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Series GSE230035 Query DataSets for GSE230035
Status Public on Nov 05, 2023
Title A new pipeline SPICE identifies novel JUN-IKZF1 composite elements
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. SPICE de novo predicted known composite elements, including AP1-IRF composite elements (AICE) and STAT5 tetramers, and also predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We confirmed cooperative binding of JUN and IKZF1 to an upstream conserved noncoding region, CNS9, in the human IL10 gene, that contains a non-canonical IKZF1 site, and the activity of an IL10-luciferase reporter construct depended on both this site and the AP1 binding site within this composite element in primary B and T cells. Our findings reveal an unappreciated global association of IKZF1 and AP1, and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.
Overall design ChIP-Seq experiments with antibodies to IKZF1 and JUN in primary mouse B cells that were either untreated or treated with LPS or LPS + IL-21 for 3 hours.
Contributor(s) Li P, Pulugulla SH, Das S, Oh J, Spolski R, Lin J, Leonard WJ
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Submission date Apr 19, 2023
Last update date Nov 06, 2023
Contact name Peng Li
Organization name NIH
Department NHLBI
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (7)
GSM7184269 ChIP-Seq B cells, untreated, anti-cJUN
GSM7184270 ChIP-Seq B cells, untreated, anti-IKZF1
GSM7184271 ChIP-Seq B cells, LPS, anti-cJUN
BioProject PRJNA957252

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Supplementary file Size Download File type/resource
GSE230035_RAW.tar 806.2 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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