183
Chromatin Remodeling during Development
enhancers to govern the endoderm gene regulatory network.
eLife 9.
Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR. 2018.
Placeholder nucleosomes underlie germline-to-embryo DNA
methylation reprogramming. Cell 172 : 993–1006.e1013.
Newport J, Kirschner M. 1982. A major developmental transition in
early Xenopus embryos. II: Control of the onset of transcription. Cell 30 : 687–696.
Nicetto D, Hahn M, Jung J, Schneider TD, Straub T, David R,
Schotta G, Rupp RA. 2013. Suv4–20h histone methyltransferases promote neuroectodermal differentiation by silencing
the pluripotency-associated Oct-25 gene. PLoS Genetics 9:
e1003188.
Nicklay JJ, Shechter D, Chitta RK, Garcia BA, Shabanowitz J, Allis
CD, Hunt DF. 2009. Analysis of histones in Xenopus laevis.
II: Mass spectrometry reveals an index of cell type-specif c
modifcations on H3 and H4. The Journal of Biological
Chemistry 284 : 1075–1085.
Niu L, Shen W, Shi Z, Tan Y, He N, Wan J, Sun J, Zhang Y, Huang
Y, Wang W, Fang C, Li J, Zheng P, Cheung E, Chen Y, Li L,
Hou C. 2021 Jul. Three-dimensional folding dynamics of the
Xenopus tropicalis genome. Nature Genetics 53(7): 1075–
1087. doi: 10.1038/s41588-021-00878-z. Epub 2021 Jun 7.
PMID: 34099928; PMCID: PMC8270788
Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V,
O’Doherty A, Falk E, Sporniak M, D’Santos C, Franklin
VNR et al. 2020. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nature Communications 11 : 3491.
Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho
KWY. 2019. Endodermal maternal transcription factors
establish super-enhancers during zygotic genome activation.
Cell Reports 27 : 2962–2977.e2965.
Paraiso KD, Cho JS, Yong J, Cho KWY. 2020. Early Xenopus gene
regulatory programs, chromatin states, and the role of maternal transcription factors. Current Topics in Developmental
Biology 139 : 35–60.
Perino M, Veenstra GJ. 2016. Chromatin control of developmental dynamics and plasticity. Developmental Cell 38:
610–620.
Petruk S, Black KL, Kovermann SK, Brock HW, Mazo A. 2013.
Stepwise histone modifcations are mediated by multiple
enzymes that rapidly associate with nascent DNA during
replication. Nature Communications 4 : 2841.
Petruk S, Cai J, Sussman R, Sun G, Kovermann SK, Mariani SA,
Calabretta B, McMahon SB, Brock HW, Iacovitti L et al.
2017. Delayed accumulation of H3K27me3 on nascent DNA
is essential for recruitment of transcription factors at early
stages of stem cell differentiation. Molecular Cell 66: 247–
257.e245.
Petruk S, Sedkov Y, Johnston DM, Hodgson JW, Black KL,
Kovermann SK, Beck S, Canaani E, Brock HW, Mazo A.
2012. TrxG and PcG proteins but not methylated histones
remain associated with DNA through replication. Cell 150:
922–933.
Potok ME, Nix DA, Parnell TJ, Cairns BR. 2013. Reprogramming
the maternal zebrafsh genome after fertilization to match the
paternal methylation pattern. Cell 153 : 759–772.
Prendergast L, Reinberg D. 2021. The missing linker: Emerging
trends for H1 variant-specifc functions. Genes & Development
35 : 40–58.
Prioleau MN, Huet J, Sentenac A, Méchali M. 1994. Competition
between chromatin and transcription complex assembly
regulates gene expression during early development. Cell 77:
439–449.
Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer
RM, Leidescher S, Markaki Y, Mentele E, Regnard C et al.
2017. Multivalent binding of PWWP2A to H2A.Z regulates
mitosis and neural crest differentiation. The EMBO Journal
36 : 2263–2279.
Putiri EL, Tiedemann RL, Liu C, Choi JH, Robertson KD. 2014.
Impact of human MLL/COMPASS and polycomb complexes
on the DNA methylome. Oncotarget 5 : 6338–6352.
Quigley IK, Heinz S. 2019. Generating a three-dimensional
genome from Xenopus with Hi-C. Cold Spring Harbor
Protocols 2019.
Quigley IK, Kintner C. 2017. Rfx2 stabilizes Foxj1 binding at
chromatin loops to enable multiciliated cell gene expression.
PLoS Genetics 13 : e1006538.
Schneider TD, Arteaga-Salas JM, Mentele E, David R, Nicetto D,
Imhof A, Rupp RA. 2011. Stage-specifc histone modif cation profles reveal global transitions in the Xenopus embryonic epigenome. PLoS One 6 : e22548.
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi
S, Fukui A, Hikosaka A, Suzuki A, Kondo M et al. 2016.
Genome evolution in the allotetraploid frog Xenopus laevis.
Nature 538 : 336–343.
Shechter D, Nicklay JJ, Chitta RK, Shabanowitz J, Hunt DF, Allis
CD. 2009. Analysis of histones in Xenopus laevis. I: A distinct index of enriched variants and modifcations exists in
each cell type and is remodeled during developmental transitions. The Journal of Biological Chemistry 284 : 1064–1074.
Sitbon D, Boyarchuk E, Dingli F, Loew D, Almouzni G. 2020.
Histone variant H3.3 residue S31 is essential for Xenopus
gastrulation regardless of the deposition pathway. Nature
Communications 11 : 1256.
Smith E, Shilatifard A. 2010. The chromatin signaling pathway:
Diverse mechanisms of recruitment of histone-modifying
enzymes and varied biological outcomes. Molecular Cell 40:
689–701.
Smith RC, Dworkin-Rastl E, Dworkin MB. 1988. Expression of a
histone H1-like protein is restricted to early Xenopus development. Genes & Development 2 : 1284–1295.
Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra
GJ, Vermeulen M. 2014. Global absolute quantif cation
reveals tight regulation of protein expression in single
Xenopus eggs. Nucleic Acids Research 42 : 9880–9891.
Soshnev AA, Josefowicz SZ, Allis CD. 2016. Greater than the sum
of parts: Complexity of the dynamic epigenome. Molecular
Cell 62 : 681–694.
Steinbach OC, Wolffe AP, Rupp RA. 1997. Somatic linker histones
cause loss of mesodermal competence in Xenopus. Nature
389 : 395–399.
Szenker E, Lacoste N, Almouzni G. 2012. A developmental
requirement for HIRA-dependent H3.3 deposition revealed
at gastrulation in Xenopus. Cell Reports 1 : 730–740.
Ura K, Nightingale K, Wolffe AP. 1996. Differential association of
HMG1 and linker histones B4 and H1 with dinucleosomal
DNA: Structural transitions and transcriptional repression.
The EMBO Journal 15 : 4959–4969.
van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y,
Veenstra GJ. 2011. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome
Research 21 : 410–421.
van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA,
Hanssen LL, Sharif N, Veenstra GJ. 2014. Principles of
nucleation of H3K27 methylation during embryonic development. Genome Research 24 : 401–410.
van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ,
Huynen MA, Veenstra GJC. 2017. Heterochromatic histone
Chromatin Remodeling during Development
enhancers to govern the endoderm gene regulatory network.
eLife 9.
Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR. 2018.
Placeholder nucleosomes underlie germline-to-embryo DNA
methylation reprogramming. Cell 172 : 993–1006.e1013.
Newport J, Kirschner M. 1982. A major developmental transition in
early Xenopus embryos. II: Control of the onset of transcription. Cell 30 : 687–696.
Nicetto D, Hahn M, Jung J, Schneider TD, Straub T, David R,
Schotta G, Rupp RA. 2013. Suv4–20h histone methyltransferases promote neuroectodermal differentiation by silencing
the pluripotency-associated Oct-25 gene. PLoS Genetics 9:
e1003188.
Nicklay JJ, Shechter D, Chitta RK, Garcia BA, Shabanowitz J, Allis
CD, Hunt DF. 2009. Analysis of histones in Xenopus laevis.
II: Mass spectrometry reveals an index of cell type-specif c
modifcations on H3 and H4. The Journal of Biological
Chemistry 284 : 1075–1085.
Niu L, Shen W, Shi Z, Tan Y, He N, Wan J, Sun J, Zhang Y, Huang
Y, Wang W, Fang C, Li J, Zheng P, Cheung E, Chen Y, Li L,
Hou C. 2021 Jul. Three-dimensional folding dynamics of the
Xenopus tropicalis genome. Nature Genetics 53(7): 1075–
1087. doi: 10.1038/s41588-021-00878-z. Epub 2021 Jun 7.
PMID: 34099928; PMCID: PMC8270788
Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V,
O’Doherty A, Falk E, Sporniak M, D’Santos C, Franklin
VNR et al. 2020. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nature Communications 11 : 3491.
Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho
KWY. 2019. Endodermal maternal transcription factors
establish super-enhancers during zygotic genome activation.
Cell Reports 27 : 2962–2977.e2965.
Paraiso KD, Cho JS, Yong J, Cho KWY. 2020. Early Xenopus gene
regulatory programs, chromatin states, and the role of maternal transcription factors. Current Topics in Developmental
Biology 139 : 35–60.
Perino M, Veenstra GJ. 2016. Chromatin control of developmental dynamics and plasticity. Developmental Cell 38:
610–620.
Petruk S, Black KL, Kovermann SK, Brock HW, Mazo A. 2013.
Stepwise histone modifcations are mediated by multiple
enzymes that rapidly associate with nascent DNA during
replication. Nature Communications 4 : 2841.
Petruk S, Cai J, Sussman R, Sun G, Kovermann SK, Mariani SA,
Calabretta B, McMahon SB, Brock HW, Iacovitti L et al.
2017. Delayed accumulation of H3K27me3 on nascent DNA
is essential for recruitment of transcription factors at early
stages of stem cell differentiation. Molecular Cell 66: 247–
257.e245.
Petruk S, Sedkov Y, Johnston DM, Hodgson JW, Black KL,
Kovermann SK, Beck S, Canaani E, Brock HW, Mazo A.
2012. TrxG and PcG proteins but not methylated histones
remain associated with DNA through replication. Cell 150:
922–933.
Potok ME, Nix DA, Parnell TJ, Cairns BR. 2013. Reprogramming
the maternal zebrafsh genome after fertilization to match the
paternal methylation pattern. Cell 153 : 759–772.
Prendergast L, Reinberg D. 2021. The missing linker: Emerging
trends for H1 variant-specifc functions. Genes & Development
35 : 40–58.
Prioleau MN, Huet J, Sentenac A, Méchali M. 1994. Competition
between chromatin and transcription complex assembly
regulates gene expression during early development. Cell 77:
439–449.
Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer
RM, Leidescher S, Markaki Y, Mentele E, Regnard C et al.
2017. Multivalent binding of PWWP2A to H2A.Z regulates
mitosis and neural crest differentiation. The EMBO Journal
36 : 2263–2279.
Putiri EL, Tiedemann RL, Liu C, Choi JH, Robertson KD. 2014.
Impact of human MLL/COMPASS and polycomb complexes
on the DNA methylome. Oncotarget 5 : 6338–6352.
Quigley IK, Heinz S. 2019. Generating a three-dimensional
genome from Xenopus with Hi-C. Cold Spring Harbor
Protocols 2019.
Quigley IK, Kintner C. 2017. Rfx2 stabilizes Foxj1 binding at
chromatin loops to enable multiciliated cell gene expression.
PLoS Genetics 13 : e1006538.
Schneider TD, Arteaga-Salas JM, Mentele E, David R, Nicetto D,
Imhof A, Rupp RA. 2011. Stage-specifc histone modif cation profles reveal global transitions in the Xenopus embryonic epigenome. PLoS One 6 : e22548.
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi
S, Fukui A, Hikosaka A, Suzuki A, Kondo M et al. 2016.
Genome evolution in the allotetraploid frog Xenopus laevis.
Nature 538 : 336–343.
Shechter D, Nicklay JJ, Chitta RK, Shabanowitz J, Hunt DF, Allis
CD. 2009. Analysis of histones in Xenopus laevis. I: A distinct index of enriched variants and modifcations exists in
each cell type and is remodeled during developmental transitions. The Journal of Biological Chemistry 284 : 1064–1074.
Sitbon D, Boyarchuk E, Dingli F, Loew D, Almouzni G. 2020.
Histone variant H3.3 residue S31 is essential for Xenopus
gastrulation regardless of the deposition pathway. Nature
Communications 11 : 1256.
Smith E, Shilatifard A. 2010. The chromatin signaling pathway:
Diverse mechanisms of recruitment of histone-modifying
enzymes and varied biological outcomes. Molecular Cell 40:
689–701.
Smith RC, Dworkin-Rastl E, Dworkin MB. 1988. Expression of a
histone H1-like protein is restricted to early Xenopus development. Genes & Development 2 : 1284–1295.
Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra
GJ, Vermeulen M. 2014. Global absolute quantif cation
reveals tight regulation of protein expression in single
Xenopus eggs. Nucleic Acids Research 42 : 9880–9891.
Soshnev AA, Josefowicz SZ, Allis CD. 2016. Greater than the sum
of parts: Complexity of the dynamic epigenome. Molecular
Cell 62 : 681–694.
Steinbach OC, Wolffe AP, Rupp RA. 1997. Somatic linker histones
cause loss of mesodermal competence in Xenopus. Nature
389 : 395–399.
Szenker E, Lacoste N, Almouzni G. 2012. A developmental
requirement for HIRA-dependent H3.3 deposition revealed
at gastrulation in Xenopus. Cell Reports 1 : 730–740.
Ura K, Nightingale K, Wolffe AP. 1996. Differential association of
HMG1 and linker histones B4 and H1 with dinucleosomal
DNA: Structural transitions and transcriptional repression.
The EMBO Journal 15 : 4959–4969.
van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y,
Veenstra GJ. 2011. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome
Research 21 : 410–421.
van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA,
Hanssen LL, Sharif N, Veenstra GJ. 2014. Principles of
nucleation of H3K27 methylation during embryonic development. Genome Research 24 : 401–410.
van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ,
Huynen MA, Veenstra GJC. 2017. Heterochromatic histone