Meissner Laboratory

Our laboratory is a mixed group of experimental and computational biologists in the Department of Stem Cell and Regenerative Biology (HSCRB).  We use genomic tools to study developmental and stem cell biology with a particular interest in the role of epigenetic regulation (Mikkelsen et al. Nature 2008; Koche, Smith et al. Cell Stem Cell 2011).

The term epigenetic refers to stable modifications of the chromatin and DNA that do not alter the primary nucleotide sequence. The global epigenetic makeup of a cell is a powerful indicator of its developmental state and potential. We have pioneered next generation sequencing technologies (Meissner et al. Nature 2008; Gu et al. Nature Methods 2010; Bock et al. Nature Biotechnology 2010) to study the epigenome in normal development and disease.

Our lab has also continued to provide important mechanistic insights into the generation of iPS cells using genomic (Mikkelsen et al. Nature 2008; Koche, Smith et al. Cell Stem Cell 2011; Bock et al. Cell 2011) and single cell imaging (Smith et al. Nature Biotechnology 2010) tools. Over the last years we have accumulated tremendous insights of the process and build many essential tools. Combined with our genomic expertise we are in a unique position to expand these studies to have a broad impact on regenerative medicine and make major contributions to our general understanding of cell states.



Epigenetics and Epigenomics

Epigenetics and Epigenomics

Chemical modifications to DNA and histone proteins form a complex regulatory network that modulates chromatin structure and genome function. The epigenome refers to the complete description of these potentially heritable changes across the genome. The composition of the epigenome within a given cell is a function of genetic determinants, lineage, and environment.

With the sequencing of the human genome completed, investigators now seek a comprehensive view of the epigenetic changes that determine how genetic information is made manifest across an incredibly varied background of developmental stages, tissue types, and disease states.

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DNA Methylation

DNA Methylation

DNA methylation is essential for mammalian development and is required in most somatic cells. It is established and maintained by three catalytically active enzymes: DNA methyltransferase (Dnmt)1, Dnmt3a and Dnmt3b. Two additional, homologous enzymes, Dnmt2 and Dnmt3l, are expressed in several cell types, including ES cells. Deletion of Dnmt2 has no apparent phenotype in vitro or in vivo. The ability of Dnmt2 to methylate a specific cytosine in the anticodon loop structure of tRNAs suggests that it might not function as a DNA methyltransferase. Loss of Dnmt1 results in embryonic lethality around embryonic day (E)8.5–9, and Dnmt1 mutant embryos retain only one-third of the normal amount of DNA methylation. Dnmt1-deficient embryos show rudiments of the major organs, but they are smaller than normal and appear to be developmentally delayed. Dnmt3b mutant embryos appear to develop normally before E9.5 but show multiple developmental defects later and do not develop to term. Conditional deletion of Dnmt3b in mouse embryonic fibroblasts (MEFs) results in partial loss of methylation, indicating the importance of this enzyme, together with Dnmt1, for maintaining epigenomic patterns in proliferating cells. Unlike mice lacking Dnmt1 or Dnmt3b, homozygous Dnmt3a knockout mice can develop to term but become runted and die ~1 month after birth. Conditional deletion of Dnmt3a results in imprinting defects in the germline. Homozygous Dnmt3l mice are viable, but male mice are sterile and heterozygous offspring of homozygous females die owing to imprinting defects. This phenotype is similar to that of Dnmt3adeficient mice and suggests that both enzymes might be involved in establishing correct imprinting patterns. Dnmt3l is a close homolog of Dnmt3a and Dnmt3b that lacks the catalytic domain but is highly expressed in the early embryo, ES cells and germ cells. It has been suggested to function as a co-regulator of both Dnmt3a and Dnmt3b and has recently been shown to interact with the N-terminal tail of histone H3 when it lacks methylation at lysine 4. Importantly, the genome is transiently hypomethylated during two phases of normal development without adverse effects. As described above, the first phase is preimplantation development. The totipotent zygote and blastomeres, the pluripotent blastomeres, the pluripotent ICM cells and trophectoderm cells do not require substantial DNA methylation. A second wave of demethylation commences after the specification of primordial germ cells (PGCs) around day E7.25. Genome-wide bisulfite sequencing was used to show that E13.5 PGCs have only 5–20% of genomic DNA methylation left36, confirming that PGCs show transient reduction of DNA methylation without adverse effects on viability.

Histone Modifications

Histone Modifications

Histone modifications provide an additional and complex layer of the epigenetic code. Many of the enzymes that regulate these modifications have been studied extensively, including histone acetyltransferases, deacetylases, methyltransferases and histone demethylases. Among the best-characterized mediators are protein complexes of the polycomb (PcG) and trithorax (trxG) groups. PcG proteins catalyze two distinct histone modifications: tri-methylation of lysine 27 of histone 3 (H3K27me3) by polycomb repressive complex (PRC) 2 and mono-ubiquitination of lysine 119 H2A (H2AK119ub1) by PRC1. H3K27 is tri-methylated by the enhancer of zeste (Ezh2 or KMT6), which contains a SET (su[var]3–9, enhancer of zeste, Trx) domain and, with Eed (embryonic ectoderm development) and Suz12 (suppressor of zeste 12), are components of PRC2. Loss of any one of the PRC2 subunits results in severe gastrulation defects, highlighting its essential role in normal development. Ezh2 knockout embryos are underdeveloped and die around E8.5. Ezh2 is upregulated upon fertilization and its expression remains high during pre-implantation development45. Its close homolog, Ezh1, is expressed in the fertilized oocyte but is barely detectable at the blastocyst stage. However, it is expressed in ES cells and found later in the adult. Eed does not appear until day E5.5, suggesting that Ezh2 and maybe Ezh1 also have roles in preimplantation development that are independent of PRC2 and Eed. Eed-deficient embryos show gastrulation defects and do not maintain X inactivation in extraembryonic cells. Like mice deficient in the other PRC2 components, Suz12 homozygous mice die during the early postimplantation stages (before day E10.5). Similar to loss of PRC2, loss of PRC1 components, such as Ring1B, results in an early embryonic lethal phenotype. Bmi-1–null mice show several hematopoietic and neurological abnormalities51, and loss of the H3K9 methyltransferases Eset (SetDB1) or G9a causes peri- and postimplantation lethality. Finally, although not discussed here, mutants for most of the chromatin remodeling and histone chaperones also show early embryonic lethality. Together, the knockout studies have clearly established that DNA methylation and histone modification are essential for normal development. But many questions remain regarding the specific contributions of these epigenetic marks to the regulation of gene expression throughout development. The genomic distribution and global patterns of these marks have not been studied in detail. Mice with mutations in most of these genes die early, probably owing to failure to establish early epigenetic patterns that are presumed to dictate later developmental decisions. It is less clear what the effect of such mutations would be after initial specification has taken place. Strategies for exploring these questions in future research include conditional deletions in mouse somatic lineages and cell types and genome-wide mapping of epigenetic modifications in early development.

NIH Roadmap Epigenomics Project

The Reference Epigenome Mapping Centers (REMC) will aim to transform our understanding of human epigenetics through production and integrative analysis of comprehensive reference epigenomes for ES cells, differentiated cells and tissues. In pursuit of this goal, we have assembled a unique scientific team and infrastructure with broad expertise and capabilities in stem cell biology, epigenomics, technology, production research and computation. We recently demonstrated two complementary methods that leverage ultra high-throughput sequencing for epigenomic analysis. In the first method, genome-wide chromatin maps are acquired by deep sequencing chromatin IP DNA (ChlP-Seq). In the second, nucleotide-resolution DNA methylation maps are generated by high-throughput bisulfite-sequencing (HTBS). These methods represent major improvements over prior tools as they yield precise digital information, have high genome coverage, require fewer cells and are cost-effective. Multiple epigenomic maps have already been produced for stem cells and primary tissues, and pipelines have been assembled for efficient data collection, processing and analysis. For the REMC project, we propose to apply ChlP-Seq and HTBS pipelines to generate comprehensive high-resolution maps of chromatin state and DNA methylation for 100 diverse cell types. Cell types were selected for their biological and medical importance, and for their potential to maximize the comprehensiveness of acquired epigenomic data. They include human ES cells, ES-derived cells, mesenchymal stem cells, reprogrammed stem cells and primary tissues. ChlP-Seq will be used to map highly informative chromatin modifications and related chromatin proteins in each cell type. HTBS will be used to generate nucleotide-resolution DNA methylation maps. Reference epigenomes will reveal the locations and activation states of diverse functional genomic elements, inform on the developmental state and potential of studied cell populations, and provide a framework for understanding complex epigenetic regulatory mechanisms. All data will be made available to the scientific community upon verification. PUBLIC HEALTH RELEVANCE: Comprehensive characterization of epigenetic marks ('the epigenome') is a critical step towards a global understanding of the human genome in health and disease. The proposed mapping studies will provide unprecedented views of the human epigenetic landscape and its variation across cell states, offer fundamental insight into the functions and interrelationships of epigenetic marks, and provide a framework for future studies of normal and diseased epigenomes.

Read more about the project:

Data generated by the consortium:

Publications from the consortium:

NIGMS Program Project

Induced pluripotent stem (iPS) cells have a tremendous potential for advancing our understanding of human development and disease. To help unlock this potential we have organized a program to (A) comprehensively identify the genetic and epigenetic components of the regulatory network that maintains cells in a pluripotent state; (B) characterize culture-induced variation in the activities of these components in pluripotent cells; and (C) characterize temporal variation in their activities during induction of pluripotency with defined factors. To achieve these goals, we have formulated four interdependent projects: Project I (Meissner) will (1) characterize transcriptional coregulators and small non-coding RNAs that modulate the activity of the core pluripotency transcription factors, and (2) define and isolate subpopulations from pluripotent cell cultures to characterize their transcriptional and epigenetic states. Project II (Rinn) will characterize long non-coding RNAs expressed in pluripotent cells and elucidate their role in remodeling the epigenetic landscape during reprogramming. Project III (Mikkelsen) will characterize the cis-regulatory modules that direct activation, maintenance and repression of gene expression in pluripotent cells by recruiting transcription factors and their coregulators to key genomic loci. Project IV (Eggan) will characterize the inheritance patterns and maintenance of inactivated X chromosomes during reprogramming and in pluripotent cell cultures. The four projects rely on complementary use of innovative high-throughput genomic and proteomic technologies to profile high-quality iPS cell lines. The integration of data and insights from each of the projects will generate a comprehensive view of protein-protein, protein-RNA and protein-DNA interactions essential to the maintenance of pluripotency (goal A). This integrated view will then guide studies of culture- induced and temporal variation in the network (goals B and C). PUBLIC HEALTH RELEVANCE: Induced pluripotent stem cells are a potential revolutionary tool for disease modeling, drug screening and regenerative medicine. This program is organized to fully characterize the molecular properties of these cells, which is essential to ensure that their use in biomedicine is effective and safe.

Epigenome Data

Primary data for published Broad Institute RRBS experiments have been deposited to the NCBI GEO database and/or are available through the supporting websites.


Meissner and Mikkelsen et al. (2008): GSE11034 pdf
Koche, Smith et al. (2011): GSE26100 pdf
Bock, Kiskinis, Verstappen et al. (2011): GSE25970 pdf
Smith et al. (2012): GSE34864 pdf
Chan et al. (2012): GSE38711 pdf
Boyle et al. (2012): GSE40429 zip

Supporting Websites:

Gu, Bock et al. (2010)

Bock, Tomazou et al. (2010)

Bock, Kiskinis, Verstappen et al. (2011)

Carone et al. (2011)

Shearstone et al. (2011)

Bock et al. (2012)

Other protocols (Roadmap project)



Broad Institute Epigenome Program

NIH Roadmap Epigenomics Project

Epigenome Atlas

Epigenome at NCBI

Starr Cancer Consortium



UMass Stem Cell Registry


SCRB 155

Epigenetic Regulation in Stem Cells and Development

Catalog Number: 63211
Alexander Meissner
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14

Cloning of Dolly the sheep suggests that all of our cells have exactly the same genes as a fertilized egg. If this is true, then how is it that each of our cells reads out those genes differently? This course will explain the developmental events that regulate the expression of genes, as well as how this developmental expression is established and maintained.
Prerequisite: Life and Physical Sciences A or Life Sciences 1a; Life Sciences 1b; MCB 52; SCRB 10 or permission of the instructor.


Continuous single cell imaging of fibroblasts to iPS cell reprogramming