Contributors:David Y. Rhee, Dong-Yeon Cho, Bo Zhai, Matthew Slattery, Lijia Ma, Julian Mintseris, Christina Y. Wong, Kevin P. White, Susan E. Celniker, Teresa M. Przytycka, Steven P. Gygi, Robert A. Obar, Spyros Artavanis-Tsakonas
Table containing both overlapping and nonoverlapping targets between interacting TF pairs identified by ChIP-seq.
... Table containing information regarding the dominant-negative mastermind genetic screen, including Drosophila stock IDs and controls used.
... Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA... Drosophila Transcription Factor Interaction Network
High-confidence interaction network map representing interactions involving 229 site-specific TFs (red nodes). The network contains 647 proteins connected by 624 edges. A total of 117 putative protein complexes were defined using MCL clustering (Enright et al., 2002; Table S3); 9.46% of interactions are binary TF-TF interactions, 21.79% are nonTF-nonTF interactions, and 68.75% are interactions between a TF and a non-TF protein. Protein interactions are shown as gray lines, with line thickness proportional to the HGSCore for the interaction and intercomplex interactions shown in light gray. A number of previously characterized protein complexes are labeled.
See also Tables S1 and S2 and Data S1.
... Inferred Regulatory Edges for Transcriptional Complexes
(A) Transcriptional regulatory motifs, representing instances in which an interacting protein regulates its binding partner (1:1), combinatorial regulation of a target by two interacting factors (2:1), and regulation of interacting proteins by a single factor (1:2). Red edges indicate PPIs and gray edges with arrows indicate directional regulatory edges.
(B) Components of the Drosophila dREAM complex recovered in our interaction network.
(C) Transcriptional regulators of Dp-E2f.
(D) Basal transcription machinery components.
(E) Cell-cycle proteins.
(F) DNA replication-related proteins.
(H) Chromatin related.
(I) Unannotated targets of Dp/E2f.
See also Table S8 and Data S3.
... Tissue-Specific Protein Complexes
(A) Tissue-specificity distribution for all proteins in the high-confidence interaction network scored using the TSPS algorithm. Low-specificity proteins are labeled in green, moderate-specificity proteins are labeled in yellow, and high-specificity proteins are labeled in blue. Distribution was fit to a trimodal distribution and bins were defined with cutoffs of 0.4781 and 1.1741.
(B) Testis-specific protein complex. Rounded squares represent “core” network proteins and blue circles represent “specific” proteins. CG8117 is an ortholog of a human testis-specific transcription elongation factor, also expressed specifically in the Drosophila testis. The other polymerase II components are expressed broadly.
(C) Larval CNS-specific protein complex. Nerfin-1 is highly specific to the larval CNS. It interacts with two low-specificity proteins: the TF sd and the transcription coactivator yki.
See also Table S6 and Data S2.
... Table S7. Overlapping for Interacting TF Pairs Identified by ChIP-Seq, Related to Figure 5
Contributors:Ci Chu, Kun Qu, Franklin L. Zhong, Steven E. Artandi, Howard Y. Chang
ChIRP-Seq Reveals roX2 Binding Sites on X Chromosome
(A) roX2 colocalizes with MSL complex and CES.
(B) 308 roX2 binding sites are all on the X chromosome, indicating an FDR ∼0.
(C) roX2 ChIRP-seq is overall highly correlated to MSL3 ChIP-seq (R = 0.77 for log2 intensity > 10).
(D) roX2 binds across X-linked gene bodies with bias toward the 3′ end, in a manner similar to MSL3 but with higher dynamic range. ChIRP-seq or ChIP-seq signal intensity for all bound genes on X or genes on chromosome 2L were averaged and aligned to gene start and end annotations.
(E) roX2 binding sites are strongly enriched for a sequence motif that is nearly identical to MSL3 motif.
Contributors:Arnau Sebé-Pedrós, Cecilia Ballaré, Helena Parra-Acero, Cristina Chiva, Juan J. Tena, Eduard Sabidó, José Luis Gómez-Skarmeta, Luciano Di Croce, Iñaki Ruiz-Trillo
Comparative Proximal Distribution of Chromatin Marks across Opisthokonta Species
For each species, a plot shows the average normalized read coverage of four different histone modifications around the TSS (±5 kb), and heatmaps represent the same coverage for all genes sorted by level of expression. ChIP-seq data were obtained from publicly available datasets: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Nematostella vectensis, and Saccharomyces cerevisiae.
... Table S1. Sequencing Statistics and ChIP-Seq/ATAC-Seq Peak Coordinates, Related to Supplemental Experimental Procedures