Biology subjects

Kugelberg, U.

Publications and source records attributed to Kugelberg, U..

4 recordsLinked to original sources

bioRxiv2021

Early embryonic heat shock induces long-term epigenetic memory by affecting the transition to zygotic independence

Early-life stress can generate persistent life-long effects that impact adult health and disease risk, but little is known of how such programming is established and maintained. Previous use of the Drosophila strain wm4h show that an early embryonic heat shock result in stable epigenetic alteration in the adult fly. To investigate the potential role of small non-coding RNA (sncRNA) in the initiation of such long-term epigenetic effects, we here generated a fine timeline of sncRNA expression during the first 5 stages of Drosophila embryogenesis in this strain. Building on this, we show that (1) miRNA is increased following early embryonic heat shock, and (2) the increased miRNA is coming from two separate sources, maternal and zygotic. By performing long RNA sequencing on the same single embryo, we found that a subgroup of miRNA with maternal origin, had a strong negative correlation with a group of early zygotic transcripts. Critically, we found evidence that one such early zygotic transcript, the insulator binding factor Elba1, is a Su(var) for wm4h. The findings provide insights of the dynamics and stress-sensitivity of sncRNA during the first embryonic stages in Drosophila and suggest an interplay between miRNA, Elba1 and long-term epigenetic alteration. HIGHLIGHTSO_LIWe provide a high-resolution timeline for sncRNA for Drosophila stage 1-5 embryos C_LIO_LIHeat shock before midblastula transition (MBT) results in a massive upregulation of miRNA at cellularization C_LIO_LIHeat shock-induced miRNAs negatively associate with downregulation of a specific subset of pre-MBT genes C_LIO_LIElba1 is a position-effect-variegation (PEV) modifier for wm4h C_LIO_LIHeat shock-induces an "leaky" expression of genes that overlap with Elba 1-3 binding sites C_LI

developmental biology↗

bioRxiv2021

Nutritional dependence of sperm mitochondrial metabolism and small RNA biogenesis

A wide spectrum of exogenous factors, including diet, environmental pollutants, stress, and seasonal changes have major impact on sperm quality and function. The molecular basis, however, that explains this susceptibility remains largely unknown. Using a combination of proteomics and small RNA (sRNA) sequencing, we show that Drosophila sperm display rapid molecular changes in response to dietary sugar, both in terms of metabolic/redox proteins and sRNA content, particularly miRNA and mitochondria derived sRNA (mt-sRNA). Thus, results from two independent omics point at the dynamics of mitochondria as the central aspect in rapid metabolic adjustments in sperm. Using specific stains and in vivo redox reporter flies, we show that diet indeed rapidly alters the production of mitochondrial derived reactive oxygen species (ROS). Quenching ROS via supplementation of N acetyl cysteine reduces diet-upregulated miRNA, but not mitochondrial-sRNA. Together, these results open new territories in our search for the mechanistic understanding of sperm health and disease. HighlightsO_LIDiet rapidly changes the proteomic and sRNA profiles in sperm C_LIO_LIDiet sensitive sperm proteins are found in human infertility studies C_LIO_LISperm mitochondrial ROS levels are modulated by diet C_LIO_LIdme-miR-10 regulation is secondary to diet-induced ROS C_LIO_LIDiet, but not diet-induced ROS, alters the expression of mitochondrial small RNA, especially tsRNA C_LI

molecular biology↗

bioRxiv2021

Intergenerational metabolic priming by sperm piRNAs

SummaryPreconception parental environment can reproducibly program offspring phenotype without altering the DNA sequence, yet the mechanisms underpinning this epigenetic inheritance remains elusive. Here, we demonstrate the existence of an intact piRNA-pathway in mature Drosophila sperm and show that pathway modulation alters offspring gene transcription in a sequence-specific manner. We map a dynamic small RNA content in developing sperm and find that the mature sperm carry a highly distinct small RNA cargo. By biochemical pulldown, we identify a small RNA subset bound directly to piwi protein. And, we show that piRNA-pathway controlled sperm small RNAs are linked to target gene repression in offspring. Critically, we find that full piRNA-pathway dosage is necessary for the intergenerational metabolic and transcriptional reprogramming events triggered by high paternal dietary sugar. These data provide a direct link between regulation of endogenous mature sperm small RNAs and transcriptional programming of complementary sequences in offspring. Thus, we identify a novel mediator of paternal intergenerational epigenetic inheritance.

developmental biology↗

bioRxiv2020

5'XP sRNA-seq: A simple sequencing method to identify small RNA with and without 5' phosphorylation in a single library from low input samples

Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5 nucleotide modifications, makes many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that solves this problem. By tagging 5P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5-terminal modifications (5X), with a selective approach for 5-phosphorylated sRNA (5P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5 insensitive library strategies with 5 sensitive tagging, we have solved an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.

molecular biology↗