Interesting article. Naive question: Is there any possibility that the transcription factors of gene regulation could be determined during DNA sequencing? If you know which genes are turned on then you would know which proteins are being produced. Any possibility nanopore sequencing, or a specialized variant, might possibly pick off the regulatory proteins as DNA passes through the pore?
Thanks for the question, Tom. One can certainly do RNA-sequencing to figure out which genes are expressed in a cell at a given moment in time. And that is cheap and highly scalable. But as far as I know, it's not possible to figure out which transcription factor regulates which gene (if that's what you're asking) solely for sequencing data. You need to do some kind of biochemical or biophysical assay to figure that out.
Also, as Paul Rudnick comments below, there are some exciting protein sequencing technologies on the horizon, mainly using nanopores (which are themselves proteins).
Interesting article and interesting company! Single cell proteomics is indeed hard, largely do with the vast concentration range of proteins w/in a cell - much easier task if millions of cells are pooled. DNA scientists are fortunate to have PCR which will exponentially amplify target from minimal template - proteomics scientists have no such luxury. The other major difference is that proteomics sequencing efforts are not "de novo", meaning that the sequences must match a reference database in order to be identified in the experiment. That falls short when the goal is detecting variant proteins. There is a new DARPA program focused on the development of better "sequencing" methods for proteomics (https://www.darpa.mil/research/programs/protein-sequencing-prose) which promises large investment. I am excited to see how that develops.
Interesting article. Naive question: Is there any possibility that the transcription factors of gene regulation could be determined during DNA sequencing? If you know which genes are turned on then you would know which proteins are being produced. Any possibility nanopore sequencing, or a specialized variant, might possibly pick off the regulatory proteins as DNA passes through the pore?
Thanks for the question, Tom. One can certainly do RNA-sequencing to figure out which genes are expressed in a cell at a given moment in time. And that is cheap and highly scalable. But as far as I know, it's not possible to figure out which transcription factor regulates which gene (if that's what you're asking) solely for sequencing data. You need to do some kind of biochemical or biophysical assay to figure that out.
Also, as Paul Rudnick comments below, there are some exciting protein sequencing technologies on the horizon, mainly using nanopores (which are themselves proteins).
Interesting article and interesting company! Single cell proteomics is indeed hard, largely do with the vast concentration range of proteins w/in a cell - much easier task if millions of cells are pooled. DNA scientists are fortunate to have PCR which will exponentially amplify target from minimal template - proteomics scientists have no such luxury. The other major difference is that proteomics sequencing efforts are not "de novo", meaning that the sequences must match a reference database in order to be identified in the experiment. That falls short when the goal is detecting variant proteins. There is a new DARPA program focused on the development of better "sequencing" methods for proteomics (https://www.darpa.mil/research/programs/protein-sequencing-prose) which promises large investment. I am excited to see how that develops.