脊椎动物进化过程中的三个调控创新期。
Three periods of regulatory innovation during vertebrate evolution.
机构信息
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
出版信息
Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702.
Abstract
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
摘要
基因调控元件的获得、丧失和修饰可能是动物谱系中表型变化的主要原因。为了研究整个脊椎动物进化过程中调控元件的获得，我们鉴定了包括人类在内的五种脊椎动物的全基因组假定调控区。这些假定的调控区是保守的非编码元件（CNEE），它们在进化上是保守的，但不与任何编码或非编码成熟转录本重叠。然后，我们推断了每个 CNEE 受到选择约束的分支。我们的分析确定了基因调控元件进化过程中的三个扩展时期。早期脊椎动物进化的特征是转录因子和发育基因附近的调控获得，但这一趋势被细胞外信号基因附近的创新所取代，然后是翻译后蛋白修饰物附近的创新。
相似文献
1
Three periods of regulatory innovation during vertebrate evolution.脊椎动物进化过程中的三个调控创新期。
Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702.
2
Evolution. CNCing is believing.进化。数控即信仰。
Science. 2011 Aug 19;333(6045):946-7. doi: 10.1126/science.1210771.
3
Organization of conserved elements near key developmental regulators in vertebrate genomes.脊椎动物基因组中关键发育调节因子附近保守元件的组织
Adv Genet. 2008;61:307-38. doi: 10.1016/S0065-2660(07)00012-0.
4
Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis.通过系统发育足迹分析揭示脊椎动物 Hox 簇中保守非编码序列在两轮全基因组复制过程中的演化。
J Mol Evol. 2010 Dec;71(5-6):427-36. doi: 10.1007/s00239-010-9396-1. Epub 2010 Oct 28.
5
cis-Regulatory remodeling of the SCL locus during vertebrate evolution.脊椎动物进化过程中 SCL 基因座的顺式调控重塑。
Mol Cell Biol. 2010 Dec;30(24):5741-51. doi: 10.1128/MCB.00870-10. Epub 2010 Oct 18.
6
Tuning in to the signals: noncoding sequence conservation in vertebrate genomes.解读信号：脊椎动物基因组中的非编码序列保守性
Trends Genet. 2008 Jul;24(7):344-52. doi: 10.1016/j.tig.2008.04.005. Epub 2008 May 29.
7
Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters.脊椎动物Hox基因簇中调控元件的进化保守性。
Genome Res. 2003 Jun;13(6A):1111-22. doi: 10.1101/gr.700503.
8
Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates.牙形类脊椎动物中 Dlx 旁系同源物共表达的异质保守性。
PLoS One. 2013 Jun 28;8(6):e68182. doi: 10.1371/journal.pone.0068182. Print 2013.
9
Pan-vertebrate conserved non-coding sequences associated with developmental regulation.与发育调控相关的泛脊椎动物保守非编码序列。
Brief Funct Genomic Proteomic. 2009 Jul;8(4):256-65. doi: 10.1093/bfgp/elp033.
10
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.靶向从蠕虫到人类的一组共同发育调控基因的保守非编码元件的平行进化。
Genome Biol. 2007;8(2):R15. doi: 10.1186/gb-2007-8-2-r15.
引用本文的文献
1
Six million years of vole dental evolution shaped by tooth development.六百万年的田鼠牙齿进化受牙齿发育影响。
Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2505624122. doi: 10.1073/pnas.2505624122. Epub 2025 Jul 31.
2
The therapeutic futility paradox: insights from oncological drug litigation in Ecuador.治疗无效悖论：来自厄瓜多尔肿瘤药物诉讼的见解。
Front Med (Lausanne). 2025 Mar 14;12:1434524. doi: 10.3389/fmed.2025.1434524. eCollection 2025.
3
On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution.论蛋白质内在无序在生命起源与进化中的作用
Life (Basel). 2024 Oct 15;14(10):1307. doi: 10.3390/life14101307.
4
SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function.SCAR-6 lncRNA 基因座通过表观遗传调控 PROZ 并调节凝血和血管功能。
EMBO Rep. 2024 Nov;25(11):4950-4978. doi: 10.1038/s44319-024-00272-w. Epub 2024 Oct 2.
5
Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators.在冬眠哺乳动物中，特定保守非编码元件趋同加速进化。
Sci Rep. 2024 May 23;14(1):11754. doi: 10.1038/s41598-024-62455-8.
6
Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.早期硬骨鱼进化过程中广泛的保守非编码元件的丢失和获得。
Genome Biol Evol. 2024 Apr 2;16(4). doi: 10.1093/gbe/evae061.
7
Patterns of enrichment and acceleration in evolutionary rates of promoters suggest a role of regulatory regions in cetacean gigantism.启动子进化速率的富集和加速模式表明调控区域在鲸目动物巨型化中起作用。
BMC Ecol Evol. 2023 Oct 24;23(1):62. doi: 10.1186/s12862-023-02171-5.
8
Convergent and complementary selection shaped gains and losses of eusociality in sweat bees.趋同和互补选择塑造了社会性蜜蜂中群居性的得失。
Nat Ecol Evol. 2023 Apr;7(4):557-569. doi: 10.1038/s41559-023-02001-3. Epub 2023 Mar 20.
9
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network.CNEReg 通过发育基因调控网络解释反刍动物特异性保守非编码元件。
Genomics Proteomics Bioinformatics. 2023 Jun;21(3):632-648. doi: 10.1016/j.gpb.2022.11.007. Epub 2022 Dec 7.
10
Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.适应性序列分歧在人类中形成了新的神经发育增强子。
Cell. 2022 Nov 23;185(24):4587-4603.e23. doi: 10.1016/j.cell.2022.10.016.
本文引用的文献
1
GREAT improves functional interpretation of cis-regulatory regions.GREAT 提高了顺式调控区域的功能解释。
Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.
2
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population.逐步修饰模块化增强子是果蝇种群适应的基础。
Science. 2009 Dec 18;326(5960):1663-7. doi: 10.1126/science.1178357.
3
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.棘鱼的骨盆缩小是通过 Pitx1 增强子的反复缺失实现的适应性进化。
Science. 2010 Jan 15;327(5963):302-5. doi: 10.1126/science.1182213. Epub 2009 Dec 10.
4
Detection of nonneutral substitution rates on mammalian phylogenies.检测哺乳动物系统发育上的非中性替代率。
Genome Res. 2010 Jan;20(1):110-21. doi: 10.1101/gr.097857.109. Epub 2009 Oct 26.
5
The Universal Protein Resource (UniProt) in 2010.2010 年的通用蛋白质资源（UniProt）。
Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846. Epub 2009 Oct 20.
6
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.共有编码序列（CCDS）计划：鉴定人类和小鼠基因组的共同蛋白质编码基因集。
Genome Res. 2009 Jul;19(7):1316-23. doi: 10.1101/gr.080531.108. Epub 2009 Jun 4.
7
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.全基因组关联位点对人类疾病和性状的潜在病因学及功能影响。
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7. doi: 10.1073/pnas.0903103106. Epub 2009 May 27.
8
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.基于染色质免疫沉淀测序（ChIP-Seq）数据的转录因子结合位点全基因组分析。
Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.
9
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.文昌鱼基因组揭示了脊椎动物的起源和头索动物生物学。
Genome Res. 2008 Jul;18(7):1100-11. doi: 10.1101/gr.073676.107. Epub 2008 Jun 18.
10
High-resolution mapping and characterization of open chromatin across the genome.全基因组开放染色质的高分辨率图谱绘制与特征分析。
Cell. 2008 Jan 25;132(2):311-22. doi: 10.1016/j.cell.2007.12.014.
Zotero 插件