Sean M. Cullen

Wild-type microglia do not reverse pathology in mouse models of Rett syndrome.

arising from N. C. Derecki et al. 484, 105–109 (2012); doi:10.1038/nature10907Rett syndrome is a severe neurodevelopmental disorder caused by mutations in the X chromosomal gene MECP2 (ref. 1), and its treatment so far is symptomatic. Mecp2 disruption in mice phenocopies major features of the syndrome that can be reversed after Mecp2 re-expression. Recently, Derecki et al. reported that transplantation of wild-type bone marrow into lethally irradiated Mecp2-null (Mecp2tm1.1Jae/y) mice prevented neurological decline and early death by restoring microglial phagocytic activity against apoptotic targets, and clinical trials of bone marrow transplantation (BMT) for patients with Rett syndrome have thus been initiated. We aimed to replicate and extend the BMT experiments in three different Rett syndrome mouse models, but found that despite robust microglial engraftment, BMT from wild-type donors did not prevent early death or ameliorate neurological deficits. Furthermore, early and specific Mecp2 genetic expression in microglia did not rescue Mecp2-deficient mice.

Hematopoietic stem cell development: an epigenetic journey.

Hematopoietic development and homeostasis are based on hematopoietic stem cells (HSCs), a pool of ancestor cells characterized by the unique combination of self-renewal and multilineage potential. These two opposing forces are finely orchestrated by several regulatory mechanisms, comprising both extrinsic and intrinsic factors. Over the past decades, several studies have contributed to dissect the key role of niche factors, signaling transduction pathways, and transcription factors in HSC development and maintenance. Accumulating evidence, however, suggests that a higher level of intrinsic regulation exists; epigenetic marks, by controlling chromatin accessibility, directly shape HSC developmental cascades, including their emergence during embryonic development, maintenance of self-renewal, lineage commitment, and aging. In addition, aberrant epigenetic marks have been found in several hematological malignancies, consistent with clinical findings that mutations targeting epigenetic regulators promote leukemogenesis. In this review, we will focus on both normal and malignant hematopoiesis, covering recent findings that illuminate the epigenetic life of HSCs.

Dynamic DNA methylation discovered during HSC differentiation.

Methylation of DNA at CpG dinucleotides is dynamic at many genomic loci during normal development. The continuously differentiating hematopoietic system offers a wellcharacterized model to study these changes in the adult. During normal hematopoietic differentiation, DNA methylation levels have been shown to both increase and decrease as hematopoietic stem cell (HSC) lineage specification progresses. Recent studies of DNA methylation in hematopoietic stem and progenitor (HSPC) populations have elucidated finely tuned methylation changes taking place during differentiation, as well as identified some of the key regulators and drivers of this epigenetic process. Major questions remain, however, regarding the relationship between DNA methylation status, including location in the genome (intron, exon, promoter, intergenic, etc.), and the resultant effect on overall gene expression. Following up on their recent generation and analysis of DNA methylomes in murine HSCs and 4 closely related multipotent progenitor populations (MPPs) using tagmentation-based whole genome bisulfite sequencing (TWGBS), Lipka et al. further categorize the molecular landscape changes in HSPCs during the very early stages of HSC differentiation. They found a number of epigenetic changes that were inversely correlated with gene expression during HSPC differentiation (Fig. 1). During the HSC to MPP1 transition, for example, genes known to be important for normal HSC function, such as Gata2, exhibited increased DNA methylation and decreased gene expression. Across the genome, they identified nearly 16 thousand differentially methylated regions (DMRs), distinguishing several distinct clusters of methylation dynamics. Importantly, the TWGBS approach enabled two-to-three times as many DMRs to be identified as in previous reports of hematopoietic differentiation and better correlation with gene expression changes. Previous studies of DNA methylation during HSPC differentiation used reduced representation bisulfite sequencing (RRBS) or comprehensive highthroughput array-based relative methylation (CHARM) arrays, and a general correlation between DNA methylation levels and gene expression was not observed. In the current study, the majority of DMRs (85%) were exclusively identified by TWGBS, and were found within intragenic regions (57%), which were more likely to be missed by other assays due to an overrepresentation of CpG-rich genomic regions. Lipka et al. also identify a group of 264 “core-enriched” genes, which exhibited an inverse relationship between DNA methylation and gene expression during the HSC to MPP1 transition, but their functional significance remains to be determined. The newly identified DMRs were further analyzed for overlap with regulatory regions associated with hematopoietic-specific transcription factors (TFs); each differentiation stage produced examples of DMRs associated with differentially expressed hematopoietic-specific TFs. The authors propose some of these stage-specific DMRs represent novel cis-acting regulatory regions of TFs important for hematopoietic differentiation, but this will require experimental validation. In addition, probing the DMRs for the presence of canonical TF binding motifs revealed potential involvement of about 30 TFs. The binding site enrichments for specific TF groups were, in turn, limited to specific DMR clusters, possibly implicating a more distinctive, active role for DNA methylation in regulating TF binding in early hematopoiesis. The regulation of, and downstream effects of, DNA methylation changes in the hematopoietic system are crucial to elucidate because a main driver of DNA methylation in HSCs, DNA methyltransferase 3a (DNMT3A), both directly regulates DNA methylation levels in HSCs, and is recurrently mutated in hematologic malignancies, including acute myeloid leukemia. The connection between regulation of DNA methylation in HSCs and development of cancer is still largely unknown, but understanding the epigenetic mechanisms governing differentiation, and the downstream cellular impacts, could provide a great deal of insight. Overall, this study provides important insights into DNA methylation dynamics of early HSC differentiation, and a roadmap for experimental exploration of potential downstream effects of epigenetic aberrations, such as DNMT3A mutations, in hematologic malignancy and disease. Many important questions remain for the future. For example, the functional relevance of the 9 DMR clusters, particularly given the enrichment of specific TF binding motifs, is intriguing. As the authors suggest, genomewide mapping of protein binding via chromatin-Immunoprecipitation sequencing (ChIP-Seq) will be required to address this question, as well as determining the effect of DNA methylation dynamics on TF binding. It would additionally be useful to

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

Direct reprogramming of fibroblasts to neurons induces widespread cellular and transcriptional reconfiguration. In this study, we characterized global epigenomic changes during direct reprogramming using whole-genome base-resolution DNA methylome (mC) sequencing. We found that the pioneer transcription factor Ascl1 alone is sufficient for inducing the uniquely neuronal feature of non-CG methylation (mCH), but co-expression of Brn2 and Mytl1 was required to establish a global mCH pattern reminiscent of mature cortical neurons. Ascl1 alone induced strong promoter CG methylation (mCG) of fibroblast specific genes, while BAM overexpression additionally targets a competing myogenic program and directs a more faithful conversion to neuronal cells. Ascl1 induces local demethylation at its binding sites. Surprisingly, co-expression with Brn2 and Mytl1 inhibited the ability of Ascl1 to induce demethylation, suggesting a contextual regulation of transcription factor - epigenome interaction. Finally, we found that de novo methylation by DNMT3A is required for efficient neuronal reprogramming.

DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells

BackgroundDNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5mC), which can be further oxidized by the TET dioxygenases to ultimately cause DNA demethylation. However, the genome-wide cooperation and functions of these two families of proteins, especially at large under-methylated regions, called canyons, remain largely unknown.ResultsHere we demonstrate that DNMT3A and TET1 function in a complementary and competitive manner in mouse embryonic stem cells to mediate proper epigenetic landscapes and gene expression. The longer isoform of DNMT3A, DNMT3A1, exhibits significant enrichment at distal promoters and canyon edges, but is excluded from proximal promoters and canyons where TET1 shows prominent binding. Deletion of Tet1 increases DNMT3A1 binding capacity at and around genes with wild-type TET1 binding. However, deletion of Dnmt3a has a minor effect on TET1 binding on chromatin, indicating that TET1 may limit DNA methylation partially by protecting its targets from DNMT3A and establishing boundaries for DNA methylation. Local CpG density may determine their complementary binding patterns and therefore that the methylation landscape is encoded in the DNA sequence. Furthermore, DNMT3A and TET1 impact histone modifications which in turn regulate gene expression. In particular, they regulate Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 enrichment to constrain gene expression from bivalent promoters.ConclusionsWe conclude that DNMT3A and TET1 regulate the epigenome and gene expression at specific targets via their functional interplay.

Corrigendum: Wild-type microglia do not reverse pathology in mouse models of Rett syndrome

This corrects the article DOI: 10.1038/nature14444

Erratum: Wild-type microglia do not reverse pathology in mouse models of Rett syndrome (Nature (2015) 521 (E1-E4) DOI:10.1038/nature14444)

This corrects the article DOI: 10.1038/nature14444

Erratum: Corrigendum: Wild-type microglia do not reverse pathology in mouse models of Rett syndrome

This corrects the article DOI: 10.1038/nature14444

Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine

The differentiation of intestinal stem cells involves few DNA methylation changes, assayed by bisulfite sequencing, in contrast to other adult somatic stem cell hierarchies.Please see related Research article: http://genomebiology.com/2013/14/5/R50