182
Xenopus
Blythe SA, Cha SW, Tadjuidje E, Heasman J, Klein PS. 2010. Betacatenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2. Developmental
Cell 19 : 220–231.
Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB,
Gomez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra
GJ. 2011. Temporal uncoupling of the DNA methylome and
transcriptional repression during embryogenesis. Genome
Research 21 : 1313–1327.
Bogdanovic O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford
E, Williams R, Senanayake U, Schultz MD, Hontelez S, van
Kruijsbergen I et al. 2016. Active DNA demethylation at
enhancers during the vertebrate phylotypic period. Nature
Genetics 48 : 417–426.
Bogdanovic O, van Heeringen SJ, Veenstra GJ. 2012. The epigenome in early vertebrate development. Genesis (New York,
NY: 2000) 50 : 192–206.
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L,
Kirschner MW, Klein AM. 2018. The dynamics of gene
expression in vertebrate embryogenesis at single-cell resolution. Science (New York, NY) 360.
Bright AR, van Genesen S, Li Q, Grasso A, Frölich S, van der Sande
M, van Heeringen SJ, Veenstra GJC. 2021. Combinatorial
transcription factor activities on open chromatin induce
embryonic heterogeneity in vertebrates. The EMBO Journal:
e104913.
Bright AR, Veenstra GJC. 2019. Assay for transposase-accessible
chromatin-sequencing using Xenopus embryos. Cold Spring
Harbor Protocols 2019.
Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD,
Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X et al. 2017a.
Foxh1 occupies cis-regulatory modules prior to dynamic
transcription factor interactions controlling the mesendoderm gene program. Developmental Cell 40 : 595–607.e594.
Charney RM, Paraiso KD, Blitz IL, Cho KWY. 2017b. A gene
regulatory program controlling early Xenopus mesendoderm
formation: Network conservation and motifs. Seminars in
Cell & Developmental Biology 66 : 12–24.
Dunican DS, Ruzov A, Hackett JA, Meehan RR. 2008. xDnmt1
regulates transcriptional silencing in pre-MBT Xenopus
embryos independently of its catalytic function. Development
135 : 1295–1302.
Dworkin-Rastl E, Kandolf H, Smith RC. 1994. The maternal histone H1 variant, H1M (B4 protein), is the predominant H1
histone in Xenopus pregastrula embryos. Developmental
Biology 161 : 425–439.
Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I,
Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA,
van Heeringen SJ et al. 2017. Regulatory remodeling in the
allo-tetraploid frog Xenopus laevis. Genome Biology 18 : 198.
Esmaeili M, Blythe SA, Tobias JW, Zhang K, Yang J, Klein
PS. 2020. Chromatin accessibility and histone acetylation in the regulation of competence in early development.
Developmental Biology 462 : 20–35.
Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJ.
2016. Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development 143:
1340–1350.
Gentsch GE, Spruce T, Owens NDL, Smith JC. 2019. Maternal
pluripotency factors initiate extensive chromatin remodelling to predef ne frst response to inductive signals. Nature
Communications 10 : 4269.
Gilchrist MJ, Cho KWY, Veenstra GJC. 2020. Genomics methods for Xenopus embryos and tissues. Cold Spring Harbor
Protocols 2020 : 097915.
Greenberg RS, Long HK, Swigut T, Wysocka J. 2019. Single amino
acid change underlies distinct roles of H2A.Z subtypes in
human syndrome. Cell 178 : 1421–1436.e1424.
Gupta R, Wills A, Ucar D, Baker J. 2014. Developmental enhancers are marked independently of zygotic Nodal signals in
Xenopus. Developmental Biology 395 : 38–49.
Gurdon JB. 2013. The egg and the nucleus: A battle for supremacy.
Development 140 : 2449–2456.
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ,
Bogdanovic O, Lister R, Veenstra GJ. 2015. Embryonic transcription is controlled by maternally defned chromatin state.
Nature Communications 6 : 10148.
Hontelez S, van Kruijsbergen I, Veenstra GJC. 2019. ChIPsequencing in Xenopus embryos. Cold Spring Harbor
Protocols 2019.
Hörmanseder E, Simeone A, Allen GE, Bradshaw CR, Figlmüller
M, Gurdon J, Jullien J. 2017. H3K4 methylation-dependent
memory of somatic cell identity inhibits reprogramming and
development of nuclear transfer embryos. Cell Stem Cell 21:
135–143.e136.
Jallow Z, Jacobi UG, Weeks DL, Dawid IB, Veenstra GJ. 2004.
Specialized and redundant roles of TBP and a vertebrate-specifc TBP paralog in embryonic gene regulation in Xenopus.
Proceedings of the National Academy of Sciences of the
United States of America 101 : 13525–13530.
Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma
X, Sun X, Cai J et al. 2013. Sperm, but not oocyte, DNA
methylome is inherited by zebrafsh early embryos. Cell 153:
773–784.
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger
N, Strouboulis J, Wolffe AP. 1998. Methylated DNA and
MeCP2 recruit histone deacetylase to repress transcription.
Nature Genetics 19 : 187–191.
Kakebeen AD, Chitsazan AD, Williams MC, Saunders LM, Wills
AE. 2020. Chromatin accessibility dynamics and single cell
RNA-Seq reveal new regulators of regeneration in neural
progenitors. eLife 9.
Koster JG, Destrée OH, Westerhoff HV. 1988. Kinetics of histone
gene expression during early development of Xenopus laevis.
Journal of Theoretical Biology 135 : 139–167.
Kuznetsov JN, Aguero TH, Owens DA, Kurtenbach S, Field MG,
Durante MA, Rodriguez DA, King ML, Harbour JW. 2019.
BAP1 regulates epigenetic switch from pluripotency to differentiation in developmental lineages giving rise to BAP1mutant cancers. Science Advances 5 : eaax1738.
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup
O, Winata C, Mathavan S, Muller F, Alestrom P et al. 2011.
Prepatterning of developmental gene expression by modif ed
histones before zygotic genome activation. Developmental
Cell 21 : 993–1004.
Liu X, Wang C, Liu W, Li J, Li C, Kou X, Chen J, Zhao Y, Gao
H, Wang H et al. 2016. Distinct features of H3K4me3 and
H3K27me3 chromatin domains in pre-implantation embryos.
Nature 537 : 558–562.
Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML,
Grutzner F, Odom DT, Patient R, Ponting CP et al. 2013.
Epigenetic conservation at gene regulatory elements revealed
by non-methylated DNA profling in seven vertebrates. eLife
2 : e00348.
Martire S, Banaszynski LA. 2020. The roles of histone variants
in fne-tuning chromatin organization and function. Nature
Reviews Molecular Cell Biology 21 : 522–541.
Mukherjee S, Chaturvedi P, Rankin SA, Fish MB, Wlizla M,
Paraiso KD, MacDonald M, Chen X, Weirauch MT, Blitz IL
et al. 2020. Sox17 and β-catenin co-occupy Wnt-responsive
Xenopus
Blythe SA, Cha SW, Tadjuidje E, Heasman J, Klein PS. 2010. Betacatenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2. Developmental
Cell 19 : 220–231.
Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB,
Gomez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra
GJ. 2011. Temporal uncoupling of the DNA methylome and
transcriptional repression during embryogenesis. Genome
Research 21 : 1313–1327.
Bogdanovic O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford
E, Williams R, Senanayake U, Schultz MD, Hontelez S, van
Kruijsbergen I et al. 2016. Active DNA demethylation at
enhancers during the vertebrate phylotypic period. Nature
Genetics 48 : 417–426.
Bogdanovic O, van Heeringen SJ, Veenstra GJ. 2012. The epigenome in early vertebrate development. Genesis (New York,
NY: 2000) 50 : 192–206.
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L,
Kirschner MW, Klein AM. 2018. The dynamics of gene
expression in vertebrate embryogenesis at single-cell resolution. Science (New York, NY) 360.
Bright AR, van Genesen S, Li Q, Grasso A, Frölich S, van der Sande
M, van Heeringen SJ, Veenstra GJC. 2021. Combinatorial
transcription factor activities on open chromatin induce
embryonic heterogeneity in vertebrates. The EMBO Journal:
e104913.
Bright AR, Veenstra GJC. 2019. Assay for transposase-accessible
chromatin-sequencing using Xenopus embryos. Cold Spring
Harbor Protocols 2019.
Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD,
Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X et al. 2017a.
Foxh1 occupies cis-regulatory modules prior to dynamic
transcription factor interactions controlling the mesendoderm gene program. Developmental Cell 40 : 595–607.e594.
Charney RM, Paraiso KD, Blitz IL, Cho KWY. 2017b. A gene
regulatory program controlling early Xenopus mesendoderm
formation: Network conservation and motifs. Seminars in
Cell & Developmental Biology 66 : 12–24.
Dunican DS, Ruzov A, Hackett JA, Meehan RR. 2008. xDnmt1
regulates transcriptional silencing in pre-MBT Xenopus
embryos independently of its catalytic function. Development
135 : 1295–1302.
Dworkin-Rastl E, Kandolf H, Smith RC. 1994. The maternal histone H1 variant, H1M (B4 protein), is the predominant H1
histone in Xenopus pregastrula embryos. Developmental
Biology 161 : 425–439.
Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I,
Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA,
van Heeringen SJ et al. 2017. Regulatory remodeling in the
allo-tetraploid frog Xenopus laevis. Genome Biology 18 : 198.
Esmaeili M, Blythe SA, Tobias JW, Zhang K, Yang J, Klein
PS. 2020. Chromatin accessibility and histone acetylation in the regulation of competence in early development.
Developmental Biology 462 : 20–35.
Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJ.
2016. Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors. Development 143:
1340–1350.
Gentsch GE, Spruce T, Owens NDL, Smith JC. 2019. Maternal
pluripotency factors initiate extensive chromatin remodelling to predef ne frst response to inductive signals. Nature
Communications 10 : 4269.
Gilchrist MJ, Cho KWY, Veenstra GJC. 2020. Genomics methods for Xenopus embryos and tissues. Cold Spring Harbor
Protocols 2020 : 097915.
Greenberg RS, Long HK, Swigut T, Wysocka J. 2019. Single amino
acid change underlies distinct roles of H2A.Z subtypes in
human syndrome. Cell 178 : 1421–1436.e1424.
Gupta R, Wills A, Ucar D, Baker J. 2014. Developmental enhancers are marked independently of zygotic Nodal signals in
Xenopus. Developmental Biology 395 : 38–49.
Gurdon JB. 2013. The egg and the nucleus: A battle for supremacy.
Development 140 : 2449–2456.
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ,
Bogdanovic O, Lister R, Veenstra GJ. 2015. Embryonic transcription is controlled by maternally defned chromatin state.
Nature Communications 6 : 10148.
Hontelez S, van Kruijsbergen I, Veenstra GJC. 2019. ChIPsequencing in Xenopus embryos. Cold Spring Harbor
Protocols 2019.
Hörmanseder E, Simeone A, Allen GE, Bradshaw CR, Figlmüller
M, Gurdon J, Jullien J. 2017. H3K4 methylation-dependent
memory of somatic cell identity inhibits reprogramming and
development of nuclear transfer embryos. Cell Stem Cell 21:
135–143.e136.
Jallow Z, Jacobi UG, Weeks DL, Dawid IB, Veenstra GJ. 2004.
Specialized and redundant roles of TBP and a vertebrate-specifc TBP paralog in embryonic gene regulation in Xenopus.
Proceedings of the National Academy of Sciences of the
United States of America 101 : 13525–13530.
Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma
X, Sun X, Cai J et al. 2013. Sperm, but not oocyte, DNA
methylome is inherited by zebrafsh early embryos. Cell 153:
773–784.
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger
N, Strouboulis J, Wolffe AP. 1998. Methylated DNA and
MeCP2 recruit histone deacetylase to repress transcription.
Nature Genetics 19 : 187–191.
Kakebeen AD, Chitsazan AD, Williams MC, Saunders LM, Wills
AE. 2020. Chromatin accessibility dynamics and single cell
RNA-Seq reveal new regulators of regeneration in neural
progenitors. eLife 9.
Koster JG, Destrée OH, Westerhoff HV. 1988. Kinetics of histone
gene expression during early development of Xenopus laevis.
Journal of Theoretical Biology 135 : 139–167.
Kuznetsov JN, Aguero TH, Owens DA, Kurtenbach S, Field MG,
Durante MA, Rodriguez DA, King ML, Harbour JW. 2019.
BAP1 regulates epigenetic switch from pluripotency to differentiation in developmental lineages giving rise to BAP1mutant cancers. Science Advances 5 : eaax1738.
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup
O, Winata C, Mathavan S, Muller F, Alestrom P et al. 2011.
Prepatterning of developmental gene expression by modif ed
histones before zygotic genome activation. Developmental
Cell 21 : 993–1004.
Liu X, Wang C, Liu W, Li J, Li C, Kou X, Chen J, Zhao Y, Gao
H, Wang H et al. 2016. Distinct features of H3K4me3 and
H3K27me3 chromatin domains in pre-implantation embryos.
Nature 537 : 558–562.
Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML,
Grutzner F, Odom DT, Patient R, Ponting CP et al. 2013.
Epigenetic conservation at gene regulatory elements revealed
by non-methylated DNA profling in seven vertebrates. eLife
2 : e00348.
Martire S, Banaszynski LA. 2020. The roles of histone variants
in fne-tuning chromatin organization and function. Nature
Reviews Molecular Cell Biology 21 : 522–541.
Mukherjee S, Chaturvedi P, Rankin SA, Fish MB, Wlizla M,
Paraiso KD, MacDonald M, Chen X, Weirauch MT, Blitz IL
et al. 2020. Sox17 and β-catenin co-occupy Wnt-responsive