# Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy

**Authors:** Tyrese Boddie, Arianna Lacen, Hui-Ting Lee

PMC · DOI: 10.1021/acs.jpcb.5c07484 · The Journal of Physical Chemistry. B · 2026-03-17

## TL;DR

This review discusses how advanced microscopy improves RNA quantification by providing spatial and real-time data, enhancing understanding of gene regulation and disease.

## Contribution

The paper highlights the novel use of high-resolution microscopy for RNA quantification, offering spatial and dynamic insights beyond traditional methods.

## Key findings

- Advanced microscopy enables precise RNA localization and real-time tracking.
- It improves understanding of cell-specific gene regulation and disease states.
- This method reveals cellular architecture and RNA dynamics not visible with conventional techniques.

## Abstract

RNA plays a crucial role in gene expression, regulation,
protein
synthesis, and other cellular functions. The diversity that exists
between different RNAs makes information beyond their expression
level necessary for understanding more about their complex functions
in a cell. Conventional ensemble approaches to RNA quantification
have been used extensively to measure the quantity of RNA but lack
cellular-level spatial information. This review highlights important
contributions that high resolution microscopy has made to RNA quantification
and cellular biophysics. Using advanced microscopy for precise localization,
real-time tracking, and quantitative measurements of RNA increases
our understanding of different disease states, cell- and tissue-specific
gene regulation, and cellular architecture.

## Full-text entities

- **Genes:** ORF1ab (ORF1a polyprotein;ORF1ab polyprotein) [NCBI Gene 43740578], POTEF (POTE ankyrin domain family member F) [NCBI Gene 728378] {aka A26C1B, POTE2alpha, POTEACTIN}, Glb1 (galactosidase, beta 1) [NCBI Gene 12091] {aka Bge, Bgl, Bgl-e, Bgl-s, Bgl-t, Bgs}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, POLRMT (RNA polymerase mitochondrial) [NCBI Gene 5442] {aka APOLMT, COXPD55, MTRNAP, MTRPOL, h-mtRPOL}, Actb (actin, beta) [NCBI Gene 81822] {aka Actx}, PRORP (protein only RNase P catalytic subunit) [NCBI Gene 9692] {aka COXPD54, KIAA0391, MRPP3}, NOTCH2 (notch receptor 2) [NCBI Gene 4853] {aka AGS2, HJCYS, hN2}, CXCL1 (C-X-C motif chemokine ligand 1) [NCBI Gene 2919] {aka FSP, GRO1, GROa, MGSA, MGSA-a, NAP-3}, MUC4 (mucin 4, cell surface associated) [NCBI Gene 4585] {aka ASGP, HSA276359, MUC-4}, COX1 (cytochrome c oxidase subunit I) [NCBI Gene 4512] {aka COI, MTCO1}, TK1 (thymidine kinase 1) [NCBI Gene 7083], CYTB (cytochrome b) [NCBI Gene 4519] {aka MTCYB}, Cr1l (complement C3b/C4b receptor 1 like) [NCBI Gene 12946] {aka Crry, Mcp, mCRY}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Spen (spen family transcription repressor) [NCBI Gene 56381] {aka Mint, mKIAA0929}, COX3 (cytochrome c oxidase subunit III) [NCBI Gene 4514] {aka COIII, MTCO3}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, PPIB (peptidylprolyl isomerase B) [NCBI Gene 5479] {aka CYP-S1, CYPB, HEL-S-39, OI9, SCYLP}, PALM (paralemmin) [NCBI Gene 5064] {aka PALM1}, ACTB (actin, beta) [NCBI Gene 396526] {aka Bact, actin}, SEC61B (SEC61 translocon subunit beta) [NCBI Gene 10952], MAP1B (microtubule associated protein 1B) [NCBI Gene 4131] {aka DFNA83, FUTSCH, MAP5, PPP1R102, PVNH9}, AAAS (aladin WD repeat nucleoporin) [NCBI Gene 8086] {aka AAA, AAASb, ADRACALA, ADRACALIN, ALADIN, GL003}, HPRT1 (hypoxanthine phosphoribosyltransferase 1) [NCBI Gene 3251] {aka HGPRT, HPRT}, SEC61A1 (SEC61 translocon subunit alpha 1) [NCBI Gene 29927] {aka ADTKD5, CVID15, HNFJ4, HSEC61, SEC61, SEC61A}, Xist (inactive X specific transcripts) [NCBI Gene 213742] {aka A430022B11}, Palm (paralemmin) [NCBI Gene 18483], CAPG (capping actin protein, gelsolin like) [NCBI Gene 822] {aka AFCP, HEL-S-66, MCP}, NEAT1 (nuclear paraspeckle assembly transcript 1) [NCBI Gene 283131] {aka LINC00084, NCRNA00084, TP53LC15, TncRNA, VINC}, KRT88P (keratin 88, pseudogene) [NCBI Gene 85348] {aka HBC, KRT122P, KRTHBP3}, H2BC21 (H2B clustered histone 21) [NCBI Gene 8349] {aka GL105, H2B, H2B-GL105, H2B.1, H2BE, H2BFQ}
- **Diseases:** bacterial infection (MESH:D001424), infection (MESH:D007239), STORM (MESH:D009901), cancer (MESH:D009369), Viral Infection (MESH:D014777), autoimmune diseases (MESH:D001327), SARS-CoV-2 infection (MESH:D000086382), SMLM (MESH:D012640), MERFISH (MESH:D015456), breast cancer (MESH:D001943)
- **Chemicals:** carbon (MESH:D002244), PNAS (MESH:D020135), oxygen (MESH:D010100), rhodamine (MESH:D012235), DCP (MESH:C580746), thiol (MESH:D013438), uridine (MESH:D014529), Label X (-), Cy5 (MESH:C085321), biotin (MESH:D001710), AF647 (MESH:C569686), KTiOPO4 (MESH:C064806), polyelectrolyte (MESH:D000071228), ribose (MESH:D012266), alkyne (MESH:D000480), formalin (MESH:D005557), paraffin (MESH:D010232), doxycycline (MESH:D004318), water (MESH:D014867), guanine (MESH:D006147), oligonucleotide (MESH:D009841), metal (MESH:D008670), LNA (MESH:C477371), carbohydrate (MESH:D002241)
- **Species:** Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Danio rerio (leopard danio, species) [taxon 7955], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Mus musculus (house mouse, species) [taxon 10090], Drosophila melanogaster (fruit fly, species) [taxon 7227], Homo sapiens (human, species) [taxon 9606], C. elegans [taxon 328850], Gallus gallus (bantam, species) [taxon 9031], Ambystoma mexicanum (axolotl, species) [taxon 8296], Rattus norvegicus (brown rat, species) [taxon 10116], Hantaan virus [taxon 1980471], Influenza A virus (no rank) [taxon 11320], Bacteriophage sp. (species) [taxon 38018], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932]
- **Cell lines:** IMR90 — Homo sapiens (Human), Finite cell line (CVCL_0347), MEF — Mus musculus (Mouse), Finite cell line (CVCL_9115), HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), NIH/3T3 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0594), MCF-7 — Homo sapiens (Human), Invasive breast carcinoma of no special type, Cancer cell line (CVCL_0031), CHO — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_0213)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC13034423/full.md

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13034423/full.md

## References

185 references — full list in the complete paper: https://tomesphere.com/paper/PMC13034423/full.md

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Source: https://tomesphere.com/paper/PMC13034423