Biology subjects

Steg, L. C.

Publications and source records attributed to Steg, L. C..

3 recordsLinked to original sources

bioRxiv2026

Paternal diet shapes paternal and maternal transcriptomes in the early embryo through parallel sperm-associated mechanisms

Life experiences in fathers can influence phenotypes in the offspring. While it is known that acquired paternal information can be transferred to descendants via the germline, how such transfer operates between sperm and embryo remains unclear. We examined the effects of low protein diet (LPD) on males of different genotypes and their hybrid offspring generated by reciprocal outcross and on their genome. We found that LPD induces genotype-specific effects in fathers and different phenotypes in their male and female offspring. Allele-specific analyses revealed that paternal LPD modifies paternal and maternal transcriptomes differently in early two-cell embryos. Changes in the paternal transcriptome overlap with the sperm transcriptome and are associated with sperm chromatin features, suggesting that sperm-inherited transcripts and chromatin states may shape the paternal transcriptome in the embryo. The maternal transcriptome, by contrast, is linked to sperm-derived small RNAs, consistent with a possible role of sperm-derived small RNAs in modulating maternal transcript levels in the embryo. Analyses of undifferentiated spermatogonia populations suggest that LPD-induced sperm states can originate from early stages of germ cells. These findings provide evidence that paternal experiences can influence the early embryo via processes involving each parental allele differently.

molecular biology↗

bioRxiv2024

NanoTag - an IgG-free method for mapping DNA-protein interactions

Genome-wide profiling of DNA-protein interactions in cells can provide important information about mechanisms of gene regulation. Most current methods for genome-wide profiling of DNA-bound proteins, such as ChIP-seq and CUT&Tag, use conventional IgG antibodies to bind target protein(s), which limits their applicability to targets for which high affinity and high specificity antibodies are available. Here we describe NanoTag, a novel method derived from CUT&Tag that is IgG-free and uses a nanobody to profile DNA-protein interactions. NanoTag is based on an anti-GFP nanobody-Tn5 transposase fusion that allows mapping GFP-tagged proteins associated with chromatin in a fast and cost-effective manner. We demonstrate the utility of NanoTag by profiling the histone mark H3K4me3 via its binding partner TATA box-binding protein-associated factor 3 (TAF3) and the transcription factors Nanog and CTCF in mouse embryonic stem cells expressing GFP-tagged targets. For the targets examined, NanoTag data shows high correlation to CUT&Tag data and displays a similarly high signal-to-noise ratio. Overall, NanoTag provides a flexible, IgG-free and cost-effective method to generate high resolution DNA-binding profiles in cells or tissues.

molecular biology↗

bioRxiv2020

Novel epigenetic clock for fetal brain development predicts fetal epigenetic age for iPSCs and iPSC-derived neurons.

Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and iPSC-derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.

neuroscience↗