Ron L Shanderson, PhD 🦀
@theshanderson.bsky.social
Postdoc Stanford Bioengineering Interested in how signaling networks regulate transcription
tinyurl.com/Raf1GLS We learn that Raf1 can be localized to the mitochondria and interact with GLS to regulate glutamine metabolism in cancer. A combination of cross-linking mass spec, AlphaFold predicted structures, and docking allowed us to identify and mutate the interaction interface.
As instruments and approaches emerge for single-molecule protein analysis, some developers and early users share their first impressions with Nature Methods. 🧪
Is single-molecule protein sequencing here yet?
Nature Methods
go.nature.com
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏 www.science.org/doi/10.1126/...
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
science.org
Beautiful single-molecule footprinting study from the Greenleaf and Bintu labs www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression - Nature
A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...
nature.com
Cancer cells often harbor oncogenes outside chromosomes on extrachromosomal DNA (ecDNA), which is unevenly inherited by dividing cells. We reported in Nature last week that collectives of ecDNAs are inherited together by dividing cancer cells. 1/ www.nature.com/articles/s41...
Coordinated inheritance of extrachromosomal DNAs in cancer cells - Nature
Cooperative species of extrachromosomal DNAs are coordinately inherited through mitotic co-segregation.
nature.com
Too often we spend only two weeks choosing a problem and then many years trying solving it, but this limits our potential impact. A must read for PhD students: Problem choice and decision trees in science and engineering. pubmed.ncbi.nlm.nih.gov/38608651/
www.nature.com/articles/s41...
Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription - Nature Communications
Androgen receptor (AR) is the critical driver of nearly all prostate cancer. The authors show that AR activation causes specific pre-existing chromatin loops to increase contact frequency with target ...
nature.com
Republicizing my preprint from earlier this year! We found that mitochondrial Raf1 upregulates glutamine catabolism in cancer cells. www.biorxiv.org/content/10.1...
Mitochondrial Raf1 Regulates Glutamine Catabolism
Raf1 is present within the mitochondrial matrix, where it binds GLS to regulate glutamine catabolism and tumorigenesis. In cancer, Raf1 activation occurs via mechanisms that include mutation of upstr...
biorxiv.org
