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| Status |
Public on Sep 08, 2013 |
| Title |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: Thymocytes) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros, a critical regulator of lymphopoiesis and leukemogenesis. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling (this GEO submission: RNA-Seg of whole thymus from wt and the two ZnF mutants), reveal that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions, and they demonstrate that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors.
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| Overall design |
RNA-Seq from Whole Thymus comparing wt (3 replicates), Ikaros-ZnF1-/- mutant (2 replicates) and Ikaros-ZnF4-/- mutant (2 replicates)
RPKM_Thymocytes.txt (linked below as a supplementary file) reports the relative mRNA expression levels (RPKM)values for all annotated Refseq genes that had at least one read in at least one of the samples, with duplicates for the same gene (different transcripts for same gene) filtered out. RPKM (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
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| Contributor(s) |
Schjerven H, Smale ST |
| Citation(s) |
24013668 |
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| Submission date |
Sep 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Hilde Schjerven |
| Organization name |
UCSF
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| Department |
Laboratory Medicine
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| Street address |
513 Parnassus Ave
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE33693 |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros |
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| Relations |
| SRA |
SRP008272 |
| BioProject |
PRJNA154865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32190_RAW.tar |
16.4 Gb |
(http)(custom) |
TAR (of BAM, BEDGRAPH, BIGWIG, SAM) |
| GSE32190_RPKM_Thymocytes.txt.gz |
377.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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