Defining the age-dependent and tissue-specific circadian transcriptome in male mice

Christopher A. Wolff, Miguel A. Gutierrez-Monreal, Lingsong Meng, Xiping Zhang, Lauren G. Douma, Hannah M. Costello, Collin M. Douglas, Elnaz Ebrahimi, Ann Pham, Aline C. Oliveira, Chunhua Fu, Amy Nguyen, Bryan R. Alava, Stuart J. Hesketh, Andrew R. Morris, Mehari M. Endale, G. Ryan Crislip, Kit yan Cheng, Elizabeth A. Schroder, Brian P. DelisleAndrew J. Bryant, Michelle L. Gumz, Zhiguang Huo, Andrew C. Liu, Karyn A. Esser

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

Cellular circadian clocks direct a daily transcriptional program that supports homeostasis and resilience. Emerging evidence has demonstrated age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profile the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in three age groups. We find age-dependent and tissue-specific clock output changes. Aging reduces the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. REGs are enriched for the hallmarks of aging, adding another dimension to our understanding of aging. Analyzing differential gene expression within a tissue at four different times of day identifies distinct clusters of differentially expressed genes (DEGs). Increased variability of gene expression across the day is a common feature of aged tissues. This analysis extends the landscape for understanding aging and highlights the impact of aging on circadian clock function and temporal changes in gene expression.

Original languageEnglish
Article number111982
JournalCell Reports
Volume42
Issue number1
DOIs
StatePublished - Jan 31 2023

Bibliographical note

Funding Information:
We thank the members of the Esser, Liu, Bryant, Gumz, and Huo laboratories for their work with the circadian collection, sample preparations, and lively discussions while developing this dataset and manuscript. We also thank Drs. Yanping Zhang and David Moraga from the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) for library preparation and sequencing (RRID: SCR_019152 ) and the UF high-performance computing cluster. This work was supported by grants ( R01HL141343 to B.P.D.; R01HL142776 and R01HL142887 to A.J.B.; R56DK128271 and R01DK109570 to M.L.G.; R01NS054794 and R01NS117457 to A.C.L.; R01HL153042 to B.P.D. and K.A.E.; and R01AR079220 to K.A.E.) and support from the UF NIH Claude D. Pepper Older Americans Independence Center ( P30AG028740 ) to A.C.L. and K.A.E. and the Office of Research Affairs , UF College of Medicine.

Funding Information:
We thank the members of the Esser, Liu, Bryant, Gumz, and Huo laboratories for their work with the circadian collection, sample preparations, and lively discussions while developing this dataset and manuscript. We also thank Drs. Yanping Zhang and David Moraga from the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) for library preparation and sequencing (RRID:SCR_019152) and the UF high-performance computing cluster. This work was supported by grants (R01HL141343 to B.P.D.; R01HL142776 and R01HL142887 to A.J.B.; R56DK128271 and R01DK109570 to M.L.G.; R01NS054794 and R01NS117457 to A.C.L.; R01HL153042 to B.P.D. and K.A.E.; and R01AR079220 to K.A.E.) and support from the UF NIH Claude D. Pepper Older Americans Independence Center (P30AG028740) to A.C.L. and K.A.E. and the Office of Research Affairs, UF College of Medicine. Conceptualization, C.A.W. M.A.G. A.C.L. M.L.G. A.J.B. and K.A.E.; methodology, C.A.W. L.M. Z.H.; investigation, C.A.W. X.Z. M.A.G. C.M.D. A.R.M. M.M.E. E.E. E.A.S. and B.P.D.; writing – original draft, C.A.W. M.A.G. A.C.L. and K.A.E.; writing – review & editing, all authors reviewed and approved the final version of this manuscript; funding acquisition, B.P.D. A.J.B. M.L.G. Z.H. A.C.L. and K.A.E.; resources, A.C.L. M.L.G. A.J.B. Z.H. and K.A.E.; supervision, A.C.L. M.L.G. Z.H. A.J.B. and K.A.E. The authors declare no competing interests. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in their field of research or within their geographical location. One or more authors of this paper self-identifies as a member of the LGBTQIA+ community. One or more of the authors of this paper received support from a program designed to increase minority representation in their field of research.

Publisher Copyright:
© 2022 The Author(s)

Keywords

  • adrenal gland
  • aging
  • circadian clock
  • CP: Developmental biology
  • CP: Molecular biology
  • heart
  • hypothalamus
  • kidney
  • lung
  • RNA-seq
  • skeletal muscle

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology

Fingerprint

Dive into the research topics of 'Defining the age-dependent and tissue-specific circadian transcriptome in male mice'. Together they form a unique fingerprint.

Cite this