Geneticist @Bayer4Crops. Views and opinions are my own.
Joined February 2012
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Nathan Springer retweeted
Special issue for Epigenetics and gene regulation 2023 in Current Opinion in Plant Biology, co-edited with @SpringerNathan !
#epigenome #transposon #plant
sciencedirect.com/journal/cu…
authors.elsevier.com/a/1iDJg…
Cool opportunity to work on developing applications of single-cell technologies for crop improvement on a fantastic team led by @rebeccalowdon jobs.bayer.com/job/Chesterfi…
Nathan Springer retweeted
🚨 We've got a new preprint out 🚨 - We developed a series of logical frameworks for analyzing how transposable element content contributes to structural variation (SV) within maize 🌽🧬🌽. How'd we do this + what did we find?? - 1/11
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion biorxiv.org/cgi/content/shor… #bioRxiv
After ~20 years at the UMN today was my last day . I have been so lucky to work with wonderful people in my group and to have a fantastic set of collaborators. A huge thank you to all of my colleagues, collaborators and friends. Excited for a new journey @Bayer4Crops
Nathan Springer retweeted
Why do the same gene in different varieties respond differentially under the environmental stimuli? We seek to answer the question using both population transcriptomics and chromatin signatures.
Figuring out the promoter sequences that control variation in how genes respond to heat stress in corn using RNA-seq from 120 diverse maize genotypes. New preprint from @shanwai1234 and @SpringerNathan. doi.org/10.1101/2022.06.23.4…
Nathan Springer retweeted
Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel biorxiv.org/cgi/content/shor… #biorxiv_plants
Nathan Springer retweeted
Plant Cell author Peng Zhou bit.ly/3l6zQfs first author of Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information @orionzhou @taraenders @AuthenticZAM @erikalanemag @pete_crisp @noshjac @shanwai1234 @SpringerNathan
Excited to share @noshjac's last thesis chapter research. Monitoring accessible chromatin and DNA methylation in four maize genomes. Reveals that a large amount of variable methylation is due to shifting boundaries at the edge of methylated domains
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes biorxiv.org/cgi/content/shor… #biorxiv_plants
Nathan Springer retweeted
Recognizing Plant Physiology first author Zhikai Liang plantae.org/recognizing-plan… @shanwai1234 author of Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize
This was a fun project led by @orionzhou which taught me that many of my conceptions about cis-regulatory elements are flawed. Peng is a fantastic science, he'll be sorely missed at MN as he begins a new position.
Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize biorxiv.org/cgi/content/shor… #biorxiv_plants
While 2020 has certainly had some glaring deficiencies there is still much to be thankful for. Thank you to all my colleagues and friends for the kind words the last couple days 1/n
I am very thankful for the wonderful people I get to work with on a regular basis - @noshjac @orionzhou @erikalanemag @shanwai1234 @Hashtag_Read @AuthenticZAM @swedishenvy I miss in person interactions
2/n
I also am thankful for, and miss, a set of people that have recently gone on to new endeavors @pete_crisp @sna8 @taraenders
3/3
This is a nice study led by @shanwai1234 that shows the variability of TE responses to abiotic stresses in different maize inbreds. Both genetics and epigenetics are important factors. Couldn't have happened without @sna8 @pete_crisp @noshjac @taraenders
Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize biorxiv.org/cgi/content/shor… #biorxiv_plants
Nathan Springer retweeted
Our latest: we use DNA methylation profiles to distill large genomes down to a small fraction of unmethylated regions (UMRs) biorxiv.org/content/10.1101/…
I should have included the link - old person twitter issues...
biorxiv.org/content/10.1101/…
Really nice work led by @noshjac that finds evidence for a subset of TEs that influence regulation of nearby genes. Made possible by great collaborations with @Schmitz_Lab @HirschCandice and many others!
Nathan Springer retweeted
Really nice work led by @noshjac that finds evidence for a subset of TEs that influence regulation of nearby genes. Made possible by great collaborations with @Schmitz_Lab @HirschCandice and many others!
Really nice work led by @noshjac that finds evidence for a subset of TEs that influence regulation of nearby genes. Made possible by great collaborations with @Schmitz_Lab @HirschCandice and many others!
Very nice work on imprinting by @sna8 When you develop new approaches that shine light in the corners you were ignoring sometimes you find some really cool things.
“Widespread imprinting of transposable elements and young genes in the maize endosperm”
Preprint online now - big thanks to collaborators @orionzhou @km_higgins26 @yanivbrandvain @SpringerNathan
Highlights below