Decoding the signature of sperm RNA & RNA modification of environmental stressors on the intergenerational transmission of metabolic phenotypes

Project Summary
Emerging evidence has shown that small non-coding RNAs (sRNAs) harbor a diversity of RNA modifications.
RNA modifications have the potential to store a secondary layer of labile biological information that is responsive
to various environmental exposures and can modulate RNA properties such as stability and interaction potential,
thus contributing to complex physiological/pathological processes. In our previous mouse model of paternal high-
fat diet (HFD)-induced intergenerational inheritance, we found that tRNA-derived small RNAs (tsRNAs) and RNA
methylatranserase (Dnmt2)-mediated site-specific RNA modification established a “sperm RNA code” that is
required for intergenerational transmission of paternally acquired metabolic disorders (Science 2016; Nat Cell
Biol 2018). These data, along with others, support an emerging concept that RNA modifications in sperm small
RNAs serve as an additional layer of paternal hereditary information that can be modulated by environmental
input, and is essential for regulating offspring phenotype via embryo development. These advances have set the
stage to further examine whether a wider range of paternal environmental exposures, such as tributyltin (TBT)
and arsenite (both are known to associate with obesity and metabolic disorders) will similarly alter sperm RNAs
to confer offspring phenotype. This concerns the nature of the core sperm RNA code (i.e. a group of modified
tsRNAs) shared by different exposure that is responsible for the intergenerational phenotype transmission; and
also the molecular mechanism by which the modified sperm tsRNAs regulate embryo development to dictate
offspring’s metabolic performance. In present project, we aim to first decipher the essential sperm tsRNAs &
associated RNA modifications that responsible for programming offspring metabolic health, by comparatively
studying different paternal environmental stressors (HFD, TBT & arenite exposure) with improved small RNA-
seq protocol, which reduces sequencing bias by enzymatically removing RNA modifications that block reverse
transcriptase and terminal adaptor ligation; we also explore the upstream regulators of the altered sperm tsRNAs,
with a focus on RNA modifications enzymes (Aim 1). We will further isolate individual tsRNAs followed by RNA
modification quantification using Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS), and test their
function in conferring offspring phenotype by zygotic RNA injection and offspring phenotype tracking (Aim 2).
Mechanistically, we will test the hypothesis whether modified sperm tsRNAs can program the metabolic state by
regulating ribosome heterogeneity that control distinct translational pool of mRNAs (Aim3). In other words, we
propose that environmental stressor-induced “sperm RNA code” is transformed into an “embryonic ribosome
code”, which generates translational specificity to define the metabolic phenotype of offspring. Data from the
proposed study may not only reveal the nature and mechanism of metabolic disorder related sperm RNA code,
but also generate fundamental knowledge for future therapeutic intervention facing the obesogenic environment.

Grant Number: 5R01ES032024-05
NIH Institute/Center: NIH
Principal Investigator: Qi Chen