GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis.
We report the genomic occupancy profiles of the key hematopoietic transcription factor GATA-1 in pro-erythroblasts and mature erythroid cells fractionated from day E12.5 mouse fetal liver cells. Integration of GATA-1 occupancy profiles with available genome-wide transcription factor and epigenetic p...
| Hoofdauteurs: | , , , , , , |
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| Formaat: | Journal article |
| Taal: | English |
| Gepubliceerd in: |
2013
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| _version_ | 1826301290029776896 |
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| author | Papadopoulos, G Karkoulia, E Tsamardinos, I Porcher, C Ragoussis, J Bungert, J Strouboulis, J |
| author_facet | Papadopoulos, G Karkoulia, E Tsamardinos, I Porcher, C Ragoussis, J Bungert, J Strouboulis, J |
| author_sort | Papadopoulos, G |
| collection | OXFORD |
| description | We report the genomic occupancy profiles of the key hematopoietic transcription factor GATA-1 in pro-erythroblasts and mature erythroid cells fractionated from day E12.5 mouse fetal liver cells. Integration of GATA-1 occupancy profiles with available genome-wide transcription factor and epigenetic profiles assayed in fetal liver cells enabled as to evaluate GATA-1 involvement in modulating local chromatin structure of target genes during erythroid differentiation. Our results suggest that GATA-1 associates preferentially with changes of specific epigenetic modifications, such as H4K16, H3K27 acetylation and H3K4 di-methylation. Furthermore, we used random forest (RF) non-linear regression to predict changes in the expression levels of GATA-1 target genes based on the genomic features available for pro-erythroblasts and mature fetal liver-derived erythroid cells. Remarkably, our prediction model explained a high proportion of 62% of variation in gene expression. Hierarchical clustering of the proximity values calculated by the RF model produced a clear separation of upregulated versus downregulated genes and a further separation of downregulated genes in two distinct groups. Thus, our study of GATA-1 genome-wide occupancy profiles in mouse primary erythroid cells and their integration with global epigenetic marks reveals three clusters of GATA-1 gene targets that are associated with specific epigenetic signatures and functional characteristics. |
| first_indexed | 2024-03-07T05:30:09Z |
| format | Journal article |
| id | oxford-uuid:e1f97a8f-a362-4be5-b99b-198a97ba646b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:30:09Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:e1f97a8f-a362-4be5-b99b-198a97ba646b2022-03-27T09:57:56ZGATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:e1f97a8f-a362-4be5-b99b-198a97ba646bEnglishSymplectic Elements at Oxford2013Papadopoulos, GKarkoulia, ETsamardinos, IPorcher, CRagoussis, JBungert, JStrouboulis, JWe report the genomic occupancy profiles of the key hematopoietic transcription factor GATA-1 in pro-erythroblasts and mature erythroid cells fractionated from day E12.5 mouse fetal liver cells. Integration of GATA-1 occupancy profiles with available genome-wide transcription factor and epigenetic profiles assayed in fetal liver cells enabled as to evaluate GATA-1 involvement in modulating local chromatin structure of target genes during erythroid differentiation. Our results suggest that GATA-1 associates preferentially with changes of specific epigenetic modifications, such as H4K16, H3K27 acetylation and H3K4 di-methylation. Furthermore, we used random forest (RF) non-linear regression to predict changes in the expression levels of GATA-1 target genes based on the genomic features available for pro-erythroblasts and mature fetal liver-derived erythroid cells. Remarkably, our prediction model explained a high proportion of 62% of variation in gene expression. Hierarchical clustering of the proximity values calculated by the RF model produced a clear separation of upregulated versus downregulated genes and a further separation of downregulated genes in two distinct groups. Thus, our study of GATA-1 genome-wide occupancy profiles in mouse primary erythroid cells and their integration with global epigenetic marks reveals three clusters of GATA-1 gene targets that are associated with specific epigenetic signatures and functional characteristics. |
| spellingShingle | Papadopoulos, G Karkoulia, E Tsamardinos, I Porcher, C Ragoussis, J Bungert, J Strouboulis, J GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title | GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title_full | GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title_fullStr | GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title_full_unstemmed | GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title_short | GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. |
| title_sort | gata 1 genome wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis |
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