Abstract
Developmental biologists are interested in the question of how a fertilized egg, equipped with only about 22,000 genes in its nucleus, is able to transform into a complete human being. In this chapter we discuss the functional genomics analysis of mammalian kidney development, using the kidney as a model system to better understand the basic principles of organogenesis. The formation of an organ requires a complex orchestration of gene expression in many different cell types at multiple developmental stages. The driving gene expression patterns can be captured in a variety of ways. Laser capture microdissection (LCM) can be used to isolate developmental compartments of the kidney, such as the forming glomerulus, for gene expression profiling. Transgenic lines of mice can be used to fluorescently label specific cell types that can then be purified by fluorescent activated cell sorting (FACS). And more recent very high resolution technologies allow high throughput RNA-seq of single cells of a developing organ. These methodologies produce immense datasets that require powerful informatics tools for their analysis. The purpose of this chapter is to illustrate how these various tools can be used to address important questions in developmental biology that are highly relevant to child health, and development of the kidney. The huge amounts of data generated need to be captured and annotated in a systematic way, stored, integrated and analyzed. The goal is to identify basic principles as well as precise pathways that drive organogenesis. The results will provide a better understanding of developmental disorders, and guide efforts to recapitulate organogenesis in vitro, for example in the generation of replacement organs from induced pluripotent stem cells.
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References
Brunskill EW, Potter SS. RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes. Dev Biol. 2012;368:4–17.
Brunskill EW, Potter SS. Pathogenic pathways are activated in each major cell type of the glomerulus in the Cd2ap mutant mouse model of focal segmental glomerulosclerosis. BMC Nephrol. 2015;16:71.
Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius MT, Aronow J, Kaimal V, Jegga AG, Yu J, Grimmond S, et al. Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell. 2008;15:781–91.
Brunskill EW, Park JS, Chung E, Chen F, Magella B, Potter SS. Single cell dissection of early kidney development: multilineage priming. Development. 2014;141:3093–101.
Carroll TJ, Park JS, Hayashi S, Majumdar A, McMahon AP. Wnt9b plays a central role in the regulation of mesenchymal to epithelial transitions underlying organogenesis of the mammalian urogenital system. Dev Cell. 2005;9:283–92.
Challen G, Gardiner B, Caruana G, Kostoulias X, Martinez G, Crowe M, Taylor DF, Bertram J, Little M, Grimmond SM. Temporal and spatial transcriptional programs in murine kidney development. Physiol Genomics. 2005;23:159–71.
Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature. 2008;453:544–7.
Chiang MK, Melton DA. Single-cell transcript analysis of pancreas development. Dev Cell. 2003;4:383–93.
Chubb JR, Trcek T, Shenoy SM, Singer RH. Transcriptional pulsing of a developmental gene. Curr Biol. 2006;16:1018–25.
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods. 2008;5:613–9.
Costantini F, Kopan R. Patterning a complex organ: branching morphogenesis and nephron segmentation in kidney development. Dev Cell. 2010;18:698–712.
De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010;8:e1000384.
Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002;297:1183–6.
Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei CL, et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity. 2010;32:317–28.
Golding I, Paulsson J, Zawilski SM, Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005;123:1025–36.
Guo M, Wang H, Potter SS, Whitsett JA, Xu Y. SINCERA: a pipeline for single-cell RNA-Seq profiling analysis. PLoS Comput Biol. 2015;11:e1004575.
Jackson DA, Hassan AB, Errington RJ, Cook PR. Visualization of focal sites of transcription within human nuclei. EMBO J. 1993;12:1059–65.
Johansson T, Broll I, Frenz T, Hemmers S, Becher B, Zeilhofer HU, Buch T. Building a zoo of mice for genetic analyses: a comprehensive protocol for the rapid generation of BAC transgenic mice. Genesis. 2010;48:264–80.
Keller G, Zimmer G, Mall G, Ritz E, Amann K. Nephron number in patients with primary hypertension. N Engl J Med. 2003;348:101–8.
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465:182–7.
Ko MS, Nakauchi H, Takahashi N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 1990;9:2835–42.
Lowik MM, Groenen PJ, Pronk I, Lilien MR, Goldschmeding R, Dijkman HB, Levtchenko EN, Monnens LA, van den Heuvel LP. Focal segmental glomerulosclerosis in a patient homozygous for a CD2AP mutation. Kidney Int. 2007;72:1198–203.
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202–14.
Mikkola HK, Orkin SH. Gene targeting and transgenic strategies for the analysis of hematopoietic development in the mouse. Methods Mol Med. 2005;105:3–22.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320:1344–9.
Novick A, Weiner M. Enzyme induction as an all-or-none phenomenon. Proc Natl Acad Sci U S A. 1957;43:553–66.
Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet. 2004;36:1065–71.
Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet. 2002;31:69–73.
Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008;5:877–9.
Ross IL, Browne CM, Hume DA. Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunol Cell Biol. 1994;72:177–85.
Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010;107:10514–9.
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015;33:495–502.
Schmidt-Ott KM, Yang J, Chen X, Wang H, Paragas N, Mori K, Li JY, Lu B, Costantini F, Schiffer M, et al. Novel regulators of kidney development from the tips of the ureteric bud. J Am Soc Nephrol. 2005;16:1993–2002.
Schwab K, Patterson LT, Aronow BJ, Luckas R, Liang HC, Potter SS. A catalogue of gene expression in the developing kidney. Kidney Int. 2003;64:1588–604.
Schwarz K, Simons M, Reiser J, Saleem MA, Faul C, Kriz W, Shaw AS, Holzman LB, Mundel P. Podocin, a raft-associated component of the glomerular slit diaphragm, interacts with CD2AP and nephrin. J Clin Invest. 2001;108:1621–9.
Self M, Lagutin OV, Bowling B, Hendrix J, Cai Y, Dressler GR, Oliver G. Six2 is required for suppression of nephrogenesis and progenitor renewal in the developing kidney. EMBO J. 2006;25:5214–28.
Shih NY, Li J, Cotran R, Mundel P, Miner JH, Shaw AS. CD2AP localizes to the slit diaphragm and binds to nephrin via a novel C-terminal domain. Am J Pathol. 2001;159:2303–8.
Stuart RO, Bush KT, Nigam SK. Changes in global gene expression patterns during development and maturation of the rat kidney. Proc Natl Acad Sci U S A. 2001;98:5649–54.
Takasuka N, White MR, Wood CD, Robertson WR, Davis JR. Dynamic changes in prolactin promoter activation in individual living lactotrophic cells. Endocrinology. 1998;139:1361–8.
Temin HM, Baltimore D. RNA-directed DNA synthesis and RNA tumor viruses. Adv Virus Res. 1972;17:129–86.
Tietjen I, Rihel JM, Cao Y, Koentges G, Zakhary L, Dulac C. Single-cell transcriptional analysis of neuronal progenitors. Neuron. 2003;38:161–75.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381–6.
Tsuboi A, Yoshihara S, Yamazaki N, Kasai H, Asai-Tsuboi H, Komatsu M, Serizawa S, Ishii T, Matsuda Y, Nagawa F, et al. Olfactory neurons expressing closely linked and homologous odorant receptor genes tend to project their axons to neighboring glomeruli on the olfactory bulb. J Neurosci. 1999;19:8409–18.
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A. 1990;87:1663–7.
Vassar R, Ngai J, Axel R. Spatial segregation of odorant receptor expression in the mammalian olfactory epithelium. Cell. 1993;74:309–18.
Wansink DG, Schul W, van der Kraan I, van Steensel B, van Driel R, de Jong L. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J Cell Biol. 1993;122:283–93.
Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I, Desplan C. Stochastic spineless expression creates the retinal mosaic for colour vision. Nature. 2006;440:174–80.
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Potter, S.S. (2016). Functional Genomics-Renal Development and Disease. In: Hutton, J. (eds) Pediatric Biomedical Informatics. Translational Bioinformatics, vol 10. Springer, Singapore. https://doi.org/10.1007/978-981-10-1104-7_20
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DOI: https://doi.org/10.1007/978-981-10-1104-7_20
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