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| Status |
Public on Aug 16, 2013 |
| Title |
Diverse patterns of genome-wide DNA targeting by transcriptional regulators in Drosophila melanogaster |
| Project |
modENCODE
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| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Understanding the regulatory genome remains a significant challenge. Annotation of regulatory elements and identification of the transcription factors (TFs) targeting these elements are key steps in understanding how a given cell interprets its genetic blueprint. One goal of the modENCODE (model organism Encyclopedia of DNA Elements) project is to survey a diverse sampling of TFs, both DNA-binding and non-DNA binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also suggest the existence of a partially self-contained Polycomb regulatory network, and highlight the importance of Trithorax-like (Trl) in maintaining hotspots of DNA binding throughout development. Furthermore, the data identify over 5,800 instances in which TFs target DNA regions with demonstrated enhancer activity. Regions of high TF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. A putative regulatory network generated based on these 84 regulators reveals hundreds of co-binding events, thousands of potential regulatory interactions, and distinct regulatory strategies at developmental and housekeeping genes. These data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and
http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago.
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| Contributor(s) |
Slattery M, Ma L, Spokony R, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran J, Rehm EJ, Grossman RL, Kellis M, White KP |
| Citation(s) |
24985916 |
| Submission date |
Aug 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Institute for Genomics and Systems Biology
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| Street address |
900 E. 57th STR. 10th FL.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (47)
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| GSM1209172 |
Stat92E_ChIP-seq, replicate1 |
| GSM1209173 |
Stat92E_ChIP-seq, replicate2 |
| GSM1209174 |
Stat92E_Input, replicate1 |
| GSM1209175 |
Notch_ChIP-seq, replicate1 |
| GSM1209176 |
Notch_ChIP-seq, replicate2 |
| GSM1209177 |
Notch_Input, replicate1 |
| GSM1209178 |
dm_ChIP-seq, replicate1 |
| GSM1209179 |
dm_ChIP-seq, replicate2 |
| GSM1209180 |
Lola_ChIP-seq, replicate1 |
| GSM1209181 |
Lola_ChIP-seq, replicate2 |
| GSM1209182 |
Lola_Input, replicate1 |
| GSM1209183 |
insv_ChIP-seq, replicate1 |
| GSM1209184 |
insv_ChIP-seq, replicate2 |
| GSM1209185 |
insv_ChIP-seq, replicate3 |
| GSM1209186 |
Hr78_W3L_ChIP-seq, replicate1 |
| GSM1209187 |
Hr78_W3L_ChIP-seq, replicate2 |
| GSM1209188 |
Hr78_W3L_Input, replicate1 |
| GSM1209189 |
Hr78_E8-16_ChIP-seq, replicate1 |
| GSM1209190 |
Hr78_E8-16_ChIP-seq, replicate2 |
| GSM1209191 |
Hr78_E8-16_Input, replicate1 |
| GSM1209192 |
h_ChIP-seq, replicate1 |
| GSM1209193 |
h_ChIP-seq, replicate2 |
| GSM1209194 |
h_ChIP-seq, replicate3 |
| GSM1209195 |
Cmi_ChIP-seq, replicate1 |
| GSM1209196 |
Cmi_ChIP-seq, replicate2 |
| GSM1209197 |
Cmi_Input, replicate1 |
| GSM1209198 |
CG8478_ChIP-seq, replicate1 |
| GSM1209199 |
CG8478_ChIP-seq, replicate2 |
| GSM1209200 |
AbdB_ChIP-seq, replicate1 |
| GSM1209201 |
AbdB_ChIP-seq, replicate2 |
| GSM1209202 |
AbdB_Input, replicate1 |
| GSM1209203 |
S2_Input, replicate1 |
| GSM1209204 |
Kc167_Input, replicate1 |
| GSM1210920 |
br_ChIP-seq replicate1 |
| GSM1210921 |
br_ChIP-seq replicate2 |
| GSM1210922 |
br_Input replicate1 |
| GSM1210923 |
cnc_ChIP-seq replicate1 |
| GSM1210924 |
cnc_ChIP-seq replicate2 |
| GSM1210925 |
cnc_Input replicate1 |
| GSM1210926 |
prd-RF12_ChIP-seq replicate1 |
| GSM1210927 |
prd-RF12_ChIP-seq replicate2 |
| GSM1210928 |
prd-RF13_ChIP-seq replicate1 |
| GSM1210929 |
prd-RF13_ChIP-seq replicate2 |
| GSM1210930 |
E0-12_Input replicate1 |
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| Relations |
| BioProject |
PRJNA215278 |
| SRA |
SRP028841 |
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