Protein product

1. a. Protein products Stabilized mRNA (loss of NMD) mRNA AAAA b. Protein product Silent variant (pseudogene) expressed mRNA AAAA c. Protein product Destabilized mRNA (nonstop decay) AAAA mRNA d. Protein product Addition of C-terminal sequences mRNA AAAA 3’UTR Lindquist Supplementary Figure 1

2. Supplementary Figure 1. [PSI+]-mediated phenotypic diversity stems from uncovering genetic variants. Many types of gene products may be affected by the [PSI+] state. a) More protein may be produced from a gene containing a premature stop codon due to the initial read through event inactivating nonsense mediated decay (NMD), thereby stabilizing the mRNA. b) Pseudogenes or other genes disrupted by an inactivating stop codon mutation (ISCM) may acquire genetic variation and be expressed in the [PSI+] state. c) mRNA may be destabilized by translational read through if the ribosome reaches the end of a message and does not encounter a stop codon (nonstop decay degrades the message). d) Additional amino acids can be added onto the end of a protein with a read through event in [PSI+] and may impact the folding and/or function of that gene product.

3. Lindquist Supplementary Figure 3a [PSI+] cells appear condition B [psi-] cells thrive condition A [PSI+] cells thrive [psi-] cells appear

4. Supplementary Figure 3a. The advantage of the epigenetic switch to [PSI+]. Cells growing in a population are largely in the [psi-] state (at the star, [psi-] cells represented by the darker cells with a smooth cell border). As the population becomes larger, [PSI+] variants appear in the population ([PSI+] represented by the lighter cells with ruffled edges). Without any change in the environment they are stable as a population of largely [psi-] cells. If the condition changes (to condition B) and the [PSI+] variants are beneficial, the genome is not lost but the [PSI+] variants thrive in that condition and [psi-] cells die off. Again the population of cells grows (this time in the [PSI+] state) and eventually the population gets large enough that some [psi-] variants appear. If condition B persists, the population of mostly [PSI+] cells persists. If the condition changes again (to condition A) and the [psi-] cells have a beneficial phenotype, then the [psi-] cells thrive and the [PSI+] cells die off. In this manner, the genome is maintained by the ability to display phenotypic plasticity in the population by simply selecting the [PSI+] or [psi-] variants.

5. 1 2 3 Lindquist Supplementary Figure 3b

6. Supplementary Figure 3b. The advantage of the epigenetic switch to [PSI+]. Silent genetic variants arise and accumulate in a population of [psi-] cells (represented by the darker cell border). (1) [PSI+] variants (represented by the cells with ruffled edges) appear in the population as it grows. (2) Certain [PSI+] variants are more fit when the environment changes and are selected. (3) When the cells begin to revert to [psi-] that variant is prominent in the population.