非编码DNA调控元件在动物适应性性状演化中的研究进展

doi:10.16288/j.yczz.24-272

遗传 ›› 2024, Vol. 46 ›› Issue (12): 995-1016.doi: 10.16288/j.yczz.24-272

非编码DNA调控元件在动物适应性性状演化中的研究进展

吴秀红¹(), 汪亚军¹(), 车利锋², 王晓萍¹()

1.云南大学省部共建云南生物资源保护与利用国家重点实验室，生命科学学院，昆明 650091
2.陕西省动物研究所，西安710032

收稿日期:2024-09-19 修回日期:2024-10-31 出版日期:2024-12-20 发布日期:2024-11-18
通讯作者: 王晓萍，博士，副研究员，研究方向：动物遗传与进化。E-mail: wangxp@ynu.edu.cn
作者简介:吴秀红，硕士研究生，专业方向：遗传学。E-mail: xiuzi.wu@foxmail.com;
汪亚军，硕士研究生，专业方向：遗传学。E-mail: yajunwang2024@foxmail.com
第一联系人：
吴秀红和汪亚军并列第一作者。
基金资助:
国家自然科学基金项目(32360120);云南省教育厅科学研究基金项目(2024Y017)

Research progresses on non-coding DNA regulatory elements in the evolution of animal adaptive traits

Xiuhong Wu¹(), Yajun Wang¹(), Lifeng Che², Xiaoping Wang¹()

1. State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, School of Life Sciences of Yunnan University, Kunming 650091, China
2. Shaanxi Institute of Zoology, Xi’an 710032, China

Received:2024-09-19 Revised:2024-10-31 Published:2024-12-20 Online:2024-11-18
Supported by:
National Natural Science Foundation of China(32360120);Yunnan Provincial Department of Education Science Research Fund Project(2024Y017)

摘要/Abstract

摘要：

在适应性演化的推动下，动物发展出了多种适应性特征，这些特征对它们的生存和繁衍至关重要。揭示适应性演化的分子机制对理解物种多样化、表型趋同等重要生物学现象具有关键意义。随着多组学技术的发展与成熟，基因组非编码DNA调控元件已被证明在动物适应性性状演化过程中发挥着重要调控作用。本文概述了非编码DNA调控元件的特征及其作用机制，并从动物附肢适应性状、动物极端环境适应性状以及动物其他特殊表型适应性状这3个方面综述了其在动物适应性性状演化中的分子机制，为理解动物适应性性状演化分子机制提供重要参考。

关键词: 非编码DNA, 调控元件, 动物, 适应性性状

Abstract:

Driven by adaptive evolution, animals have developed a variety of adaptive traits that are critical to their survival and reproduction. Unraveling the molecular mechanisms of adaptive evolution is of key significance for understanding important biological phenomena such as species diversification and phenotypic convergence, etc. With the development and maturation of multi-omics technologies, genomic non-coding DNA regulatory elements have been proven to play important regulatory roles in the evolution of adaptive traits in animals. In this review, we summarize the characteristics and mechanisms of non-coding DNA regulatory elements and reviews their molecular mechanisms in the evolution of adaptive traits in animals from three aspects: adaptive traits of animal appendages, traits for adaptation to extreme environments, and other special phenotypic adaptive traits. It offers significant insights for understanding the molecular mechanisms of adaptive trait evolution in animals.

Key words: non-coding DNA, regulatory elements, animal, adaptive traits

吴秀红, 汪亚军, 车利锋, 王晓萍. 非编码DNA调控元件在动物适应性性状演化中的研究进展[J]. 遗传, 2024, 46(12): 995-1016.

Xiuhong Wu, Yajun Wang, Lifeng Che, Xiaoping Wang. Research progresses on non-coding DNA regulatory elements in the evolution of animal adaptive traits[J]. Hereditas(Beijing), 2024, 46(12): 995-1016.

图/表 3

图1

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表1

非编码DNA调控元件与动物适应性性状研究汇总"

适应性状	研究对象	适应性状特征	主要研究方法	非编码DNA 调控元件	基因/通路	参考文献
动物附肢适应性状	三刺鱼(Gasterosteus aculeatus)	骨盆刺退化	全基因组连锁图谱、转基因实验	CRE	Pitx1	[53,54]
	小鳐鱼(Leucoraja erinacea)	翼状鳍	比较基因组、RNA-seq、HiChIP、ATAC-seq	CRE	Hoxa1/Hoxa2	[55]
	非洲肺鱼(Protopterus annectens)	五趾肢起源	比较基因组、RNA-seq	CNE	Hoxa11	[11]
	非洲肺鱼(Protopterus annectens) 南美洲肺鱼 (Lepidosiren paradoxa) 澳州肺鱼(Neoceratodus forsteri)	远端鳞状鳍的减少	比较基因组、Hi-C	CRE	Shh/SHH	[61]
	蛇类(Serpentiformes)	四肢退化或丢失	比较基因组、转基因实验	CRE	Shh、Ets1	[67]
	球蟒(Python regius)	四肢退化	RNA原位杂交、转基因实验	CRE	Shh、HoxD	[68]
	有鳞类(Squamata)	四肢丢失	比较基因组、ATAC-seq、双荧光素酶报告实验	CNE	Tbx4/Fgf10/ Gli3	[14]
	平胸总目(Ratitae)	前肢缩小	比较基因组、ATAC-seq、ChIP-seq、电穿孔转化实验	CNE	Tbx5/Dach1/Pax9	[10]
	牛(Bos taurus)	趾退化	比较基因组、ChIP-seq	CNE	Ptch1/SHH	[73]
	猪(Sus scrofa)	趾退化	比较基因组、ATAC-seq	CRE	Gli1/SHH	[74]
	短尾蝠(Carollia perspicillata)	前肢指延长	转基因实验、原位杂交、PCR扩增	CRE	Prx1	[75]
	纳塔尔长翼蝠(Miniopterus natalensis)	前肢指延长	比较基因组、RNA-seq、ChIP-seq	AR	BMP/FGF/ Wnt-PCP	[77]
	小棕蝠(Myotis lucifugus)	前肢指延长	比较基因组、ChIP-seq、转基因实验	AR	HoxD	[78]
	长臂猿科(Hylobatidae)	前肢延长	比较基因组、转基因实验	AR	Dlx5/Emx2	[16]
	蒙古五趾跳鼠 (Orientallactaga sibirica)	后肢增大	比较基因组、双荧光素酶报告实验	CNE	Xylt1	[80]
动物极端环境适应性状	狮尾狒(Theropithecus gelada)	低氧环境氧化应激适应	比较基因组、全基因组群体重测序	AR	Htatip2/Rcan1/Fbn1	[85]
	绵羊(Ovis aries)	低氧环境氧化应激适应	RNA-seq、Hi-C、ATAC-seq	CRE	Limd1/Hippo	[86]
	猎隼(Falco cherrug)	低氧环境血氧运输适应	比较基因组、Hi-C、ATAC-seq	CRE	Hbz/Hbad/ Hba1	[87]
	非洲鼹鼠(Heterocephalus glaber)	低氧环境血氧运输适应低氧环境适应	比较基因组、ChIP-seq	CNE	Foxpi/MEF	[88]
	南极鱼亚目(Notothenioidei)	富氧环境血氧运输适应富氧环境适应	比较基因组、结节血分析、红细胞形态定量	CNE	血红细胞分化相关基因	[90]
	海洋哺乳动物	低温环境体温调节适应	比较基因组、ATAC-seq	CNE	体温调节相关基因	[91]
	冬眠哺乳动物	低温、食物贫乏环境新陈代谢适应	比较基因组	CNE	Mgmt/Qki	[93]
	墨西哥脂鲤(Astyanax mexicanus)	食物贫乏环境能量代谢适应	比较基因组、ChIP-seq、ATAC-seq、RNA-seq	CRE	Hpdb	[94]
	远东鲥鱼(Pseudaspius)	高渗环境渗透调节适应	比较基因组、双荧光素酶报告实验	CNE	Atg7/Usp45	[96]
	近江牡蛎(Crassostrea ariakensis)	高渗环境保水能力适应	Hi-C、ATAC-seq、双荧光素酶报告实验	CRE	ManⅡa	[97]
	蒙古五趾跳鼠 (Orientallactaga sibirica)	干旱环境渗透调节适应	比较基因组、双荧光素酶报告实验	CNE	Ror2	[80]
	鼹鼠金毛鼹 (Chrysochloris asiatica) 星鼻鼹(Condylura cristata) 裸鼹鼠(Heterocephalus glaber) 盲鼹鼠(Nannospalax galili)	黑暗环境视觉退化适应	比较基因组、ATAC-seq	CNE	Bfsp2/Pax6/ Vista	[98]
	盲鼹鼠(Nannospalax galili)	黑暗环境视觉退化适应	双荧光素酶报告实验、转基因实验、PCR	CNE	Tdrd7	[99]
动物其他特殊表型适应性状	人猿总科(Hominoidea)	尾巴丢失	比较基因组	CRE	Kiaa1217	[100]
	袋狼(Thylacinus cynocephalus) 灰狼(Canis lupus)	颅面结构趋同	比较基因组	CRE	TGF β/BMP	[101]
	蜜袋鼯(Petaurus breviceps)	翼膜形成	比较基因组、ATAC-seq、ChIP-seq、Micro-C	AR	Emx2	[102]
	反刍亚目(Ruminantia)	鹿角再生	比较基因组、RNA-seq	CNE	Runx2/Sp7	[104]
	虎尾海马(Hippocampus comes)	体型变化	比较基因组、转基因实验	CNE	Hox	[105]
	黑妹袖蝶(Heliconius himera)	黑色花纹	转基因实验、ATAC-seq、Hi-C	CRE	WntA	[110]
	艺神袖蝶(Heliconius erato) 诗神袖蝶(Heliconius melpomene)	红色花纹	转基因实验、ChIP-seq、Hi-C、ATAC-seq	CRE	Optix	[13,111]
	艺神袖蝶(Heliconius erato) 诗神袖蝶 (Heliconius melpomene)	黄色条纹	转基因实验、原位杂交、RNA-seq、ATAC-seq	CRE	Cortex	[112]

表1

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非编码DNA调控元件在动物适应性性状演化中的研究进展

Research progresses on non-coding DNA regulatory elements in the evolution of animal adaptive traits

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