Developmentally Conserved Brain Designs Quantifiable with Transcriptome Tomography
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1
RIKEN Center for Advanced Photonics, Japan
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2
Brain Research Network (BReNt), Japan
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3
National Center for Global Health and Medicine, Japan
We have invented a framework for gene expression density mapping on the whole three dimensional (3D) anatomical context, transcriptome tomography, in which tissue sections in each of three orthogonal planes are fractionated (fractions), and gene expression densities in them measured with microarrays (fraction data) are then reconstructed to generate 3D maps (PLoS One 2012; 7, e45373). The fractions are exactly in the same thickness, so the fraction number of a coronal section, for instance, represents the distance from the starting point of the sections, the spino-cerebral (SC) border. Thus, besides 3D reconstructed maps, comprehensive expression densities along the body axes are measurable in the fractions. This unique feature of the data has encouraged us to test how gene expression gradients along the anterior-posterior (AP) body axis can be measured in the framework. Homeobox gene family members, Hox genes, are sequentially activated in time and space in a way of evolutionally conserved co-linear genomic position of the paralog genes (Figure 1A) and are participated in definitions of positional information along the AP axis in developmental stages of wide ranges of animals including mammals. Using the fraction data, we would show that the spatially co-linear expression patterns of Hox genes along the AP axis were also observed in the adult mouse brain. Intriguingly, the expression densities exponentially declined when plotted against the fraction numbers representing distances of from the SC border (Figure 1B), and the inclination was correlated to the genomic location of the paralogs. We would also show co-linear density gradients of Dlx genes that belonged to another homeobox gene family. The 3D expression maps of Hox and Dlx genes in the adult brain were seen in the ViBrism-DB for the first dataset created with transcriptome tomography ( http://vibrism.riken.jp/3dviewer/ex/index.html ; some seen in Figure 1C). Quantified expression density data exclusively produced with our framework provided evidences of the direct co-relation of them to the genomic organization. This may contribute to clarify a developmentally conserved regulatory mechanism underlying complex brain function.
Acknowledgements
This research was supported by Strategic Programs for R&D (President’s Discretionary Fund) RIKEN to Y.O., K.S. H.Y. et al.
Keywords:
digital atlasing,
Gene Expression Profiling,
Hox genes,
Dlx genes,
genomic organisation,
Transcriptome Tomography
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Digital atlasing
Citation:
Okamura-Oho
Y,
Shimokawa
K,
Takemoto
S and
Yokota
H
(2013). Developmentally Conserved Brain Designs Quantifiable with Transcriptome Tomography.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00023
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Received:
08 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Yuko Okamura-Oho, RIKEN Center for Advanced Photonics, Wako-Shi, Japan, yoho-tky@umin.ac.jp