177
Chromatin Remodeling during Development
results in craniofacial defects and aberrant neural crest
migration, suggesting that this protein mediates the function
of H2A.Z in neural crest gene expression.
Linker histones bind to the dyad axis of nucleosomes
(where DNA enters and exits the nucleosome) and generally have a role in chromatin compaction (Prendergast and
Reinberg 2021). However, this does not mean that all linker
histones repress transcription. Studies in Xenopus have
made important early contributions in the emerging roles
of variant linker histones in embryonic development (Smith
et al. 1988; Dworkin-Rastl et al. 1994; Steinbach et al. 1997 ).
Canonical histone H1 is virtually absent in oocytes and
early embryos. Instead, they contain a variant linker histone
encoded by the h1–8 gene (also referred to as linker histone
B4, H1M, or h1foo). This early embryonic linker histone is
gradually diluted and replaced by canonical (somatic) H1
during development. In animal cap explants, somatic H1
promotes the loss of mesodermal competence, suggesting
that somatic H1 but not maternal H1–8/B4 represses genes
involved in mesoderm induction (Steinbach et al. 1997 ).
H1–8/B4 has a relatively low affnity for chromatin compared to somatic H1 (Ura et al. 1996 ), which may explain the
transcriptionally permissive nature of chromatin associated
with developmental competence in early embryos. These
data illustrate how variant core and linker histone are critically important for chromatin accessibility and gene regulation during development.
11.3.2. CHROMATIN ASSEMBLY AND THE ONSET
OF ZYGOTIC GENOME ACTIVATION
The nucleosomes that are formed by the very abundant
maternal stores of histone proteins generally provide a
barrier towards transcription; this is especially the case in
early development, in which chromatin assembly is very
repressive towards transcription. Before ovulation, oocytes
are arrested in prophase of meiosis I and transcriptionally
active. Meiotic maturation under the infuence of progesterone leads to completion of meiosis I and an arrest at
metaphase of meiosis II. These eggs are transcriptionally
quiescent. After fertilization, the maternal gene products
of the egg need to sustain the embryo until well into blastula stages, when the embryo starts to transcribe its own
genes (zygotic genome activation, ZGA). Injected promoterreporter templates recapitulate this pattern of endogenous
transcription: they are active in oocytes but repressed in
embryos until the mid-blastula stage, when they become
active again. This was frst demonstrated with an RNA
polymerase III-dependent tRNA promoter and subsequently
with a number of RNA polymerase II-dependent promoters,
such as the c-Myc promoter, one of the histone H2B promoters, and the CMV promoter (Newport and Kirschner 1982;
Prioleau et al. 1994; Veenstra et al. 1999). Excess competitor DNA that is co-injected with the promoter construct
interferes effectively with chromatin assembly, as judged
from supercoiling assays, and relieves the repression of
transcription before the mid-blastula stage. Injection of the
general transcription factor TBP stimulates this precocious
transcription by one to two orders of magnitude (Prioleau
et al. 1994; Veenstra et al. 1999). This is because TBP (Tbp)
is only minimally present before the mid-blastula stage.
TBP is also virtually absent in transcriptionally active
oocytes, but oocytes contain TBP2 (Tbpl2), a TBP replacement factor in oocytes that is largely degraded during
oocyte maturation (Jallow et al. 2004; Akhtar and Veenstra
2009). In cleavage-stage embryos, neither TBP nor TBP2
is abundant, but TBP accumulates during blastula stages
due to translation of maternal tbp mRNA. Interestingly, in
cleavage-stage embryos with exogenous TBP, injected promoter constructs become transiently active, to be repressed
coincident with chromatin assembly (Prioleau et al. 1994;
Veenstra et al. 1999). Chromatin assembly is much more
effcient in egg extract than in oocyte extract (Wang and
Shechter 2016). Moreover, depletion of free histones leads
to an earlier ZGA (Amodeo et al. 2015). This suggests that
repression of transcription before ZGA occurs at multiple
levels: chromatin assembly is repressive towards transcription, and, in addition, the abundance of TBP and TBP2
determines the capacity of the transcription machinery in
early development.
11.3.3. CHROMATIN ACCESSIBILITY AND
TRANSCRIPTION FACTOR BINDING
Chromatin accessibility, as interrogated using ATACsequencing, is observed from late blastula stages onward
(Bright et al. 2021), suggesting an important role for maternal factors in chromatin opening. Indeed, maternal factors
may contribute to chromatin opening, pluripotency, and
germ layer specif cation (Paraiso et al. 2020). Many regulatory elements that are active in early embryos contain binding sites for the pluripotency factors Oct4 (Pou5f3.1, 3.2, and
3.3) and Sox2/3. Of these proteins, Pou5f3.2, Pou5f3.3, and
Sox3 are maternally expressed and are required for establishing chromatin accessibility at approximately 40% of
putative regulatory elements (Gentsch et al. 2019). Another
maternal factor, Foxh1, is bound to regulatory elements as
early as the 32-cell stage (Charney et al. 2017a). In early
blastula embryos, Foxh1 recruits Tle, a co-repressor that
can associate with the histone deacetylase Hdac1. In prospective endoderm, early Foxh1-Tle binding to regulatory
elements of endoderm-expressed genes precedes the recruitment of the zygotically expressed Foxa activator and the
co-activator Ep300. This suggests a molecular “hand-off”
between maternal and zygotic forkhead transcription factors
that coincides with a switch from repression to activation of
transcription (Charney et al. 2017a). Maternal factors Vegt
and Otx1 also bind to regulatory elements in cleavage stage
embryos and orchestrate endoderm formation together with
Foxh1 (Paraiso et al. 2019). The mediator of canonical Wnt
signaling, β-Catenin (Ctnnb1), is also associated with DNA
before the mid-blastula stage (Blythe et al. 2010; Afouda
et al. 2020). It recruits Prmt2, a histone methyl transferase,
methylating histone H3 on arginine 8 and priming target
Chromatin Remodeling during Development
results in craniofacial defects and aberrant neural crest
migration, suggesting that this protein mediates the function
of H2A.Z in neural crest gene expression.
Linker histones bind to the dyad axis of nucleosomes
(where DNA enters and exits the nucleosome) and generally have a role in chromatin compaction (Prendergast and
Reinberg 2021). However, this does not mean that all linker
histones repress transcription. Studies in Xenopus have
made important early contributions in the emerging roles
of variant linker histones in embryonic development (Smith
et al. 1988; Dworkin-Rastl et al. 1994; Steinbach et al. 1997 ).
Canonical histone H1 is virtually absent in oocytes and
early embryos. Instead, they contain a variant linker histone
encoded by the h1–8 gene (also referred to as linker histone
B4, H1M, or h1foo). This early embryonic linker histone is
gradually diluted and replaced by canonical (somatic) H1
during development. In animal cap explants, somatic H1
promotes the loss of mesodermal competence, suggesting
that somatic H1 but not maternal H1–8/B4 represses genes
involved in mesoderm induction (Steinbach et al. 1997 ).
H1–8/B4 has a relatively low affnity for chromatin compared to somatic H1 (Ura et al. 1996 ), which may explain the
transcriptionally permissive nature of chromatin associated
with developmental competence in early embryos. These
data illustrate how variant core and linker histone are critically important for chromatin accessibility and gene regulation during development.
11.3.2. CHROMATIN ASSEMBLY AND THE ONSET
OF ZYGOTIC GENOME ACTIVATION
The nucleosomes that are formed by the very abundant
maternal stores of histone proteins generally provide a
barrier towards transcription; this is especially the case in
early development, in which chromatin assembly is very
repressive towards transcription. Before ovulation, oocytes
are arrested in prophase of meiosis I and transcriptionally
active. Meiotic maturation under the infuence of progesterone leads to completion of meiosis I and an arrest at
metaphase of meiosis II. These eggs are transcriptionally
quiescent. After fertilization, the maternal gene products
of the egg need to sustain the embryo until well into blastula stages, when the embryo starts to transcribe its own
genes (zygotic genome activation, ZGA). Injected promoterreporter templates recapitulate this pattern of endogenous
transcription: they are active in oocytes but repressed in
embryos until the mid-blastula stage, when they become
active again. This was frst demonstrated with an RNA
polymerase III-dependent tRNA promoter and subsequently
with a number of RNA polymerase II-dependent promoters,
such as the c-Myc promoter, one of the histone H2B promoters, and the CMV promoter (Newport and Kirschner 1982;
Prioleau et al. 1994; Veenstra et al. 1999). Excess competitor DNA that is co-injected with the promoter construct
interferes effectively with chromatin assembly, as judged
from supercoiling assays, and relieves the repression of
transcription before the mid-blastula stage. Injection of the
general transcription factor TBP stimulates this precocious
transcription by one to two orders of magnitude (Prioleau
et al. 1994; Veenstra et al. 1999). This is because TBP (Tbp)
is only minimally present before the mid-blastula stage.
TBP is also virtually absent in transcriptionally active
oocytes, but oocytes contain TBP2 (Tbpl2), a TBP replacement factor in oocytes that is largely degraded during
oocyte maturation (Jallow et al. 2004; Akhtar and Veenstra
2009). In cleavage-stage embryos, neither TBP nor TBP2
is abundant, but TBP accumulates during blastula stages
due to translation of maternal tbp mRNA. Interestingly, in
cleavage-stage embryos with exogenous TBP, injected promoter constructs become transiently active, to be repressed
coincident with chromatin assembly (Prioleau et al. 1994;
Veenstra et al. 1999). Chromatin assembly is much more
effcient in egg extract than in oocyte extract (Wang and
Shechter 2016). Moreover, depletion of free histones leads
to an earlier ZGA (Amodeo et al. 2015). This suggests that
repression of transcription before ZGA occurs at multiple
levels: chromatin assembly is repressive towards transcription, and, in addition, the abundance of TBP and TBP2
determines the capacity of the transcription machinery in
early development.
11.3.3. CHROMATIN ACCESSIBILITY AND
TRANSCRIPTION FACTOR BINDING
Chromatin accessibility, as interrogated using ATACsequencing, is observed from late blastula stages onward
(Bright et al. 2021), suggesting an important role for maternal factors in chromatin opening. Indeed, maternal factors
may contribute to chromatin opening, pluripotency, and
germ layer specif cation (Paraiso et al. 2020). Many regulatory elements that are active in early embryos contain binding sites for the pluripotency factors Oct4 (Pou5f3.1, 3.2, and
3.3) and Sox2/3. Of these proteins, Pou5f3.2, Pou5f3.3, and
Sox3 are maternally expressed and are required for establishing chromatin accessibility at approximately 40% of
putative regulatory elements (Gentsch et al. 2019). Another
maternal factor, Foxh1, is bound to regulatory elements as
early as the 32-cell stage (Charney et al. 2017a). In early
blastula embryos, Foxh1 recruits Tle, a co-repressor that
can associate with the histone deacetylase Hdac1. In prospective endoderm, early Foxh1-Tle binding to regulatory
elements of endoderm-expressed genes precedes the recruitment of the zygotically expressed Foxa activator and the
co-activator Ep300. This suggests a molecular “hand-off”
between maternal and zygotic forkhead transcription factors
that coincides with a switch from repression to activation of
transcription (Charney et al. 2017a). Maternal factors Vegt
and Otx1 also bind to regulatory elements in cleavage stage
embryos and orchestrate endoderm formation together with
Foxh1 (Paraiso et al. 2019). The mediator of canonical Wnt
signaling, β-Catenin (Ctnnb1), is also associated with DNA
before the mid-blastula stage (Blythe et al. 2010; Afouda
et al. 2020). It recruits Prmt2, a histone methyl transferase,
methylating histone H3 on arginine 8 and priming target