Single-Cell RNA-seq Reveals Principles of Allelic Expression in Mammalian Cells
Event details
| Date | 01.05.2014 |
| Hour | 11:00 |
| Speaker | Prof. Rickard Sandberg, Karolinska Institutet and Ludwig Institute for Cancer Research, Stockholm (SE) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
Assessing gene expression in single cells will be critical to better understand cellular behaviors and compositions in developing, adult and pathological tissues. To this end, my lab has been developing single-cell RNA-seq methods (e.g. Smart-seq2) that combine full-length transcript coverage with high sensitivity and accuracy. We have performed global analyses of gene expression in hundreds of individual cells from mouse preimplantation embryos of mixed genetic background (CAST/EiJ x C57BL/6J). Using strain-specific SNPs we investigate allelic expression in these cells during preimplantation development to characterize X-chromosome imprinting and allelic expression patterns of autosomal genes. Although expression from both paternal alleles is generally observed in analyses of diploid cell populations, no study has addressed allelic expression patterns genome-wide in single cells. Importantly, we demonstrate that allelic expression is independent for genes across all expression levels making this a genomic principle. Additionally, our study revealed that allelic transcription fluctuations generated widespread random monoallelic expression in single cells, and we discuss its functional consequences.
Bio:
2009 - Present Member at Ludwig Institute for Cancer Research, Stockholm (SE)
2007 - present Professor (Assistant, then Associate), Karolinska Institutet, Stockholm (SE)
Education:
2004 - 2006 Postdoctoral Fellow, MIT, Cambridge, MA (USA)
2003 PhD, Karolinska Institutet, Stockholm (SE)
Abstract:
Assessing gene expression in single cells will be critical to better understand cellular behaviors and compositions in developing, adult and pathological tissues. To this end, my lab has been developing single-cell RNA-seq methods (e.g. Smart-seq2) that combine full-length transcript coverage with high sensitivity and accuracy. We have performed global analyses of gene expression in hundreds of individual cells from mouse preimplantation embryos of mixed genetic background (CAST/EiJ x C57BL/6J). Using strain-specific SNPs we investigate allelic expression in these cells during preimplantation development to characterize X-chromosome imprinting and allelic expression patterns of autosomal genes. Although expression from both paternal alleles is generally observed in analyses of diploid cell populations, no study has addressed allelic expression patterns genome-wide in single cells. Importantly, we demonstrate that allelic expression is independent for genes across all expression levels making this a genomic principle. Additionally, our study revealed that allelic transcription fluctuations generated widespread random monoallelic expression in single cells, and we discuss its functional consequences.
Bio:
2009 - Present Member at Ludwig Institute for Cancer Research, Stockholm (SE)
2007 - present Professor (Assistant, then Associate), Karolinska Institutet, Stockholm (SE)
Education:
2004 - 2006 Postdoctoral Fellow, MIT, Cambridge, MA (USA)
2003 PhD, Karolinska Institutet, Stockholm (SE)
Practical information
- General public
- Free