dbMAE


NAR Molecular Biology Database Collection entry number 1870
Savova, Virginia; Patsenker, Jonathan; Vigneau, Sebatien; Gimelbrant, Alexander
1 Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215, USA
2 Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02215, USA

Database Description

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele- specific expression of autosomal genes, with the initial non-predetermined ('random') choice of the transcriptional activity of the two alleles maintained in a given clonal cell lineage [recent reviews include refs. (1-3)]. The database of autosomal monoallelic expression (dbMAE) incorporates data from multiple recent reports of genome-wide analyses. These include transcriptome-wide analyses of allelic imbalance in clonal cell populations based on sequence polymorphisms, as well as indirect identification, based on a specific chromatin signature present in MAE gene bodies. The database maintains a clear distinction between these types of evidence, listing the entry's MAE status according to all available sources. The user can also access the full set of data for each gene. At the time of publication, the database contains MAE calls for over 700 human and 16,000 mouse genes with experimental evidence of allelic bias as assessed in four tissue types. There are close to 5,000 corresponding positively confirmed instances of biallelic expression in human and more than 21,000 in mouse. In addition, the database includes MAE and biallelic calls based on genome-wide chromatin analysis for seven human and 21 murine cell types and tissues.

Acknowledgements

We thank early users for their comments and suggestions: Jason Alvarez, Suzanne Gaudet, Marko Horb, Anwesha Nag, Clara Pereira, and Leon Peshkin. We would also like to thank the anonymous reviewers for the improvements that resulted from their testing, and Andy Bergman, an Orchestra system administrator, for his help and support. AAG was supported in part by the Pew scholar award; VS and SV were supported in part by NIH grant R01GM114864 to AAG. dbMAE is hosted on the Orchestra High Performance Compute Cluster at Harvard Medical School. This NIH supported shared facility is partially provided through grant NCRR 1S10RR028832-01. See http://rc.hms.harvard.edu for more information.

References

1. Chess, A. (2012) Mechanisms and consequences of widespread random monoallelic expression. Nature reviews. Genetics, 13, 421-428.
2. Savova, V., Vigneau, S. and Gimelbrant, A.A. (2013) Autosomal monoallelic expression: genetics of epigenetic diversity? Current opinion in genetics & development, 23, 642-648.
3. Eckersley-Maslin, M.A. and Spector, D.L. (2014) Random monoallelic expression: regulating gene expression one allele at a time. Trends in genetics : TIG, 30, 237-244.
4. Gimelbrant, A., Hutchinson, J.N., Thompson, B.R. and Chess, A. (2007) Widespread monoallelic expression on human autosomes. Science (New York, N.Y, 318, 1136-1140.
5. Nag, A., Savova, V., Fung, H.L., Miron, A., Yuan, G.C., Zhang, K. and Gimelbrant, A.A. (2013) Chromatin signature of widespread monoallelic expression. Elife, 2, e01256.
6. Nag, A., Vigneau, S., Savova, V., Zwemer, L.M. and Gimelbrant, A.A. (2015) Chromatin Signature Identifies Monoallelic Gene Expression Across Mammalian Cell Types. G3, 5, 1713-1720.


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