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| Status |
Public on May 19, 2022 |
| Title |
Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Congenital dyserythropoietic anemia type I (CDA-I) is an autosomal recessive disorder marked by ineffective erythropoiesis, abnormal morphology of bone marrow erythroblasts, and iron overload. Most cases of CDA-I are caused by mutations in the CDAN1 gene, which encodes for a ubiquitous protein of unknown function, codanin-1. To study the function of codanin-1 in CDA-I erythroid pathophysiology several erythroid models were developed. Here we show that codanin-1 expression is required for erythroid progenitor development and normal erythroid cell differentiation. Erythroid cells lacking codanin-1 demonstrated morphologic changes similar to that observed in CDA-I. Global gene expression changes after codanin-1 knockdown revealed alterations in a set of key erythroid genes. In particular, the AHSP gene, which showed decreased mRNA expression after codanin-1 knockdown in CD34+ cells, also demonstrated increased codanin-1 occupancy at its gene regulatory region by chromatin immunoprecipitation coupled to high-throughput sequencing. Using cell models recapitulating many features of CDA-I, we have confirmed the importance of codanin-1 during erythroid differentiation and provide mechanistic insight into how loss of codanin-1 expression results in CDA-I.
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| Overall design |
ChIP-Seq analysis of codanin-1 binding sites in human K562 erythroleukemia cells. ChIP assays were performed using anti-codanin-1 antibodies (Cod1, Cod2). Cod1 corresponds to homemade antibody raised against N-terminal fragment of codanin-1 (amino acids 123-142, ProteinTech). Cod2 corresponds to commercial antibody raised against C-terminal fragment of codanin-1 from Santa Cruz (sc-68404, Santa Cruz). As controls, anti-GATA1 antibody (N6) (sc-265X, Santa Cruz) and rabbit IgG (sc-2027, Santa Cruz) were used.
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| Contributor(s) |
Bosques L, Hattangadi SM, Tang C, Mehta S, Kupfer GM |
| Citation missing |
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| Submission date |
May 20, 2019 |
| Last update date |
May 21, 2022 |
| Contact name |
Gary Kupfer |
| E-mail(s) |
gary.kupfer@yale.edu
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| Organization name |
Yale
|
| Street address |
333 Cedar St
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| City |
New Haven |
| ZIP/Postal code |
06460 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE131515 |
Codanin-1 binding sites in human K562 erythroleukemia cells; Global Gene expression changes in response codanin-1 knockdown in erythroid-committed cells |
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| Relations |
| BioProject |
PRJNA543943 |
| SRA |
SRP199088 |
