Grounded: Transcriptional Pausing in Naive mESCs
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Citation
Guenther, Matthew G., and Richard A. Young. “Grounded:
Transcriptional Pausing in Naive mESCs.” Cell Stem Cell 10, no.
5 (May 2012): 484–485. © 2012 Elsevier Inc.
As Published
http://dx.doi.org/10.1016/j.stem.2012.04.016
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Elsevier
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Final published version
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Fri May 27 02:09:27 EDT 2016
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http://hdl.handle.net/1721.1/91606
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Cell Stem Cell
Previews
Grounded: Transcriptional Pausing in Naive mESCs
Matthew G. Guenther1 and Richard A. Young1,2,*
1Whitehead
Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
*Correspondence: young@wi.mit.edu
DOI 10.1016/j.stem.2012.04.016
2Department
Growing mouse pluripotent stem cells in defined media with signaling inhibitors establishes a naive ground
state different from that of cells grown in serum. Recently in Cell, Marks et al. (2012) reported differences in
the transcriptional and epigenomic landscapes of naive and serum-exposed mouse stem cells that improve
our understanding of the pluripotent ground state.
Embryonic stem cells (ESCs) provide
a powerful model system for studying early
development because of their capacity to
differentiate into any cell type or tissue in
the adult organism, a property known as
pluripotency. Murine ESCs (mESCs) were
originally explanted and cultured in the
presence of ‘‘feeder’’ embryonic fibroblasts, fetal calf serum, and other growth
supplements to produce cells that selfrenew indefinitely in culture and retain pluripotency (Evans and Kaufman, 1981;
Martin, 1981). Heterogeneity in cellular
morphology and in expression of key pluripotency factors suggested that mESCs
grown in serum may be in a metastable
and more developmentally advanced state
that is not representative of the ground
state of cells in the inner cell mass of the
preimplantation embryo. Erk pathway
stimulation by serum exposure is thought
to predispose these cells to lineage
commitment and prevent them from
acquiring a naive pluripotent state (reviewed in Nichols and Smith, 2009). Propagation of mESCs in the presence of Mek/
Fgf pathway and Gsk3 inhibitors and in
the absence of serum factors, a condition
known as 2i, effectively blocks differentiation signals and allows capture of the naive
pluripotent state. Thus, mESCs grown in
the 2i condition may more accurately
represent the naive state of pluripotent
cells in the inner cell mass of the blastocyst.
In a recent issue of Cell, Marks et al.
(2012) compared the transcriptional and
chromatin profiles of serum-grown and
2i-grown cells to gain insights into the
naive pluripotent state. They found that
many lineage-specification genes expressed in serum-grown mESCs are
repressed in 2i conditions. Interestingly,
they also found that reduced expression
of lineage-specification and other genes
in 2i cells is associated with enhanced
promoter-proximal pausing (Figure 1).
Transcription initiation and promoter-proximal pausing by RNA polymerase II (Pol II)
has previously been shown to occur at
genes that encode lineage-specific regulators in embryonic cells, and is a mechanism
that allows these silent genes to be
precisely and synchronously induced in
response to developmental cues or
extrinsic stimuli (reviewed in Levine, 2011).
mESCs grown in serum and 2i conditions have similar levels of transcripts for
genes encoding key pluripotency factors
(Pou5f1, Nanog, Sox2, Esrrb, Klf2, Klf4,
and Tbx3) and exhibit similar proliferation
behavior and differentiation potential,
but cells propagated in the 2i condition
exhibit more uniform expression of key
pluripotency factors and cellular morphology. When Marks et al. (2012)
examined genes that are differentially
expressed in the two conditions, they
found that cells grown in the 2i condition
have increased levels of transcripts for
genes encoding metabolic functions and
decreased levels of transcripts for many
ectodermal and mesodermal specification
genes. The precocious transcription of
such genes in ESCs, which has
been called lineage priming, might poise
stem cells for differentiation. However, as
the authors note, the repression of
lineage-specification genes in 2i conditions
suggests that multilineage priming is not an
essential feature of the pluripotent state.
Trithorax Group and Polycomb Group
protein complexes, which catalyze histone H3K4me3 and H3K27me3 modifications, play prominent roles in development. Nucleosomes with H3K4me3
occur at sites of Pol II initiation and
those with H3K27me3 occur at repressed
lineage-specification
genes,
among
484 Cell Stem Cell 10, May 4, 2012 ª2012 Elsevier Inc.
others. Marks et al. (2012) mapped the
genome-wide locations of H3K4me3and H3K27me3-modified nucleosomes
in ESCs grown in serum and 2i conditions,
and found that H3K4me3 profiles were
highly similar, but that the levels of
H3K27me3 were reduced somewhat
in the 2i condition. The decrease in
H3K27me3 occupancy in the 2i condition
was associated with limited transcriptional changes, but the threshold for
functional occupancy is unknown, so the
biological repercussions of the different
levels of H3K27me3 await further study.
In embryonic cells from a broad range
of species, many genes experience
transcription initiation and promoter-proximal pausing by Pol II (Guenther et al.,
2007; Zeitlinger et al., 2007; Levine,
2011). Embryonic cells employ promoterproximal pausing as a mechanism to regulate genes for lineage-specific regulators
that are silent in the early embryo, but
must be activated in a precise, reliable,
and coordinated fashion in response to
developmental cues. Pol II molecules recruited to promoters by transcriptional
activators can initiate synthesis of a
short RNA species, but are subjected
to promoter-proximal pausing until phosphorylated by the elongation factor
P-TEFb, which is recruited by various
factors including Mediator and c-Myc
(Rahl et al., 2010; Takahashi et al., 2011).
Marks et al. (2012) found that promoterproximal pausing by RNA Pol II is more
prevalent in ESCs grown in the 2i condition
than in serum, and that paused Pol II was
more evident at many lineage-specification genes in the 2i condition. Their results
suggest that increased promoter-proximal pausing, which involves lineagespecification genes, among others, may
be especially important for establishing
Cell Stem Cell
Previews
described by Marks et al. (2012) are also
found in these human cells.
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Promoter-proximal
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More Pol II pausing
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Figure 1. Transcriptional Differences between 2i and Serum-Grown mESCs
Schematic diagram of mESC growth conditions (top), transcriptome (middle), and RNA Polymerase II
pausing differences (bottom, Pol II) in mESCs grown in 2i (left) or serum (right). Reads indicate ChIPSeq reads. Models for lineage-specification genes are shown below the graphs in black, and start sites
are indicated by an arrow. The transcriptional state of mESCs grown in either condition is readily interconverted by changing the growth media.
and maintaining the ground state of naive
pluripotent ESCs.
Marks et al. (2012) found that the
transcriptional and chromatin states of
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Autoimmune T Cells Lured
to a FASL Web of Death by MSCs
William J. Murphy1,2 and Jan A. Nolta2,3,*
1Department
of Dermatology
of Internal Medicine
3Stem Cell Program and Institute for Regenerative Cures
University of California, Davis, Davis, CA 95616, USA
*Correspondence: wmjmurphy@ucdavis.edu
DOI 10.1016/j.stem.2012.04.013
2Department
Achieving immune tolerance through cell transplantation is a promising approach for treating autoimmune
disease. In this issue of Cell Stem Cell, Akiyama et al. (2012) demonstrate that human and mouse mesenchymal stem cells can induce immune suppression by attracting and killing autoreactive T cells, which
stimulates TGFb production by macrophages and generates regulatory T cells.
Mesenchymal stem cells/marrow stromal
cells (MSCs) are perhaps the cell type
most commonly investigated for tissue
repair therapies. However, MSCs appear
capable of doing much more than simply
facilitating tissue repair. These interesting
cells, derived most often from the bone
marrow or fat, can serve as ‘‘paramedics’’
to help heal tissue through local and
Cell Stem Cell 10, May 4, 2012 ª2012 Elsevier Inc. 485