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Allelic Regulation SIGNED

Revealing Allele-level Regulation and Dynamics using Single-cell Gene Expression Analyses

Total Cost €


EC-Contrib. €






Project "Allelic Regulation" data sheet

The following table provides information about the project.


Organization address
address: Nobels Vag 5
postcode: 17177

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Sweden [SE]
 Total cost 1˙923˙060 €
 EC max contribution 1˙923˙060 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-CoG
 Funding Scheme ERC-COG
 Starting year 2015
 Duration (year-month-day) from 2015-07-01   to  2020-06-30


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KAROLINSKA INSTITUTET SE (STOCKHOLM) coordinator 1˙923˙060.00


 Project objective

As diploid organisms inherit one gene copy from each parent, a gene can be expressed from both alleles (biallelic) or from only one allele (monoallelic). Although transcription from both alleles is detected for most genes in cell population experiments, little is known about allele-specific expression in single cells and its phenotypic consequences. To answer fundamental questions about allelic transcription heterogeneity in single cells, this research program will focus on single-cell transcriptome analyses with allelic-origin resolution. To this end, we will investigate both clonally stable and dynamic random monoallelic expression across a large number of cell types, including cells from embryonic and adult stages. This research program will be accomplished with the novel single-cell RNA-seq method developed within my lab to obtain quantitative, genome-wide gene expression measurement. To distinguish between mitotically stable and dynamic patterns of allelic expression, we will analyze large numbers a clonally related cells per cell type, from both primary cultures (in vitro) and using transgenic models to obtain clonally related cells in vivo.

The biological significance of the research program is first an understanding of allelic transcription, including the nature and extent of random monoallelic expression across in vivo tissues and cell types. These novel insights into allelic transcription will be important for an improved understanding of how variable phenotypes (e.g. incomplete penetrance and variable expressivity) can arise in genetically identical individuals. Additionally, the single-cell transcriptome analyses of clonally related cells in vivo will provide unique insights into the clonality of gene expression per se.


year authors and title journal last update
List of publications.
2016 Björn Reinius, Jeff E Mold, Daniel Ramsköld, Qiaolin Deng, Per Johnsson, Jakob Michaëlsson, Jonas Frisén, Rickard Sandberg
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq
published pages: 1430-1435, ISSN: 1061-4036, DOI: 10.1038/ng.3678
Nature Genetics 48/11 2019-06-07
2016 Sophie Petropoulos, Daniel Edsgärd, Björn Reinius, Qiaolin Deng, Sarita Pauliina Panula, Simone Codeluppi, Alvaro Plaza Reyes, Sten Linnarsson, Rickard Sandberg, Fredrik Lanner
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
published pages: 1012-1026, ISSN: 0092-8674, DOI: 10.1016/j.cell.2016.03.023
Cell 165/4 2019-06-07
2016 Daniel Edsgärd, Björn Reinius, Rickard Sandberg
scphaser: haplotype inference using single-cell RNA-seq data
published pages: 3038-3040, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btw484
Bioinformatics 32/19 2019-06-07
2016 Åsa Segerstolpe, Athanasia Palasantza, Pernilla Eliasson, Eva-Marie Andersson, Anne-Christine Andréasson, Xiaoyan Sun, Simone Picelli, Alan Sabirsh, Maryam Clausen, Magnus K. Bjursell, David M. Smith, Maria Kasper, Carina Ämmälä, Rickard Sandberg
Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
published pages: 593-607, ISSN: 1550-4131, DOI: 10.1016/j.cmet.2016.08.020
Cell Metabolism 24/4 2019-06-07
2015 Björn Reinius, Rickard Sandberg
Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
published pages: 653-664, ISSN: 1471-0056, DOI: 10.1038/nrg3888
Nature Reviews Genetics 16/11 2019-06-07
2016 Omid R Faridani, Ilgar Abdullayev, Michael Hagemann-Jensen, John P Schell, Fredrik Lanner, Rickard Sandberg
Single-cell sequencing of the small-RNA transcriptome
published pages: 1264-1266, ISSN: 1087-0156, DOI: 10.1038/nbt.3701
Nature Biotechnology 34/12 2019-05-07

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