title: Visualization of aging-associated chromatin alterations with an engineered TALE system.
abstract: Visualization of specific genomic loci in live cells is a prerequisite for the investigation of dynamic changes in chromatin architecture during diverse biological processes, such as cellular aging. However, current precision genomic imaging methods are hampered by the lack of fluorescent probes with high specificity and signal-to-noise contrast. We find that conventional transcription activator-like effectors (TALEs) tend to form protein aggregates, thereby compromising their performance in imaging applications. Through screening, we found that fusing thioredoxin with TALEs prevented aggregate formation, unlocking the full power of TALE-based genomic imaging. Using thioredoxin-fused TALEs (TTALEs), we achieved high-quality imaging at various genomic loci and observed aging-associated (epi) genomic alterations at telomeres and centromeres in human and mouse premature aging models. Importantly, we identified attrition of ribosomal DNA repeats as a molecular marker for human aging. Our study establishes a simple and robust imaging method for precisely monitoring chromatin dynamics in vitro and in vivo.
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ruotong
authors.initials: R
authors.lastname: Ren
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.|State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Deng
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Suzuki
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Weiqi
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing 100191, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.affiliation: The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Sun
authors.affiliation: Department of Pediatrics, Beijing Shijitan Hospital Capital Medical University, Peking University Ninth School of Clinical Medicine, Beijing 100038, China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Gong
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Huiqin
authors.initials: H
authors.lastname: Luan
authors.affiliation: Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, Guangdong 510632, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, Zhejiang 311121, China.
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Ju
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Ren
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Si
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Pediatrics, Beijing Shijitan Hospital Capital Medical University, Peking University Ninth School of Clinical Medicine, Beijing 100038, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Tang
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Geng
authors.affiliation: Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Weizhou
authors.initials: W
authors.lastname: Zhang
authors.affiliation: The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing 100730, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing 100191, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiao
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.affiliation: University of Chinese Academy of Sciences, Beijing 100049, China.|State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Qu
authors.affiliation: National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.|Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, Guangdong 510632, China.|Beijing Institute for Brain Disorders, Beijing 100069, China.
authors.forename: Guang-Hui
authors.initials: GH
authors.lastname: Liu
mesh_terms: D000375:Aging / Q000235:genetics*; D000818:Animals; D064130:CRISPR-Associated Proteins / Q000378:metabolism; D002454:Cell Differentiation; D002460:Cell Line; D016922:Cellular Senescence; D002503:Centromere / Q000378:metabolism; D002843:Chromatin / Q000235:genetics*; D004275:DNA, Ribosomal / Q000378:metabolism; D005818:Genetic Engineering; D056426:Genetic Loci; D006801:Humans; D021621:Imaging, Three-Dimensional; D059630:Mesenchymal Stem Cells / Q000166:cytology; D008810:Mice, Inbred C57BL; D008938:Mitosis; D009697:Nucleolus Organizer Region / Q000235:genetics; D009865:Oocytes / Q000166:cytology; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D019098:Telomerase / Q000378:metabolism; D016615:Telomere / Q000378:metabolism; D013879:Thioredoxins / Q000378:metabolism; D000069896:Transcription Activator-Like Effector Nucleases / Q000378:metabolism*; D000094704:RNA, Guide, CRISPR-Cas Systems
chemical_list: D064130:CRISPR-Associated Proteins; D002843:Chromatin; D004275:DNA, Ribosomal; D019098:Telomerase; D013879:Thioredoxins; D000069896:Transcription Activator-Like Effector Nucleases; D000094704:RNA, Guide, CRISPR-Cas Systems