Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid

A large body of evidence from human and animal studies demonstrates that the maternal diet during pregnancy can programme physiological and metabolic functions in the developing fetus, effectively determining susceptibility to later disease. The mechanistic basis of such programming is unclear but may involve resetting of epigenetic marks and fetal gene expression. The aim of this study was to evaluate genome-wide DNA methylation and gene expression in the livers of newborn rats exposed to maternal protein restriction. On day one postnatally, there were 618 differentially expressed genes and 1183 differentially methylated regions (FDR 5%). The functional analysis of differentially expressed genes indicated a significant effect on DNA repair/cycle/maintenance functions and of lipid, amino acid metabolism and circadian functions. Enrichment for known biological functions was found to be associated with differentially methylated regions. Moreover, these epigenetically altered regions overlapped genetic loci associated with metabolic and cardiovascular diseases. Both expression changes and DNA methylation changes were largely reversed by supplementing the protein restricted diet with folic acid. Although the epigenetic and gene expression signatures appeared to underpin largely different biological processes, the gene expression profile of DNA methyl transferases was altered, providing a potential link between the two molecular signatures. The data showed that maternal protein restriction is associated with widespread differential gene expression and DNA methylation across the genome, and that folic acid is able to reset both molecular signatures

RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients

Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of early, drug naive RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.</p

TBP2 is essential for germ cell development by regulating transcription and chromatin condensation in the oocyte

Development of the germline requires consecutive differentiation events. Regulation of these has been associated with germ cell-specific and pluripotency-associated transcription factors, but the role of general transcription factors (GTFs) remains elusive. TATA-binding protein (TBP) is a GTF involved in transcription by all RNA polymerases. During ovarian folliculogenesis in mice the vertebrate-specific member of the TBP family, TBP2/TRF3, is expressed exclusively in oocytes. To determine TBP2 function in vivo, we generated TBP2-deficient mice. We found that Tbp2−/− mice are viable with no apparent phenotype. However, females lacking TBP2 are sterile due to defective folliculogenesis, altered chromatin organization, and transcriptional misregulation of key oocyte-specific genes. TBP2 binds to promoters of misregulated genes, suggesting that TBP2 directly regulates their expression. In contrast, TBP ablation in the female germline results in normal ovulation and fertilization, indicating that in these cells TBP is dispensable. We demonstrate that TBP2 is essential for the differentiation of female germ cells, and show the mutually exclusive functions of these key core promoter-binding factors, TBP and TBP2, in the mouse

Cell-Specific Interaction of Retinoic Acid Receptors with Target Genes in Mouse Embryonic Fibroblasts and Embryonic Stem Cells▿ †

All-trans retinoic acid (RA) induces transforming growth factor beta (TGF-β)-dependent autocrine growth of mouse embryonic fibroblasts (MEFs). We have used chromatin immunoprecipitation to map 354 RA receptor (RAR) binding loci in MEFs, most of which were similarly occupied by the RARα and RARγ receptors. Only a subset of the genes associated with these loci are regulated by RA, among which are several critical components of the TGF-β pathway. We also show RAR binding to a novel series of target genes involved in cell cycle regulation, transformation, and metastasis, suggesting new pathways by which RA may regulate proliferation and cancer. Few of the RAR binding loci contained consensus direct-repeat (DR)-type elements. The majority comprised either degenerate DRs or no identifiable DRs but anomalously spaced half sites. Furthermore, we identify 462 RAR target loci in embryonic stem (ES) cells and show that their occupancy is cell type specific. Our results also show that differences in the chromatin landscape regulate the accessibility of a subset of more than 700 identified loci to RARs, thus modulating the repertoire of target genes that can be regulated and the biological effects of RA

Differentially expressed genes in maternal undernutrition model.

<p>(A) Venn's diagrams showing the number of differentially expressed gene probes in comparisons MLP vs. C (P-C), MLP-F vs. C (F-C) and MLP vs. MLP-F (P-F) at FDR 5% (top) and FDR 1% (bottom). Number of gene probes whose expression was unaltered is indicated in black (right). Numbers of altered gene probes in MLP-C contrast at different FDR are indicated in green (left). (B) qRT-PCR mRNA analysis for 8 genes: <i>Dnmt1</i>, <i>Dnmt3a</i>, <i>Dnmt3b</i>, <i>Aurkb</i>, <i>Mcm6</i>, <i>Hat1</i>, <i>Gnmt</i> and <i>Gmnn</i>. Results are given in relative units, as ratio of number of copies in assessed gene and housekeeping gene GAPDH. ^× P<0.05; ^×× P<0.01; ^××× P<0.001. ns P>0.05.</p

List of loci from selected GWAS studies pertaining to metabolic and cardiovascular phenotypes associated to Low Protein diet that contain differentially methylated regions in their orthologous rat locus.

<p>The overlap between the total number of GWAS loci investigated and DMR containing loci is significant (p = 0.0025).</p

Intersection of differentially expressed (GEX), separated in up-regulated (UP) and down-regulated (DW), and DMRs-neighboring (MBD) genes.

<p>At FDR 5% only 15 genes (hypergeometric probability = 0.69) are found in both lists, of which 6 were down-regulated (<i>Dym</i>, <i>Glrx2</i>, <i>Mlph</i>, <i>Myh10</i>, <i>Pftk1</i>, And <i>Prep</i>) and 9 up-regulated (<i>Abcc8</i>, <i>Abhd6</i>, <i>Cep350</i>, <i>Ctsa</i>, <i>Eif2b3</i>, <i>Pdk1</i>, <i>Serpina11</i>, <i>Tpcn2</i>, And <i>Tyw3</i>). The total number of mapped genes is 555 in MBD and 577 in GEX.</p