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TF2Network: unravelling gene regulatory networks and transcription factor functions in Arabidopsis thaliana

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GRC Plant Molecular Biology - Dynamic Plant Systems
June 10 - 15, 2018

Published in: Science
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TF2Network: unravelling gene regulatory networks and transcription factor functions in Arabidopsis thaliana

  1. 1. TF2Network: unravelling gene regulatory networks and transcription factor functions in Arabidopsis thaliana KlaasVandepoele Gordon Research Conference Dynamic Plant Systems June 10 - 15, 2018 1 plaza_genomics
  2. 2. Experimental characterization of regulatory DNA ENCODE; Sullivan et al., 2015 2 Gene Regulatory Networks analysis • IdentifyTFs active in specific cellular conditions • Identify new gene functions, both forTFs and target genes • Study network structure and identify cooperativeTF regulation
  3. 3. Mapping regulatoryTF – target gene interactions 3 Mejia-Guerra et al., 2012 EMSA eY1H SELEX PBM ChIP-Seq DAP-Seq DNaseI ATAC-Seq
  4. 4. Computational analysis ofTF binding sites (motifs) 4 • Known transcription factor (TF) binding sites 1. Limited information about binding site for mostTFs 2. Variety in qualityTF binding site models 3. Motif redundancy & multi-geneTF families 4. How to identify functionalTF binding sites?  Simple motif mapping yields many False positives  Not everyTATA is a ‘TATA’ Database #motifs Species PLACE 469 Vascular plants AGRIS 99 Arabidopsis thaliana AtProbe 172 Arabidopsis thaliana CisBP >1000 Cross-species DAP-Seq >500 Arabidopsis thaliana JASPAR2018 >500 Cross-species
  5. 5. TF2Network: inferringTF-target interactions using publicly available binding site information 5  Data sources  Experimental TF binding site information (1793 PWMs - 916TFs)  Enrichment statistics using quality- based filtering ofTF binding site matches  Integration experimental datasets  TF2Network predicts potentialTF regulators for a set of co-expressed or functionally related genes in A. thaliana CisBP, Franco-Zorrilla et al. , Plant Cistrome Database, JASPAR 2016, UNIPROBE, AGRIS and AthaMAP
  6. 6. IntegrationTF binding site information TheTF2Network tool is available at http://bioinformatics.psb.ugent.be/webtools/TF2Network/
  7. 7. Integration gene functions (Gene Ontology) 7
  8. 8. Integration gene functions (Gene Ontology) 8
  9. 9. Integration experimental protein-DNA interactions 9 Experimental data • >170,883 protein-DNA interactions (679TFs) • 76,236 protein-protein interactions • 13M co-expression interactions (RNA-Seq)
  10. 10. Integration protein-protein and co-expression interactions 10 Experimental data • >170,883 protein-DNA interactions (679TFs) • 76,236 protein-protein interactions • 13M co-expression interactions
  11. 11. Evaluation recovery correct regulators ‘ChIP genes’ benchmark 24TFs 500 input genes ‘DE genes after TF perturbation’ benchmark 23TFs; 500 input genes Three gene region types: • Long: complete upstream + exon-masked gene body + 1 kb downstream • Intermediate: 1kb upstream + exon-masked gene body + 500 bp downstream • Short: 500 bp upstream core promoter 11
  12. 12. Protein-protein interactions (PPIs) between predicted regulators reveal cooperative TF regulation Intra-family PPI Inter-family PPI • Starting from DE genes for perturbed TF recovery of perturbed TF as top-ranked regulator recovery of cooperative TFs showing physical interactions with perturbed TF 12
  13. 13. Systematic regulatory annotation of Arabidopsis genes • Functional regulons combine known GO gene functions with co-expression information • Global recovery of correct regulators for 471TFs covering different biological processes defense response (15TFs), plant organ development (12TFs), hormone-mediated signaling pathway (8TFs). • Focusing on correct GO-TF regulators: 6,498/11,447 unknown Arabidopsis genes are part of functional regulons 13
  14. 14. Brassicaceae-specific genes involved in flower development • 43 unknown genes part of ‘flower development’ regulons with ≥3 incoming flowering relatedTFs 14 AT1G06420 Unknown protein; conserved in 6 Brassicaceae species Predicted regulators: AT2G45660 (AGL20);AT4G38000 (DOF4.7);AT5G13790 (AGL15); AT5G20240 (PI) AT1G05540 Protein of unknown function (DUF295); conserved in 7 Brassicaceae species Predicted regulators: AT5G10140 (AGL25);AT5G13790 (AGL15);AT5G20240 (PI)
  15. 15. Brassicaceae-specific genes involved in flower development 15 AT1G06420 BAR eFP browser: Klepikova RNA-Seq atlas
  16. 16. New regulators involved in flower development 16 AT5G12440 – CCCH-type zinc fingerfamily protein Predicted regulators: AT2G45660 (AGL20), AT4G38000 (DOF4.7), AT5G20240 (PI),AT1G17920 (HDG20), AT3G21890 (BBX31) BAR eFP browser: Klepikova RNA-Seq atlas
  17. 17. New regulators involved in flower development 17 AT5G20420 – SNF2-related protein Predicted regulators: AT4G38000 (DOF4.7); AT5G13790 (AGL15) BAR eFP browser: Klepikova RNA-Seq atlas
  18. 18. Conclusions • Different experimental –omics data types as well as integrativeTF binding site methods contribute significantly to the improved delineation of gene regulatory networks • Combined with high-throughput PPI data,TF binding site-based regulatory networks offer new insights about cooperativeTF regulation • Functional regulons are a starting point for the systematic functional and regulatory annotation of all genes in a genome new biological discoveries 18 Dries VaneechoutteShubhada Kulkarni Kulkarni et al. Nucleic Acids Res. 2018 Apr 6;46(6):e31
  19. 19. Confirming known and predicting new TF functions 19

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