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Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs

Michelle Kudron1, Wei Niu1, Zhi Lu23, Guilin Wang1, Mark Gerstein3, Michael Snyder4 and Valerie Reinke1*

Author Affiliations

1 Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA

2 MOE Key Lab of Bioinformatics and System Biology, Rm 2-111 Biotech Building, School of Life Sciences, Tsinghua University, Beijing, China 100084

3 Program in Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA

4 Department of Genetics, Stanford University School of Medicine, Mail Stop-5120, Stanford, CA 94305, USA

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Genome Biology 2013, 14:R5  doi:10.1186/gb-2013-14-1-r5

Published: 23 January 2013

Additional files

Additional file 1:

Supplementary figures and tables. Figure S1: a diagram of each tissue-specific construct and expression of each transgenic strain as determined by GFP signal. Figure S2: demonstration that the GFP-tagged constructs rescue the mutant phenotypes of dpl-1 and lin-35 mutants. Figure S3: high correlation between replicates for each factor and between different experiments and transgenic EFL-1 binding mirrors endogenous binding in the L1 soma. Figure S4: Venn diagrams that show the comparison of called binding sites for each factor in each tissue between factors within a tissue and between tissues for a given factor. Figure S5: tissue-specific binding for a subset of germline-specific and soma-specific sites using ChIP-qPCR. Figure S6: an example of other direct target genes that still retain EFL-1 binding in lin-35 mutants. Additional binding profiles at the loci encoding various candidate small RNA pathway regulatory proteins not shown in Figure 5a. EFL-1 is not ectopically recruited to the promoters of germline-specific small RNA regulators. Figure S7: MEME analysis that shows that tissue-specific targets have distinct E2F binding motifs. Table S1: a list of all the strains used for ChIP-seq analyses. Table S2: number of reads for each sample and replicate used in the analyses. Also included is a section describing the materials and methods used for the additional data files.

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Additional file 2:

Supplementary file 1. A list of binding sites for each factor in each tissue on a separate sheet.

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Additional file 3:

Supplementary file 2. Target genes and intergenic binding sites for tissue-specific datasets.

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Additional file 4:

Supplementary file 3. Targets overlapping with LIN-54 ChIP-chip study [15].

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Additional file 5:

Supplementary file 4. GO categories for each tissue-specific target gene set returned by DAVID, and summary page showing selected categories for Figure 3e.

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Additional file 6:

Supplementary file 5. Genes regulated by microarray analyses with overlaps to tissue-specific binding sites, along with statistical analysis.

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Additional file 7:

Supplementary file 6. Genes targeted by 22G RNAs [32] compared to MES-4 target genes [29].

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Additional file 8:

Supplementary file 7. Precise sequences associated with each motif identified by MEME for each set of tissue-specific binding sites.

Format: XLSX Size: 160KB Download file

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