Abstract
The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Amore G, Davidson EH (2006) Cis-regulatory control of cyclophilin, a member of the ets-dri skeletogenic gene battery in the sea urchin embryo. Dev Biol 293(2):555–64
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29
Benos PV, Bulyk ML, Stormo GD (2002) Additivity in protein–DNA interactions: how good an approximation is it?. Nucleic Acids Res 30(20):4442–4451
Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193(4):723–750
Blanchette M, Tompa M (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 12(5):739
Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR et al. (Sea Urchin Genome Sequencing Consortium) (2006) The genome of the sea urchin strongylocentrotus purpuratus. Science 314(5801):941–952
Das MK, Dai HK (2007) A survey of DNA motif finding algorithms. Feedback
Davidson EH (2006) The regulatory genome: gene regulatory networks in development and evolution. Academic Press, New York
Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C et al. (2002) A genomic regulatory network for development. Science 295(5560):1678, 1669
Elsik C, Mackey A, Reese J, Milshina N, Roos D, Weinstock G (2007) Creating a honey bee consensus gene set. Genome Biol 8(1):R13
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-encode? History and updated definition. Genome Res 17(6):669–681
Istrail S, Davidson EH (2005) Gene regulatory networks special feature: logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci 102(14):4954
Istrail S, Ben-Tabou De-Leon S, Davidson EH (2007) The regulatory genome and the computer. Dev Biol 310(2):187–195
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262(5131):208–214
Li N, Tompa M (2006) Analysis of computational approaches for motif discovery. Algorithms Mol Biol 1(8)
Livi CB, Davidson EH (2007) Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula. Gene Expr Patterns 7(1–2):1–7
Minokawa T, Wikramanayake AH, Davidson EH (2005) Cis-regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev Biology 288(2):545–558
Pevzner PA, Sze SH (2000) Combinatorial approaches to finding subtle signals in DNA sequences. In: Proceedings of the eighth international conference on intelligent systems for molecular biology, vol 8, pp 269–278
Ransick A, Davidson EH (2006) Cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol 297(2):587–602
Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V (2006) The transcriptome of the sea urchin embryo. Science 314(5801):960–962
Stormo GD (2000) DNA binding sites: representation and discovery. Bioinformatics 16(1):16–23
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23:137–144
Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5(4):276–287
Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279(5358):1896–1902
Yuh CH, Bolouri H, Davidson EH (2001) Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. Development 128(5):617–629
Yuh CH, Davidson EH (1996) Modular cis-regulatory organization of endo16, a gut-specific gene of the sea urchin embryo. Development 122(4):1069–1082
Yuh C-H, Titus Brown C, Livi CB, Rowen L, Clarke PJC, Davidson EH (2002) Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol 246(1):148–161
Yuh C-H, Dorman ER, Howard ML, Davidson EH (2004) An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. Dev Biol 269(2):536–551
Zimmer C (2008) What is a specie? Sci Am Mag 298(6):72–79
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Tarpine, R., Istrail, S. (2009). On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_36
Download citation
DOI: https://doi.org/10.1007/978-3-540-88869-7_36
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-88868-0
Online ISBN: 978-3-540-88869-7
eBook Packages: Computer ScienceComputer Science (R0)