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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

View ORCID ProfileOrsolya Symmons, Marcello Chang, View ORCID ProfileIan A. Mellis, View ORCID ProfileJennifer M. Kalish, Marisa S. Bartolomei, View ORCID ProfileArjun Raj
doi: https://doi.org/10.1101/386359
Orsolya Symmons
1Department of Bioengineering, University of Pennsylvania, Skirkanich Hall, Philadelphia, Pennsylvania 19104, USA
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  • For correspondence: osymmons@seas.upenn.edu arjunraj@seas.upenn.edu
Marcello Chang
1Department of Bioengineering, University of Pennsylvania, Skirkanich Hall, Philadelphia, Pennsylvania 19104, USA
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Ian A. Mellis
1Department of Bioengineering, University of Pennsylvania, Skirkanich Hall, Philadelphia, Pennsylvania 19104, USA
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Jennifer M. Kalish
2Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Marisa S. Bartolomei
3Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Arjun Raj
1Department of Bioengineering, University of Pennsylvania, Skirkanich Hall, Philadelphia, Pennsylvania 19104, USA
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  • For correspondence: osymmons@seas.upenn.edu arjunraj@seas.upenn.edu
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Abstract

Extensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting.

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Posted August 07, 2018.
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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting
Orsolya Symmons, Marcello Chang, Ian A. Mellis, Jennifer M. Kalish, Marisa S. Bartolomei, Arjun Raj
bioRxiv 386359; doi: https://doi.org/10.1101/386359
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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting
Orsolya Symmons, Marcello Chang, Ian A. Mellis, Jennifer M. Kalish, Marisa S. Bartolomei, Arjun Raj
bioRxiv 386359; doi: https://doi.org/10.1101/386359

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