Dux-Mediated Corrections of Aberrant H3K9ac during 2-Cell Genome Activation Optimize Efficiency of Somatic Cell Nuclear Transfer
Tài liệu tham khảo
Akagi, 2011, Treatment with a histone deacetylase inhibitor after nuclear transfer improves the preimplantation development of cloned bovine embryos, J. Reprod. Dev., 57, 120, 10.1262/jrd.10-058A
Bui, 2010, Effect of trichostatin A on chromatin remodeling, histone modifications, DNA replication, and transcriptional activity in cloned mouse embryos, Biol. Reprod., 83, 454, 10.1095/biolreprod.109.083337
Chen, 2019, Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development, Nat. Genet., 51, 947, 10.1038/s41588-019-0418-7
Chen, 2020, Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos, Nat. Commun., 11, 1813, 10.1038/s41467-020-15607-z
Choi, 2016, DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes, Nucleic Acids Res., 44, 5161, 10.1093/nar/gkw141
Choi, 2017, Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells, Science, 355, eaag1927, 10.1126/science.aag1927
Chung, 2014, Human somatic cell nuclear transfer using adult cells, Cell Stem Cell, 14, 777, 10.1016/j.stem.2014.03.015
Chung, 2015, Histone demethylase expression enhances human somatic cell nuclear transfer efficiency and promotes derivation of pluripotent stem cells, Cell Stem Cell, 17, 758, 10.1016/j.stem.2015.10.001
De Iaco, 2017, DUX-family transcription factors regulate zygotic genome activation in placental mammals, Nat. Genet., 49, 941, 10.1038/ng.3858
Djekidel, 2018, Reprogramming of chromatin accessibility in somatic cell nuclear transfer is DNA replication independent, Cell Rep., 23, 1939, 10.1016/j.celrep.2018.04.036
Eckersley-Maslin, 2016, MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs, Cell Rep., 17, 179, 10.1016/j.celrep.2016.08.087
Falco, 2007, Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells, Dev. Biol., 307, 539, 10.1016/j.ydbio.2007.05.003
Gao, 2017, Protein expression landscape of mouse embryos during pre-implantation development, Cell Rep., 21, 3957, 10.1016/j.celrep.2017.11.111
Gao, 2018, Inhibition of aberrant DNA re-methylation improves post-implantation development of somatic cell nuclear transfer embryos, Cell Stem Cell, 23, 426, 10.1016/j.stem.2018.07.017
Gates, 2017, Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation, J. Biol. Chem., 292, 14456, 10.1074/jbc.M117.802074
Gialitakis, 2006, Coordinated changes of histone modifications and HDAC mobilization regulate the induction of MHC class II genes by Trichostatin A, Nucleic Acids Res., 34, 765, 10.1093/nar/gkj462
Guo, 2019, Precise temporal regulation of Dux is important for embryo development, Cell Res., 29, 956, 10.1038/s41422-019-0238-4
Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004
Hendrickson, 2017, Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons, Nat. Genet., 49, 925, 10.1038/ng.3844
Inoue, 2010, Impeding Xist expression from the active X chromosome improves mouse somatic cell nuclear transfer, Science, 330, 496, 10.1126/science.1194174
Inoue, 2015, Trichostatin A specifically improves the aberrant expression of transcription factor genes in embryos produced by somatic cell nuclear transfer, Sci. Rep., 5, 10127, 10.1038/srep10127
Inoue, 2020, Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas, Nat. Commun., 11, 2150, 10.1038/s41467-020-16044-8
Kemp, 2005, The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells, Nucleic Acids Res., 33, 325, 10.1093/nar/gki177
Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317
Kishigami, 2006, Significant improvement of mouse cloning technique by treatment with trichostatin A after somatic nuclear transfer, Biochem. Biophys. Res. Commun., 340, 183, 10.1016/j.bbrc.2005.11.164
Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923
Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Liu, 2016, Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing, Cell Discov., 2, 16010, 10.1038/celldisc.2016.10
Liu, 2016, Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos, Nature, 537, 558, 10.1038/nature19362
Liu, 2018, Cloning of macaque monkeys by somatic cell nuclear transfer, Cell, 172, 881, 10.1016/j.cell.2018.01.020
Matoba, 2018, Somatic cell nuclear transfer reprogramming: mechanisms and applications, Cell Stem Cell, 23, 471, 10.1016/j.stem.2018.06.018
Matoba, 2014, Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation, Cell, 159, 884, 10.1016/j.cell.2014.09.055
Matoba, 2018, Loss of H3K27me3 imprinting in somatic cell nuclear transfer embryos disrupts post-implantation development, Cell Stem Cell, 23, 343, 10.1016/j.stem.2018.06.008
Munsie, 2000, Isolation of pluripotent embryonic stem cells from reprogrammed adult mouse somatic cell nuclei, Curr. Biol., 10, 989, 10.1016/S0960-9822(00)00648-5
Niu, 2017, Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9, Science, 357, 1303, 10.1126/science.aan4187
Ogura, 2013, Recent advancements in cloning by somatic cell nuclear transfer, Philos. Trans. R. Soc. Lond. B Biol. Sci., 368, 20110329, 10.1098/rstb.2011.0329
Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat. Biotechnol., 33, 290, 10.1038/nbt.3122
Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006
Qiu, 2019, BMAL1 knockout macaque monkeys display reduced sleep and psychiatric disorders, Natl. Sci. Rev., 6, 87, 10.1093/nsr/nwz002
Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033
Ramírez, 2014, deepTools: a flexible platform for exploring deep-sequencing data, Nucleic Acids Res., 42, W187, 10.1093/nar/gku365
Ruebel, 2019, SMCHD1 terminates the first embryonic genome activation event in mouse two-cell embryos and contributes to a transcriptionally repressive state, Am. J. Physiol. Cell Physiol., 317, C655, 10.1152/ajpcell.00116.2019
Rybouchkin, 2006, Role of histone acetylation in reprogramming of somatic nuclei following nuclear transfer, Biol. Reprod., 74, 1083, 10.1095/biolreprod.105.047456
Tachibana, 2013, Human embryonic stem cells derived by somatic cell nuclear transfer, Cell, 153, 1228, 10.1016/j.cell.2013.05.006
Tarasov, 2015, Sambamba: fast processing of NGS alignment formats, Bioinformatics, 31, 2032, 10.1093/bioinformatics/btv098
Wakayama, 1998, Full-term development of mice from enucleated oocytes injected with cumulus cell nuclei, Nature, 394, 369, 10.1038/28615
Wakayama, 2001, Differentiation of embryonic stem cell lines generated from adult somatic cells by nuclear transfer, Science, 292, 740, 10.1126/science.1059399
Wang, 2007, Dynamic reprogramming of histone acetylation and methylation in the first cell cycle of cloned mouse embryos, Biol. Reprod., 77, 1007, 10.1095/biolreprod.107.063149
Wang, 2018, Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development, Nat. Cell Biol., 20, 620, 10.1038/s41556-018-0093-4
Wang, 2020, Overcoming intrinsic H3K27me3 imprinting barriers improves post-implantation development after somatic cell nuclear transfer, Cell Stem Cell, 27, 315, 10.1016/j.stem.2020.05.014
Whiddon, 2017, Conservation and innovation in the DUX4-family gene network, Nat. Genet., 49, 935, 10.1038/ng.3846
Wilmut, 1997, Viable offspring derived from fetal and adult mammalian cells, Nature, 385, 810, 10.1038/385810a0
Wood, 2018, Trichostatin A inhibits deacetylation of histone H3 and p53 by SIRT6, Arch. Biochem. Biophys., 638, 8, 10.1016/j.abb.2017.12.009
Yamada, 2006, MUC2 expression is regulated by histone H3 modification and DNA methylation in pancreatic cancer, Int. J. Cancer, 119, 1850, 10.1002/ijc.22047
Yan, 2018, A Huntingtin knockin pig model recapitulates features of selective neurodegeneration in Huntington’s disease, Cell, 173, 989, 10.1016/j.cell.2018.03.005
Yang, 2007, Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning, Nat. Genet., 39, 295, 10.1038/ng1973
Yang, 2019, SQuIRE reveals locus-specific regulation of interspersed repeat expression, Nucleic Acids Res., 47, e27, 10.1093/nar/gky1301
Yang, 2020, DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state, Cell Stem Cell, 26, 234, 10.1016/j.stem.2020.01.004
Yang, 2020, Transient Dux expression facilitates nuclear transfer and induced pluripotent stem cell reprogramming, EMBO Rep., 21, e50054, 10.15252/embr.202050054
Yu, 2018, Generation of GHR-modified pigs as Laron syndrome models via a dual-sgRNAs/Cas9 system and somatic cell nuclear transfer, J. Transl. Med., 16, 41, 10.1186/s12967-018-1409-7
Zalzman, 2010, Zscan4 regulates telomere elongation and genomic stability in ES cells, Nature, 464, 858, 10.1038/nature08882
Zhang, 2009, Defective chromatin structure in somatic cell cloned mouse embryos, J. Biol. Chem., 284, 24981, 10.1074/jbc.M109.011973
Zhang, 2020, Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells, Genome Biol., 21, 45, 10.1186/s13059-020-01957-w
Zhao, 2010, Histone deacetylase inhibitors improve in vitro and in vivo developmental competence of somatic cell nuclear transfer porcine embryos, Cell. Reprogram., 12, 75, 10.1089/cell.2009.0038
Ziegenhain, 2017, Comparative analysis of single-cell RNA sequencing methods, Mol. Cell, 65, 631, 10.1016/j.molcel.2017.01.023