The Research Organization of Information and Systems (ROIS) at any time between April 1st, 2013 and the day before the starting date of this advertised position, the aforesaid term(s) of employment will be subtracted from the term of appointment.)

5. Qualifications:
A researcher with outstanding research capabilities and achievements in biophysics or molecular cell biology, who is motivated to conduct creative studies on the organization and dynamics of genome chromatin in various states of the cell such as differentiation, aging, and tumorigenesis The candidate is expected to collaborate with Professor Maeshima and contribute to the development of the Genome Dynamics Laboratory with a strong commitment to research and education.

6. Salary and Allowance: Based on ROIS Regulations

7. Social Insurance:
MEXT Mutual Society of Health Insurance
Worker’s Accident Compensation Insurance
Employment Insurance

8. Work Hours: Discretionary Labor System

9. Holiday: Saturday and Sunday, National Holidays,
From December 29th to January 3rd (New Year’s Break), Summer Break

10. Application Deadline: Noon (Japan Time) on May 7, 2025

11. Application Materials:
I. Curriculum Vitae (In English. Japanese applicants should also submit a Japanese version. Include your e-mail address.)
II. List of publications (If there are multiple authors, briefly describe your contribution. Indicate your most significant papers.)
III. Summary of past and present research and future directions (In English, max. 1,500 words. Include figures if necessary.)
IV. Names and contacts of references (two to four references including at least one international reference is desirable.)
V. Summary of career
VI. Your key papers
*All the personal data in the application is handled in strict confidentiality, and used solely for
recruitment purposes.

12. Submission:
Submit items I to VI listed above electronically as follows:
(a) The subject line should be “Application for Genome Dynamics Laboratory Assistant Professor”, which should be also noted in the e-mail body.
(b) Put items I to IV together in a single file by separating each item by page. E-mail the file as an attachment. The file format should be MS Word or PDF. Also attach item V (form can be downloaded from the NIG homepage) as a separate file.
(c) Send your key papers as PDF attachments. The file format should be PDF. If your key papers are available to access online, include a list of URLs in the e-mail body.

* We will notify you via e-mail upon receipt of your electronic application within two business days.

Based on gender equality National Institute of Genetics has been actively promoting female scientists. In case of equivalent aptitude and achievements in research, education, and social contributions, preference will be given to female candidates.

National Institute of Genetics is promoting safety and healthy working, including preventing passive smoking. (Indoor smoking is banned. / Smoking is allowed only in the designated outdoor areas.)

Send your application and inquiries to:
NIG Personnel Committee (Personnel Team)
E-mail:
Mailing Address:
National Institute of Genetics
Yata 1111, Mishima, Shizuoka 411-8540 JAPAN
TEL: +81-55-981-6716
FAX: +81-55-981-6715
Homepage: https://www.nig.ac.jp/nig/
NIG Organization Chart: https://www.nig.ac.jp/nig/research/organization-top/organization