Precise patterns of spatial and temporal gene expression are central to metazoan complexity and act as a driving force for embryonic development. While there has been substantial progress in dissecting and predicting cis-regulatory activity, our understanding of how information from multiple enhancer elements converge to regulate a gene's expression remains elusive. This is in large part due to the number of different biological processes involved in mediating regulation as well as limited availability of experimental measurements for many of them. Here, we used a Bayesian approach to model diverse experimental regulatory data, leading to accurate predictions of both spatial and temporal aspects of gene expression. We integrated whole-embryo information on transcription factor recruitment to multiple cis-regulatory modules, insulator binding and histone modification status in the vicinity of individual gene loci, at a genome-wide scale during Drosophila development. The model uses Bayesian networks to represent the relation between transcription factor occupancy and enhancer activity in specific tissues and stages. All parameters are optimized in an Expectation Maximization procedure providing a model capable of predicting tissue- and stage-specific activity of new, previously unassayed genes. Performing the optimization with subsets of input data demonstrated that neither enhancer occupancy nor chromatin state alone can explain all gene expression patterns, but taken together allow for accurate predictions of spatio-temporal activity. Model predictions were validated using the expression patterns of more than 600 genes recently made available by the BDGP consortium, demonstrating an average 15-fold enrichment of genes expressed in the predicted tissue over a na？ve model. We further validated the model by experimentally testing the expression of 20 predicted target genes of unknown expression, resulting in an accuracy of 95% for temporal predictions and 50% for spatial. While this is, to our knowledge, the first genome-wide approach to predict tissue-specific gene expression in metazoan development, our results suggest that integrative models of this type will become more prevalent in the future.
References
[1]
Azpiazu N, Frasch M (1993) tinman and bagpipe: two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila. Genes & Development 7: 1325–1325. doi: 10.1101/gad.7.7b.1325
[2]
Zaffran S, Kuchler A, Lee HH, Frasch M (2001) biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila. Genes Dev 15: 2900–2915.
[3]
Fujioka M, Wu X, Jaynes JB (2009) A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication. Development 136: 3077–3087. doi: 10.1242/dev.036467
[4]
Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117: 185–198. doi: 10.1016/s0092-8674(04)00304-6
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535–540. doi: 10.1038/nature06496
[7]
Chen X, Blanchette M (2007) Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics 8 Suppl 10: S2. doi: 10.1186/1471-2105-8-s10-s2
[8]
Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, et al. (2011) A regulatory archipelago controls Hox genes transcription in digits. Cell 147: 1132–1145. doi: 10.1016/j.cell.2011.10.023
[9]
Barolo S, Levine M (1997) hairy mediates dominant repression in the Drosophila embryo. EMBO J 16: 2883–2891. doi: 10.1093/emboj/16.10.2883
[10]
Perry MW, Boettiger AN, Levine M (2011) Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A 108: 13570–13575. doi: 10.1073/pnas.1109873108
[11]
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. (2011) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787–1797.
[12]
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148: 84–98. doi: 10.1016/j.cell.2011.12.014
[13]
Cheng C, Yan K-K, Yip KY, Rozowsky J, Alexander R, et al. (2011) A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biology 12: R15-R15. doi: 10.1186/gb-2011-12-2-r15
[14]
Karli？ R, Chung H-R, Lasserre J, Vlahovi？ek K, Vingron M (2009) Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences 107: 2926. doi: 10.1073/pnas.0909344107
[15]
Spitz F, Gonzalez F, Duboule D (2003) A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405–417. doi: 10.1016/s0092-8674(03)00310-6
[16]
Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T (2005) Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132: 797–803. doi: 10.1242/dev.01613
[17]
Wunderle VM, Critcher R, Hastie N, Goodfellow PN, Schedl A (1998) Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia. Proc Natl Acad Sci U S A 95: 10649–10654. doi: 10.1073/pnas.95.18.10649
[18]
Jack J, DeLotto Y (1995) Structure and regulation of a complex locus: the cut gene of Drosophila. Genetics 139: 1689–1700.
[19]
Cleard F, Moshkin Y, Karch F, Maeda RK (2006) Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat Genet 38: 931–935. doi: 10.1038/ng1833
[20]
Kwon D, Mucci D, Langlais KK, Americo JL, DeVido SK, et al. (2009) Enhancer-promoter communication at the Drosophila engrailed locus. Development 136: 3067–3075. doi: 10.1242/dev.036426
[21]
Splinter E, de Laat W (2011) The complex transcription regulatory landscape of our genome: control in three dimensions. EMBO J 30: 4345–4355. doi: 10.1038/emboj.2011.344
[22]
Hong JW, Hendrix DA, Levine MS (2008) Shadow enhancers as a source of evolutionary novelty. Science 321: 1314. doi: 10.1126/science.1160631
[23]
Barolo S (2011) Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy. BioEssays 34: 135–141. doi: 10.1002/bies.201100121
[24]
Prazak L, Fujioka M, Gergen JP (2010) Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors. Dev Biol 344: 1048–1059. doi: 10.1016/j.ydbio.2010.04.026
[25]
Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, et al. (2006) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159–1165. doi: 10.1038/ng1886
[26]
Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, et al. (2007) A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes & Development 21: 436. doi: 10.1101/gad.1509007
[27]
Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, et al. (2007) Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. Genes & Development 21: 2448. doi: 10.1101/gad.437607
[28]
Li X-y, MacArthur S, Bourgon R, Nix D, Pollard DA, et al. (2008) Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm. PLoS Biology 6: e27 EP. doi: 10.1371/journal.pbio.0060027
[29]
MacArthur S, Li X-Y, Li J, Brown J, Chu HC, et al. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology 10: R80. doi: 10.1186/gb-2009-10-7-r80
[30]
Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, et al. (2006) A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development. Developmental Cell 10: 797–807. doi: 10.1016/j.devcel.2006.04.009
[31]
Zinzen R, Furlong E (2008) Divergence in cis-regulatory networks: taking the ‘species’ out of cross-species analysis. Genome Biology 9: 240–240. doi: 10.1186/gb-2008-9-11-240
[32]
Liu Y-H, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, et al. (2009) A Systematic Analysis of Tinman Function Reveals Eya and JAK-STAT Signaling as Essential Regulators of Muscle Development. Developmental Cell 16: 280–291. doi: 10.1016/j.devcel.2009.01.006
[33]
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854–858. doi: 10.1038/nature07730
[34]
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311–318. doi: 10.1038/ng1966
[35]
Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, et al. (2009) Functional autonomy of distant-acting human enhancers. Genomics 93: 509–513. doi: 10.1016/j.ygeno.2009.02.002
[36]
He X, Sinha S (2010) ChIPs and regulatory bits. Nat Biotech 28: 142–143. doi: 10.1038/nbt0210-142
[37]
Engstr？m PG, Sui SJH, Drivenes ？, Becker TS, Lenhard B (2007) Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Research 17: 1898–1898. doi: 10.1101/gr.6669607
[38]
Hoff M (2008) Loopy Chromatin Brings Distant DNA to Bear on Silencing Promoter Genes. PLoS Biology 6: e313 EP -–e313 EP -. doi: 10.1371/journal.pbio.0060313
[39]
McLachlan GJ, Krishnan T (2008) The EM Algorithm and Extensions. Wiley-Interscience.
[40]
Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biology 8: R145-R145-R145-R145. doi: 10.1186/gb-2007-8-7-r145
[41]
Wilczynski B, Dojer N (2008) BNFinder: Exact and efficient method for learning Bayesian networks. Bioinformatics btn505-btn505. doi: 10.1093/bioinformatics/btn505
[42]
Nègre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, et al. (2010) A Comprehensive Map of Insulator Elements for the Drosophila Genome. PLoS Genet 6: e1000814-e1000814. doi: 10.1371/journal.pgen.1000814
[43]
Bell AC, West AG, Felsenfeld G (2001) Insulators and Boundaries: Versatile Regulatory Elements in the Eukaryotic Genome. Science 291: 447–450. doi: 10.1126/science.291.5503.447
[44]
Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, et al. (2005) Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast. Cell 122: 517–527. doi: 10.1016/j.cell.2005.06.026
[45]
Ouyang Z, Zhou Q, Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proceedings of the National Academy of Sciences 106: 21521–21521. doi: 10.1073/pnas.0904863106
[46]
Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology 3: research00881–08814-research00881–08814.
[47]
Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, et al. (2009) Unlocking the secrets of the genome. Nature 459: 927–930. doi: 10.1038/459927a
Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, et al. (2002) Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biology 3: research0079.0071–0079.0014-research0079？.0071–0079.0014.
[50]
Hanley JA, McNeil BJ (1983) A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 148: 839–843.
[51]
Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940–3941. doi: 10.1093/bioinformatics/bti623
[52]
Furlong EEM, Andersen EC, Null B, White KP, Scott MP (2001) Patterns of Gene Expression During Drosophila Mesoderm Development. Science 293: 1629–1633. doi: 10.1126/science.1062660
