The mammalian liver consists of hexagon-shaped lobules that are radially polarized by blood flow and morphogens1,2,3,4. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation5,6, but a detailed genome-wide reconstruction of this spatial division of labour has not been achieved. Here we measure the entire transcriptome of thousands of mouse liver cells and infer their lobule coordinates on the basis of a panel of zonated landmark genes, characterized with single-molecule fluorescence in situ hybridization7. Using this approach, we obtain the zonation profiles of all liver genes with high spatial resolution. We find that around 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. These include a spatial order of bile acid biosynthesis enzymes that matches their position in the enzymatic cascade. Our approach can facilitate the reconstruction of similar spatial genomic blueprints for other mammalian organs.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Gene Expression Omnibus
We thank R. Milo and all members of our laboratory for valuable comments. We thank M. Schwarz, A. Braeuning and S. Colnot for sharing their data and A. Sharp, E. Ariel, E. Hagai and Z. Gavish for help with experimental procedures. I.A. is supported by the European Research Council (309788), and the Israel Science Foundation, the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine and the Helen and Martin Kimmel award for innovative investigation. I.A. is the incumbent of the Alan and Laraine Fischer Career Development Chair. S.I. is supported by the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics, The Leir Charitable Foundations, Richard Jakubskind Laboratory of Systems Biology, Cymerman-Jakubskind Prize, The Lord Sieff of Brimpton Memorial Fund, the I-CORE program of the Planning and Budgeting Committee and the Israel Science Foundation (grants 1902/ 12 and 1796/12), the Israel Science Foundation grant No. 1486/16, the EMBO Young Investigator Program and the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement number 335122. S.I. is the incumbent of the Philip Harris and Gerald Ronson Career Development Chair.
Extended data figures
This file contains the posterior matrix, which shows the probability for each lobule layer.
The file contains the zonation matrix, which shows the average cellular expression levels at each layer in fraction of total cellular mRNA.
This file shows the signaling pathways affecting liver zonation.
This file shows the zonation of KEGG pathways.
This file shows the analysis of spatial expression of enzyme pairs from KEGG pathways.
This file shows the Parameters of Gamma distributions fitted to expression profiles of the six landmark genes in each of the 9 lobule layers.
This file contains the DNA sequences of the probes used for smFISH.