Topic: Identification of cis-regulatry sequences from large genome data
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B
A map of the cis-regulatory sequences in the mouse genome.
Nature 488: 116-120, 2012

You might think that the title of the paper that we will be discussing next week does not sound like a publication on developmental biology. In fact it is not; it's a "genome paper" that identifies many promoters and enhancers in the mouse genome.

But perhaps the paper would be also attractive for developmental biologists, if the title and abstract are modified a bit:

A genomic framework for understanding mouse development
Toshihiko Shiroishi and Yasushi Hiromi (Department of Genetics, SOKENDAI)

Development of an organism is driven by spatio- and temporal- controlled gene expressions. The regulatory information for such gene expression is encoded in the genome as "cis-regulatry sequences" --- promoters and enhancers that are associated with a gene to regulate its expression. While such regulatory elements for individual genes can be identified through conventional technology, comprehensive understanding of the developmental gene network system requires efficient identification of "all" regulatory sequences in the genome and their annotation. The work presented in this paper reports the use of ChIP-Seq (combination of chromatin immunoprecipitation and massive parallel DNA sequencing) with several marker proteins (such as RNA polymerase and histone modification) to identify promoters and enhancers in the mouse genome. In addition, CTCF binding was used to identify insulator elements and to define boundaries of genetic units. By analyzing a diverse set of 19 tissues and cell types in the mouse, a map of nearly 300,000 murine cis-regulatory sequences has been produced. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of con- served non-coding sequences. Much of the mouse genome appears to be organized into domains of coordinately regulated enhancers and promoters.

In the class we will discuss how to utilize this resource for studying developmental biology, how this resource can be further extended, and what kind of additional resources might be needed for the complete understanding of genetic networks that govern all biological phenomena of this model organism.