Genome-wide RNA polymerase stalling shapes the transcriptome during aging

Abstract

Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.

The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging

“…Recent research, including my own, has revealed that as an organism ages, its transcriptome changes in a manner that is informed by the lengths of transcript molecules. This relationship between transcript length and aging has been first observed by the lab of Jan Hoeijmakers 8 , and since then been described for C. elegans 9 , fruit flies 10 , killifish 11 , mice 8,9,[11][12][13] , rats 11 , and humans 8,11,14 . In most cases, the correlation between transcript length and age-dependent change is negative, although some tissues and cell types exhibit a positive correlation 11 .…”

“…There are many reviews on organismal 63,64 and molecular damage 39,[65][66][67][68][69] , but it is challenging to find a well-cited review on the various types of transcript damage that occur during biological aging. These damages extend beyond premature termination 9 and include intron retention 27,28 , oxidative damage 70 , and lost synchronization toward the circadian rhythm 71 . It is surprising how few reviews discuss transcript damages 22,39,72,73 , given that research by Lorena Harries and colleagues 74 found that out of 1,065 considered biological and metabolic pathways, six of the seven pathways significantly associated with age in human peripheral blood leukocytes are related to RNA metabolism.…”

“…This figure, adapted from Cohen et al 6 (licensed under CC BY 4.0), illustrates the inputs and outputs connected to length-correlated changes of the transcriptome. References for the specific inputs and outputs are provided 8,9,11,13,21,55 . Note that this figure includes references to the preprint version 55 of a recent manuscript of mine, as I had removed some material following reviewer feedback to enhance focus.…”

“…In most cases, the correlation between transcript length and age-dependent change is negative, although some tissues and cell types exhibit a positive correlation 11 . The strength of these correlations can be influenced by various factors, such as UV radiation exposure 9 or smoking 13 or caloric restriction 8 .…”

Recovery of protein synthesis to measure transcription-coupled DNA repair in living cells and tissues

“…It will be interesting to investigate if a similar reduction of TC-NER capacity can be measured in aging tissues of e.g. mouse models of aging, as accumulating DNA damage leading to transcription stress is considered one of the driving forces of the aging process (22, 64).…”