DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

Matthew S Wilken; Joseph A Brzezinski; Anna La Torre; Kyle Siebenthall; Robert Thurman; Peter Sabo; Richard S Sandstrom; Jeff Vierstra; Theresa K Canfield; R Scott Hansen; Michael A Bender; John Stamatoyannopoulos; Thomas A Reh

doi:10.1186/1756-8935-8-8

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

Epigenetics Chromatin. 2015 Feb 28:8:8. doi: 10.1186/1756-8935-8-8. eCollection 2015.

Authors

Affiliations

¹ Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Molecular and Cellular Biology Program, University of Washington, MCB Program Office, T-466 Health Sciences Building, Box 357275, Seattle, WA 98195 USA.
² Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Department of Ophthalmology, University of Colorado School of Medicine, 1675 Aurora Court, Aurora, CO 80045 USA.
³ Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA.
⁴ Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA.
⁵ Department of Pediatrics, University of Washington, 1959 NE Pacific St, Health Sciences Building, Seattle, WA Box 356320, 98195 USA ; Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA.

Abstract

Background: The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex.

Results: For the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements.

Conclusions: Overall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.

Keywords: Central nervous system; Cis-regulation; DNase-seq; Retina.

Abstract

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