Hypomethylation is necessary but not sufficient for V(D)J recombination within a transgenic substrate

Identification of Ssm1b, a novel modifier of DNA methylation, and its expression during mouse embryogenesis

The strain-specific modifier Ssm1 is responsible for the strain-dependent methylation of particular E. coli gpt-containing transgenic sequences. Here, we identify Ssm1 as the KRAB-zinc finger (ZF) gene 2610305D13Rik located on distal chromosome 4. Ssm1b is a member of a gene family with an unusual array of three ZFs. Ssm1 family members in C57BL/6 (B6) and DBA/2 (D2) mice have various amino acid changes in their ZF domain and in the linker between the KRAB and ZF domains. Ssm1b is expressed up to E8.5; its target transgene gains partial methylation by this stage as well. At E9.5, Ssm1b mRNA is no longer expressed but by then its target has become completely methylated. By contrast, in D2 embryos the transgene is essentially unmethylated. Methylation during B6 embryonic development depends on Dnmt3b but not Mecp2. In differentiating B6 embryonic stem cells methylation spreads from gpt to a co-integrated neo gene that has a similarly high CpG content as gpt, but neo alone is not methylated. In adult B6 mice, Ssm1b is expressed in ovaries, but in other organs only other members of the Ssm1 family are expressed. Interestingly, the transgene becomes methylated when crossed into some, but not other, wild mice that were kept outbred in the laboratory. Thus, polymorphisms for the methylation patterns seen among laboratory inbred strains are also found in a free-living population. This may imply that mice that do not have the Ssm1b gene may use another member of the Ssm1 family to control the potentially harmful expression of certain endogenous or exogenous genes.

DNA methylation dynamics in health and disease

DNA methylation is an epigenetic mark that is erased in the early embryo and then re-established at the time of implantation. In this Review, dynamics of DNA methylation during normal development in vivo are discussed, starting from fertilization through embryogenesis and postnatal growth, as well as abnormal methylation changes that occur in cancer.

Localized DNA demethylation at recombination intermediates during immunoglobulin heavy chain gene assembly

The dynamics of DNA methylation during the complex genomic rearrangement of antigen receptor genes in developing B lymphocytes reveal localized demethylation of the first recombination product that may serve as a mark necessary for the second step of rearrangement.

Multiple epigenetic marks have been proposed to contribute to the regulation of antigen receptor gene assembly via V(D)J recombination. Here we provide a comprehensive view of DNA methylation at the immunoglobulin heavy chain (IgH) gene locus prior to and during V(D)J recombination. DNA methylation did not correlate with the histone modification state on unrearranged alleles, indicating that these epigenetic marks were regulated independently. Instead, pockets of tissue-specific demethylation were restricted to DNase I hypersensitive sites within this locus. Though unrearranged diversity (D_H) and joining (J_H) gene segments were methylated, DJ_H junctions created after the first recombination step were largely demethylated in pro-, pre-, and mature B cells. Junctional demethylation was highly localized, B-lineage-specific, and required an intact tissue-specific enhancer, Eμ. We propose that demethylation occurs after the first recombination step and may mark the junction for secondary recombination.

DNA methylation at CpG dinucleotides is implicated in the regulation of gene expression in mammals. However, the regulation of DNA methylation itself is less clear despite recent advances in identifying enzymes that add or remove methyl groups. We have investigated the dynamics of DNA methylation during genome rearrangements that assemble antigen receptor genes in developing B lymphocytes to determine whether methylation status correlates with rearrangement potential. Two recombination events generate immunoglobulin heavy chain (IgH) genes. The first step brings together diversity (D_H) and joining (J_H) gene segments to produce DJ_H junctions. We show that both gene segments are methylated prior to rearrangement, whereas the DJ_H product is demethylated. DJ_H junctional demethylation is tissue-specific and requires an enhancer, Eμ, located within the IgH locus. The latter observations indicate that localized demethylation of the DJ_H junction occurs after the first recombination step and thus does not guide this first step of IgH gene assembly. Our working hypothesis is that recombination induces demethylation of recombinant product and may mark the junction for the second step of IgH rearrangement, juxtaposition of variable (V_H) gene segments to rearranged DJ_H products to produce fully recombined V(D)J alleles.

Chromatin topology and the regulation of antigen receptor assembly

During an organism's ontogeny and in the adult, each B and T lymphocyte generates a unique antigen receptor, thereby creating the organism's ability to respond to a vast number of different antigens. The antigen receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions. In this review, we discuss the epigenetic modifications that take place in the different antigen receptor loci, the chromatin structure adopted by the antigen receptor loci to allow recombination of elements separated by large genomic distances, and the relationship between epigenetics and chromatin structure and how they relate to the generation of antigen receptor diversity.

Local and global epigenetic regulation of V(D)J recombination

Despite using the same Rag recombinase machinery expressed in both lymphocyte lineages, V(D)J recombination of immunoglobulins only occurs in B cells and T cell receptor recombination is confined to T cells. This vital segregation of recombination targets is governed by the coordinated efforts of several epigenetic mechanisms that control both the general chromatin accessibility of these loci to the Rag recombinase, and the movement and synapsis of distal gene segments in these enormous multigene AgR loci, in a lineage and developmental stage-specific manner. These mechanisms operate both locally at individual gene segments and AgR domains, and globally over large distances in the nucleus. Here we will discuss the roles of several epigenetic components that regulate V(D)J recombination of the immunoglobulin heavy chain locus in B cells, both in the context of the locus itself, and of its 3D nuclear organization, focusing in particular on non-coding RNA transcription. We will also speculate about how several newly described epigenetic mechanisms might impact on AgR regulation.

Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines

We have developed a method for mapping unmethylated sites in the human genome based on the resistance of TspRI-digested ends to ExoIII nuclease degradation. Digestion with TspRI and methylation-sensitive restriction endonuclease HpaII, followed by ExoIII and single-strand DNA nuclease allowed removal of DNA fragments containing unmethylated HpaII sites. We then used array comparative genomic hybridization (CGH) to map the sequences depleted by these procedures in human genomes derived from five human tissues, a primary breast tumor, and two breast tumor cell lines. Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5' end of widely expressed genes, including promoter, first exon, and first intron. In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas the primary tumor exhibits a pattern between those of the normal tissue and the cell lines. A striking characteristic of tumor cell lines is the presence of megabase-sized hypomethylated zones. These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor suppressor genes, and with regions containing tissue-specific gene clusters or with gene-poor regions containing novel tissue-specific genes. Correlation with microarray analysis shows that genes with a hypomethylated sequence 2 kb up- or downstream of the transcription start site are highly expressed, whereas genes with extensive intragenic and 3' untranslated region (UTR) hypomethylation are silenced. The method described herein can be used for large-scale screening of changes in the methylation pattern in the genome of interest.

Epigenetic regulation of lymphoid specific gene sets

Coregulation of lymphoid-specific gene sets is achieved by a series of epigenetic mechanisms. Association with higher-order chromosomal structures (nuclear subcompartments repressing or favouring gene expression) and locus control regions affects recombination and transcription of clonotypic antigen receptors and expression of a series of other lymphoid-specific genes. Locus control regions can regulate DNA methylation patterns in their vicinity. They may induce tissue- and site-specific DNA demethylation and affect, thereby, accessibility to recombination-activating proteins, transcription factors, and enzymes involved in histone modifications. Both DNA methylation and the Polycomb group of proteins (PcG) function as alternative systems of epigenetic memory in lymphoid cells. Complexes of PcG proteins mark their target genes by covalent histone tail modifications and influence lymphoid development and rearrangement of IgH genes. Ectopic expression of protein noncoding microRNAs may affect the generation of B-lineage cells, too, by guiding effector complexes to sites of heterochromatin assembly. Coregulation of lymphoid and viral promoters is also possible. EBNA 2, a nuclear protein encoded by episomal Epstein-Barr virus genomes, binds to the cellular protein CBF1 (C promoter binding factor 1) and operates, thereby, a regulatory network to activate latent viral promoters and cellular promoters associated with CBF1 binding sites.Key words : lymphoid cells, coregulation of gene batteries, epigenetic regulation, nuclear subcompartment switch, locus control region, DNA methylation, Polycomb group of proteins, histone modifications, microRNA, Epstein-Barr virus, EBNA 2, regulatory network.

DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora

During the early stages of meiosis in Neurospora, the symmetry of homologous chromosomal regions is carefully evaluated by actively trans-sensing their identity. If a DNA region cannot be detected on the opposite homologous chromosome, then this lack of "sensing" activates meiotic silencing, a post-transcriptional gene silencing-like mechanism that silences all genes in the genome with homology to the loop of unpaired DNA, whether they are paired or unpaired. In this work, we genetically dissected the meiotic trans-sensing step from meiotic silencing by demonstrating that DNA methylation affects sensing without interfering with silencing. We also determined that DNA sequence is an important parameter considered during meiotic trans-sensing. Altogether, these observations assign a previously undescribed role for DNA methylation in meiosis and, on the basis of studies in other systems, we speculate the existence of an intimate connection among meiotic trans-sensing, meiotic silencing, and meiotic recombination.

Transvection effects involving DNA methylation during meiosis in the mouse

High efficiencies of recombination between LoxP elements were initially recorded when the Cre recombinase was expressed in meiotic spermatocytes. However, it was unexpectedly found that LoxP recombination fell to very low values at the second generation of mice expressing Cre during meiosis. The inability of the LoxP elements to serve as recombination substrates was correlated with cytosine methylation, initially in LoxP and transgene sequences, but later extending for distances of at least several kilobases into chromosomal sequences. It also affected the allelic locus, implying a transfer of structural information between alleles similar to the transvection phenomenon described in Drosophila. Once initiated following Cre-LoxP interaction, neither cis-extension nor transvection of the methylated state required the continuous expression of Cre, as they occurred both in germinal and somatic cells and in the fraction of the offspring that had not inherited the Sycp1-Cre transgene. Therefore, these processes depend on a physiological mechanism of establishment and extension of an epigenetic state, for which they provide an experimental model.

A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival

The role of DNA methylation and of the maintenance DNA methyltransferase Dnmt1 in the epigenetic regulation of developmental stage- and cell lineage-specific gene expression in vivo is uncertain. This is addressed here through the generation of mice in which Dnmt1 was inactivated by Cre/loxP-mediated deletion at sequential stages of T cell development. Deletion of Dnmt1 in early double-negative thymocytes led to impaired survival of TCRalphabeta(+) cells and the generation of atypical CD8(+)TCRgammadelta(+) cells. Deletion of Dnmt1 in double-positive thymocytes impaired activation-induced proliferation but differentially enhanced cytokine mRNA expression by naive peripheral T cells. We conclude that Dnmt1 and DNA methylation are required for the proper expression of certain genes that define fate and determine function in T cells.