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The local Ca2+ release from the heterogeneously distributed endoplasmic reticulum (ER) calcium store has a critical role in calcium homeostasis and cellular function. However, single fluorescent protein-based ER calcium probes experience challenges in quantifying the ER calcium store in differing live cells, and intensity-based measurements make it difficult to detect local calcium microdomains in the ER. Here, we developed a genetically encoded ratiometric ER calcium indicator (GCEPIA1-SNAPER) that can detect the real-time ER calcium store and local calcium microdomains in live cells. GCEPIA1-SNAPER was located in the lumen of the ER and showed a linear, reversible and rapid response to changes in the ER calcium store. The GCEPIA1-SNAPER probe effectively monitored the depletion of the ER calcium store by TG or starvation treatment, and through its use we identified heterogeneously distributed calcium microdomains in the ER which were correlated with the distribution of STIM1 clusters upon ER calcium store depletion. Lastly, GCEPIA1-SNAPER can be used to detect the ER calcium store by high-throughput flow cytometry and confers the ability to study the function of calcium microdomains of the ER.
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