染色质开放性与动物胚胎发育关系的研究进展

doi:10.11843/j.issn.0366-6964.2022.03.002

摘要/Abstract

摘要： 染色质开放性是指核小体或转录因子等蛋白与真核生物染色质DNA结合后,对其他蛋白能否再结合的开放程度,这一特性能够反映转录活性。染色质结构是动态变化的,染色质开放性与动物生长发育、细胞分化等过程密切相关,基因组开放染色质高效精准定位可为解析基因表达调控机制提供重要线索。本文介绍染色质开放性检测方法、染色质开放性的影响因素,重点阐述染色质开放性与动物发育的关系并对其发展及应用前景进行阐述,以期为动物发育基因表达调控等相关研究提供参考依据。

关键词: 染色质开放性, 表观遗传, 基因表达, 胚胎发育

Abstract: Chromatin accessibility refers to the openness of proteins such as nucleosomes or transcription factors to the recombination of other proteins after binding to eukaryotic chromatin DNA, which can reflect transcriptional activity. Open chromatin is closely related to animal growth and development, cell differentiation and other processes. The efficient and accurate localization of open chromatin in the genome can provide vital clues for exploring the regulation mechanism of gene expression. In this paper, the methods of chromatin accessibility detection and the factors of chromatin accessibility are introduced, and the effects of chromatin accessibility on animal development and its development and application prospects are discussed so as to provide a reference for related studies on gene expression regulation during animal development.

Key words: chromatin accessibility, epigenetics, gene expression, embryonic development

中图分类号:

S813.2

刘悦, 薛翔澜, 李晓波, 蒋琳, 浦亚斌, 何晓红, 马月辉, 赵倩君. 染色质开放性与动物胚胎发育关系的研究进展[J]. 畜牧兽医学报, 2022, 53(3): 680-687.

LIU Yue, XUE Xianglan, LI Xiaobo, JIANG Lin, PU Yabin, HE Xiaohong, MA Yuehui, ZHAO Qianjun. Research Progress of the Relationship between Chromatin Accessibility and Animal Embryo Development[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(3): 680-687.

参考文献 65

[1]	JACKSON D A.Nuclear organization:uniting replication foci,chromatin domains and chromosome structure[J].Bioessays, 1995, 17(7):587-591.
[2]	BÁRTOVÁ E,KOZUBEK S.Nuclear architecture in the light of gene expression and cell differentiation studies[J].Biol Cell,2006, 98(6):323-336.
[3]	GOTTESFELD J M,CAREY M F.Introduction to the thematic Minireview series:chromatin and transcription[J].J Biol Chem, 2018, 293(36):13775-13777.
[4]	PÁLFY M,SCHULZE G,VALEN E,et al.Chromatin accessibility established by Pou5f3,Sox19b and Nanog primes genes for activity during zebrafish genome activation[J].PLoS Genet,2020,16(1):e1008546.
[5]	STREBINGER D,DELUZ C,FRIMAN E T,et al.Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions[J]. Mol Syst Biol,2019,15(9):e9002.
[6]	GUTIÉRREZ G,MILLÁN-ZAMBRANO G,MEDINA D A,et al.Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning[J].Epigenetics Chromatin,2017,10(1):58.
[7]	MA G,BABARINDE I A,ZHUANG Q,et al.Unified analysis of multiple ChIP-Seq datasets[J].Methods Mol Biol,2021,2198:451-465.
[8]	SEGORBE D,WILKINSON D,MIZERANSCHI A,et al.An optimized FAIRE procedure for low cell numbers in yeast[J]. Yeast,2018,35(8):507-512.
[9]	SOLLNER-WEBB B,FELSENFELD G.Comparison of the digestion of nuclei and chromatin by staphylococcal nuclease[J]. Biochemistry,1975,14(13):2915-2920.
[10]	SCHONES D E,CUI K R,CUDDAPAH S,et al.Dynamic regulation of nucleosome positioning in the human genome[J].Cell, 2008,132(5):887-898.
[11]	SUNDIN O,VARSHAVSKY A.Staphylococcal nuclease makes a single non-random cut in the simian virus 40 viral minichromosome[J].J Mol Biol,1979,132(3):535-546.
[12]	GAO W W,KU W L,PAN L X,et al.Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells[J].Nucleic Acids Res,2021,49(10):e56.
[13]	BUENROSTRO J D,WU B J,CHANG H Y,et al.ATAC-seq:a method for assaying chromatin accessibility genome-wide[J].Curr Protoc Mol Biol,2015,109:21.29.1-21.29.9.
[14]	HENIKOFF S,HENIKOFF J G,KAYA-OKUR H S,et al.Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation[J].Elife,2020,9:e63274.
[15]	XU W,WEN Y,LIANG Y Y,et al.A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility[J].Nat Protoc,2021,16(8):4084-4107.
[16]	LI G Q,LIU Y P,ZHANG Y X,et al.Joint profiling of DNA methylation and chromatin architecture in single cells[J].Nat Methods,2019,16(10):991-993.
[17]	GANSEN A,FELEKYAN S,KÜHNEMUTH R,et al.High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes[J].Nat Commun,2018,9(1):4628.
[18]	KATO D,OSAKABE A,ARIMURA Y,et al.Crystal structure of the overlapping dinucleosome composed of hexasome and octasome[J].Science,2017,356(6334):205-208.
[19]	CLARK D J,FELSENFELD G.A nucleosome core is transferred out of the path of a transcribing polymerase[J].Cell,1992,71(1):11-22.
[20]	LORCH Y,LAPOINTE J W,KORNBERG R D.Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones[J].Cell,1987,49(2):203-210.
[21]	BARBIER J,VAILLANT C,VOLFF J N,et al.Coupling between sequence-mediated nucleosome organization and genome evolution[J].Genes (Basel),2021,12(6):851.
[22]	BALDI S,KORBER P,BECKER P B.Beads on a string-nucleosome array arrangements and folding of the chromatin fiber[J].Nat Struct Mol Biol,2020,27(2):109-118.
[23]	KOBAYASHI W,KURUMIZAKA H.Structural transition of the nucleosome during chromatin remodeling and transcription[J]. Curr Opin Struct Biol,2019,59:107-114.
[24]	KUBIK S,BRUZZONE M J,CHALLAL D,et al.Opposing chromatin remodelers control transcription initiation frequency and start site selection[J].Nat Struct Mol Biol,2019,26(8):744-754.
[25]	LEVENDOSKY R F,SABANTSEV A,DEINDL S,et al.The Chd1 chromatin remodeler shifts hexasomes unidirectionally[J]. eLife,2016,5:e21356.
[26]	MORRISON E A,BAWEJA L,POIRIER M G,et al.Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility[J].Nucleic Acids Res,2021,49(8):4750-4767.
[27]	BREHOVE M,SHATOFF E,DONOVAN B T,et al.DNA sequence influences hexasome orientation to regulate DNA accessibility[J]. Nucleic Acids Res,2019,47(11):5617-5633.
[28]	BARSKI A,CUDDAPAH S,CUI K R,et al.High-resolution profiling of histone methylations in the human genome[J].Cell, 2007,129(4):823-837.
[29]	ZHU X,LAN B X,YI X F,et al.HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription[J].Nucleic Acids Res,2020,48(12):6563-6582.
[30]	BOURGUET P,PICARD C L,YELAGANDULA R,et al.The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation[J].Nat Commun,2021,12(1):2683.
[31]	BUENROSTRO J D,WU B,LITZENBURGER U M,et al.Single-cell chromatin accessibility reveals principles of regulatory variation[J].Nature,2015,523(7561):486-490.
[32]	NOZAKI T,IMAI R,TANBO M,et al.Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging[J]. Mol Cell,2017,67(2):282-293.E7.
[33]	LI X Y,HARRISON M M,VILLALTA J E,et al.Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition[J].eLife,2014,3:e03737.
[34]	WANG Y M,LI W,SCHULZ V P,et al.Impairment of human terminal erythroid differentiation by histone deacetylase 5 deficiency[J].Blood,2021,138(17):1615-1627.
[35]	刘丹华,郑世民,刘晓静,等.禽网状内皮组织增生病病毒感染对SPF雏鸡血液和局部淋巴组织CD4+/CD8+细胞及相关细胞因子表达的影响[J].畜牧兽医学报,2020,51(6):1447-1454.LIU D H,ZHENG S M,LIU X J,et al.Effects of avian reticuloendotheliosis virus infection on the CD4+/CD8+ ratio and the expression of related cytokines in SPF chicks[J].Acta Veterinaria et Zootechnica Sinica,2020,51(6):1447-1454.(in Chinese)
[36]	DOR Y,CEDAR H.Principles of DNA methylation and their implications for biology and medicine[J].Lancet, 2018, 392(10149):777-786.
[37]	LI G Q,LIU Y P,ZHANG Y X,et al.Joint profiling of DNA methylation and chromatin architecture in single cells[J].Nat Methods,2019,16(10):991-993.
[38]	LIU G F,WANG W,HU S G,et al.Inherited DNA methylation primes the establishment of accessible chromatin during genome activation[J].Genome Res,2018,28(7):998-1007.
[39]	DOR Y,CEDAR H.Principles of DNA methylation and their implications for biology and medicine[J].Lancet, 2018, 392(10149):777-786.
[40]	WU J Y,XU J W,LIU B F,et al.Chromatin analysis in human early development reveals epigenetic transition during ZGA[J]. Nature, 2018,557(7704):256-260.
[41]	ZHANG Y,XIANG Y L,YIN Q Z,et al.Dynamic epigenomic landscapes during early lineage specification in mouse embryos[J].Nat Genet,2018,50:96-105.
[42]	DU Z H,ZHENG H,HUANG B,et al.Allelic reprogramming of 3D chromatin architecture during early mammalian development[J]. Nature,2017,547(7662):232-235.
[43]	KE Y W,XU Y N,CHEN X P,et al.3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis[J].Cell,2017,170(2):367-381.e20.
[44]	PIJUAN-SALA B,WILSON N K,XIA J,et al.Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis[J].Nat Cell Biol,2020,22(4):487-497.
[45]	DOGANLI C,SANDOVAL M,THOMAS S,et al.Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) protocol for zebrafish embryos[J].Methods Mol Biol,2017,1507:59-66.
[46]	LU F L,LIU Y T,INOUE A,et al.Establishing chromatin regulatory landscape during mouse Preimplantation development[J]. Cell,2016,165(6):1375-1388.
[47]	CHO J S,BLITZ I L,CHO K W Y.DNase-seq to study chromatin accessibility in early Xenopus tropicalis embryos[J].Cold Spring Harb Protoc,2019,2019(4):pdb.prot098335.
[48]	HAINES J E,EISEN M B.Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo[J]. PLoS Genet,2018,14(5):e1007367.
[49]	BLYTHE S A,WIESCHAUS E F.Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis[J]. eLife,2016,5:e20148.
[50]	CHETVERINA D,EROKHIN M,SCHEDL P.GAGA factor:a multifunctional pioneering chromatin protein[J].Cell Mol Life Sci,2021,78(9):4125-4141.
[51]	WU J Y,XU J W,LIU B F,et al.Chromatin analysis in human early development reveals epigenetic transition during ZGA[J]. Nature, 2018,557(7704):256-260.
[52]	赵天,李谷月,潘阳阳,等.Oct4在牦牛卵母细胞及早期胚胎发育过程中的表达[J].畜牧兽医学报,2017,48(3):577-584.ZHAO T,LI G Y,PAN Y Y,et al.The expression of octamer-binding transcription factor 4 gene (Oct 4) in Yak (Bos grunneins) oocytes and preimplantation embryos produced by in vitro fertilization[J].Acta Veterinaria et Zootechnica Sinica,2017,48(3):577-584.(in Chinese)
[53]	ECKERSLEY-MASLIN M,ALDA-CATALINAS C,BLOTENBURG M,et al.Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program[J].Genes Dev,2019,33(3-4):194-208.
[54]	ARZATE-MEJÍA R G,CERECEDO-CASTILLO A J,GUERRERO G,et al.In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila[J].Nat Commun,2020,11(1):894.
[55]	SHASHIKANT T,ETTENSOHN C A.Genome-wide analysis of chromatin accessibility using ATAC-seq[J].Methods Cell Biol, 2019, 151:219-235.
[56]	DAUGHERTY A C,YEO R W,BUENROSTRO J D,et al.Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans[J].Genome Res,2017,27(12):2096-2107.
[57]	LEVINE M,DAVIDSON E H.Gene regulatory networks for development[J].Proc Natl Acad Sci U S A,2005, 102(14):4936-4942.
[58]	MOUSSIAN B,ROTH S.Dorsoventral axis formation in the Drosophila embryo-shaping and transducing a morphogen gradient[J].Curr Biol,2005,15(21):R887-R899.
[59]	BOZEK M,CORTINI R,STORTI A E,et al.ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm[J].Genome Res,2019,29(5):771-783.
[60]	CROCKER J,TSAI A,STERN D L.A fully synthetic transcriptional platform for a multicellular eukaryote[J].Cell Rep,2017,18(1):287-296.
[61]	FIELD A,ADELMAN K.Evaluating enhancer function and transcription[J].Annu Rev Biochem,2020,89:213-234.
[62]	WANG Y,YUAN P,YAN Z Q,et al.Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos[J].Nat Commun, 2021,12(1):1247.
[63]	MAS G,BLANCO E,BALLARÉ C,et al.Promoter bivalency favors an open chromatin architecture in embryonic stem cells[J].Nat Genet,2018,50(10):1452-1462.
[64]	STERGACHIS A B,NEPH S,REYNOLDS A,et al.Developmental fate and cellular maturity encoded in human regulatory DNA landscapes[J].Cell,2013,154(4):888-903.
[65]	GOOLAM M,SCIALDONE A,GRAHAM S J L,et al.Heterogeneity in Oct4 and Sox2 targets biases cell fate in 4-cell mouse embryos[J].Cell,2016,165(1):61-74.