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Identification of candidate genes regulated by E4bp4 in murine bone marrow

ABSTRACT: E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP Total RNA was extracted from linege-depleted bone marrow from six wild type and six E4bp4 knockout mice. Labelled cDNA was hybridised to a GeneChip Mouse Gene 1.0 ST Array. The data generated was imported into GeneSpring GXv11 (Agilent) and normalised using the Robust Multi-Array (RMA16) algorithm. Genes were filtered on expression value between 20th and 100th percentile to remove those with very low or no expression across all the samples. A moderated t-test was applied to the data and p values were adjusted for multiple testing using a Benjamini-Hochberg False Discovery Rate correction.

ORGANISM(S): Mus musculus

SUBMITTER: Hugh Brady 

PROVIDER: E-GEOD-55014 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcription factor E4bp4/Nfil3 controls commitment to the NK lineage and directly regulates Eomes and Id2 expression.

Male Victoria V   Nisoli Ilaria I   Kostrzewski Tomasz T   Allan David S J DS   Carlyle James R JR   Lord Graham M GM   Wack Andreas A   Brady Hugh J M HJ  

The Journal of experimental medicine 20140324 4

The transcription factor E4bp4 (Nfil3) is essential for natural killer (NK) cell production. Here, we show that E4bp4 is required at the NK lineage commitment point when NK progenitors develop from common lymphoid progenitors (CLPs) and that E4bp4 must be expressed at the CLP stage for differentiation toward the NK lineage to occur. To elucidate the mechanism by which E4bp4 promotes NK development, we identified a central core of transcription factors that can rescue NK production from E4bp4(-/-  ...[more]

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