An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases-Reference-Cited by-同舟云学术

An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases

Published:2024-07-05 Issue:6704 Volume:385 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Oguchi Akiko¹²³^ORCID,Suzuki Akari⁴^ORCID,Komatsu Shuichiro¹⁵^ORCID,Yoshitomi Hiroyuki²⁶^ORCID,Bhagat Shruti²,Son Raku¹²³^ORCID,Bonnal Raoul Jean Pierre⁵^ORCID,Kojima Shohei⁷^ORCID,Koido Masaru⁸⁹¹⁰^ORCID,Takeuchi Kazuhiro¹²¹¹^ORCID,Myouzen Keiko⁴,Inoue Gyo⁴,Hirai Tomoya¹¹²,Sano Hiromi¹,Takegami Yujiro¹³,Kanemaru Ai¹³,Yamaguchi Itaru¹³,Ishikawa Yuki¹⁰^ORCID,Tanaka Nao¹⁰^ORCID,Hirabayashi Shigeki¹¹⁴¹⁵^ORCID,Konishi Riyo¹⁶^ORCID,Sekito Sho²¹⁷^ORCID,Inoue Takahiro¹⁷^ORCID,Kere Juha¹⁸¹⁹²⁰^ORCID,Takeda Shunichi²¹²²,Takaori-Kondo Akifumi¹⁴^ORCID,Endo Itaru¹²^ORCID,Kawaoka Shinpei¹⁶²³^ORCID,Kawaji Hideya²⁴²⁵²⁶^ORCID,Ishigaki Kazuyoshi²⁷^ORCID,Ueno Hideki²⁶^ORCID,Hayashizaki Yoshihide¹³²⁶^ORCID,Pagani Massimiliano⁵²⁸^ORCID,Carninci Piero²⁹³⁰^ORCID,Yanagita Motoko²³^ORCID,Parrish Nicholas⁷^ORCID,Terao Chikashi¹⁰³¹³²^ORCID,Yamamoto Kazuhiko⁴^ORCID,Murakawa Yasuhiro¹²⁵¹¹^ORCID,Guerrini Matteo,Hatano Hiroaki,Ishigaki Kazuyoshi,Ishikawa Yuki,Komatsu Shuichiro,Kono Michihiro,Murakawa Yasuhiro,Nakano Masahiro,Oguchi Akiko,Son Raku,Suzuki Akari,Takeuchi Kazuhiro,Tanaka Nao,Terao Chikashi,Tomizuka Kohei,Yamamoto Kazuhiko,Yoshino Soichiro,

Affiliation:

1. RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

2. Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.

3. Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

4. Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

5. IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy.

6. Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

7. Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

8. Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

9. Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.

10. Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

11. Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

12. Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan.

13. K.K. DNAFORM, Yokohama, Japan.

14. Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

15. Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

16. Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.

17. Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan.

18. Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.

19. Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.

20. Folkhalsan Research Center, Helsinki, Finland.

21. Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

22. Shenzhen University School of Medicine, Shenzhen, Guangdong, China.

23. Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.

24. Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

25. Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan.

26. RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan.

27. Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

28. Department of Medical Biotechnology and Translational Medicine, Università degli Studi, Milan, Italy.

29. Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

30. Human Technopole, Milan, Italy.

31. Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan.

32. Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.

Abstract

Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5′ single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4 + T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type–specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type–resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.

Publisher

American Association for the Advancement of Science (AAAS)

Link

https://www.science.org/doi/pdf/10.1126/science.add8394

Reference139 articles.

1. Integrative analysis of 111 reference human epigenomes

2. Expanded encyclopaedias of DNA elements in the human and mouse genomes

3. Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

4. The accessible chromatin landscape of the human genome

5. An atlas of gene regulatory elements in adult mouse cerebrum

Cited by 2 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. SVA Regulation of Transposable Element Clustered Transcription within the Major Histocompatibility Complex Genomic Class II Region of the Parkinson’s Progression Markers Initiative;Genes;2024-09-09

2. An autoimmune transcriptional circuit drives FOXP3 ⁺ regulatory T cell dysfunction;Science Translational Medicine;2024-08-28