Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of E2F4 double knockout mice and heterozygous littermates

ABSTRACT: We considered the possibility that removal of E2F4, as a key regulator of cellular quiescence, would cause systemic perturbations in the expression of E2F4 bound genes involved in cell cycle and proliferation. To test whether these pertubrations were reflected in the adult tissues' gene expression programs, we compared the gene expression profile of E2F4 double knockout mice to the gene expression found in identical tissues from E2F4 heterozygous littermates, that are phenotypically normal. We selected liver, testes, and kidney to profile by gene expression analysis, because two of these tissues are affected at some point during development when E2F4 is missing.

ORGANISM(S): Mus musculus

SUBMITTER: Duncan Odom

PROVIDER: E-MEXP-1131 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.

Conboy Caitlin M CM Spyrou Christiana C Thorne Natalie P NP Wade Elizabeth J EJ Barbosa-Morais Nuno L NL Wilson Michael D MD Bhattacharjee Arindam A Young Richard A RA Tavaré Simon S Lees Jacqueline A JA Odom Duncan T DT

PloS one 20071024 10

Maintaining quiescent cells in G0 phase is achieved in part through the multiprotein subunit complex known as DREAM, and in human cell lines the transcription factor E2F4 directs this complex to its cell cycle targets. We found that E2F4 binds a highly overlapping set of human genes among three diverse primary tissues and an asynchronous cell line, which suggests that tissue-specific binding partners and chromatin structure have minimal influence on E2F4 targeting. To investigate the conservatio ...[more]

PMID: 17957245

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Project description:Background and Aims: In the interleukin-10-deficient (Il10-/-) mouse model of IBD, 10 quantitative trait loci (QTL) have been shown to be associated with colitis susceptibility by linkage analyses on experimental crosses of highly susceptible C3H/HeJBir (C3Bir)-Il10-/- and partially resistant C57BL/6J (B6)-Il10-/- mice. The strongest locus (C3Bir-derived cytokine deficiency-induced colitis susceptibility [Cdcs]1 on Chromosome [Chr] 3) controlled multiple colitogenic subphenotypes and contributed the vast majority to the phenotypic variance in cecum and colon. This was demonstrated by interval-specific Chr 3 congenic mice wherein defined regions of Cdcs1 from C3Bir or B6 were bred into the IL-10-deficient reciprocal background and altered the susceptible or resistant phenotype. Furthermore, this locus likely acts by inducing innate hypo- and adaptive hyperresponsiveness, associated with impaired NFΚB responses of macrophages. The aim of the present study was to dissect the complexity of Cdcs1 by further development and characterization of reciprocal Cdcs1 congenic strains and to identify potential candidate genes in the congenic interval. Material and Methods: In total, 15 reciprocal congenic strains were generated from Il10-/- mice of either C3H/HeJBir or C57BL/6J backgrounds by 10 cycles of backcrossing. Colitis activity was monitored by histological grading. Candidate genes were identified by fine mapping of congenic intervals, sequencing, microarray analysis and a high-throughput real-time RT-PCR approach using bone marrow-derived macrophages. Results: Within the originally identified Cdcs1-interval, three independent regions were detected that likely contain susceptibility-determining genetic factors (Cdcs1.1, Cdcs1.2, and Cdcs1.3). Combining results of candidate gene approaches revealed Fcgr1, Cnn3, Larp7, and Alpk1 as highly attractive candidate genes with polymorphisms in coding or regulatory regions and expression differences between susceptible and resistant mouse strains. Conclusions: Subcongenic analysis of the major susceptibility locus Cdcs1 on mouse chromosome 3 revealed a complex genetic structure. Candidate gene approaches revealed attractive genes within the identified regions with homologs that are located in human susceptibility regions for IBD. Experiment Overall Design: Bone marrow derived macrophages (BMDM) of colitis susceptible C3Bir-Il10-/- and colitis resistant B6-Il10-/- as well as the Il10-/- reciprocal congenic strains CB-R1 (C3Bir genetic background carrying a long congenic chromosome 3 element containing Cdcs1 from B6, rendering this formerly susceptible background resistant) and BC-R3 (B6 genetic background that carries the Cdcs1-region of C3Bir) were cultured and stimulated with flagellin or left unstimulated. BMDM were obtained from 3 male mice per genotype and cultured in polystyrene 6-well culture plates. Before RNA-isolation, 3 wells per plate were stimulated with Cbir1 flagellin (and subsequently pooled for RNA isolation), the other 3 wells left unstimulated (and also pooled). In total, these experiments were replicated three times in order to perform microarray analyses in triplicates.

Dataset Information

Transcription profiling of E2F4 double knockout mice and heterozygous littermates

Publications

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.

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