Genetic reprogramming during immune activation: Decompressing the genetic information encoded in alternative transcription start sites

Thieffry, López-Márquez, et al. explore the use of alternative transcriptional start sites during immune responses. https://doi.org/10.1093/plcell/koac108

Background:

Upon sensing an attempted infection, plants change from growth to defense by reshaping gene activity. However, there is not always a 1:1 relationship between gene and protein. Rather, genes may work like zip files that are unzipped to produce multiple proteins, depending on cellular states. One way of compressing genetic information is to use different starting points for transcription, thereby producing distinct RNA copies from a single locus.

Question:

We asked two questions. (1) Does gene unzipping occur during immune activation via use of alternative starting points of transcription? (2) What is the timeline of gene activation during reprogramming? In particular, does reprogramming involve very rapidly activated genes that may affect later installments of the defense program?

Findings:

Using Arabidopsis seedlings treated to activate immune responses, we found many examples of gene unzipping via use of alternative transcription start sites. In one case, a protein is sent from one place in the cell to another, in many cases RNA variants are made that result in much larger amounts of the encoded proteins, and in yet other cases, it looks like the cell can switch between production of proteins with opposite functions from the very same genes! We also discovered an ultra-rapid, transient wave of gene activity of outstanding interest, because it contains several genes known to regulate immune responses.

Next steps:

Our findings open avenues of investigation not only on immune regulation, but also on processing of genetic information. How does gene unzipping contribute to maintenance of the immune state? Does the ultra-rapid wave of gene activity in fact drive the growth-to-defense transition? How does the cell control transcription to unzip genetic information?

Reference:

Axel Thieffry, Diego López-Márquez, Jette Bornholdtm Mojgan Gholami Malekroudi, Simon Bressendorff, Andrea Barghetti, Albin Sandelin, and Peter Brodersen (2022). PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave. https://doi.org/10.1093/plcell/koac108