后GWAS时代基因组功能变异的高通量鉴定方法及其在农业动物中的应用
收稿日期: 2025-12-04
修回日期: 2026-01-18
网络出版日期: 2026-03-04
基金资助
国家自然科学基金项目(32372867);国家农业科技重大项目(NK20221001);国家现代农业产业技术体系(CARS-41)
High-throughput identification methods of genomic functional variation in post-GWAS era and their application in agricultural animals
Received date: 2025-12-04
Revised date: 2026-01-18
Online published: 2026-03-04
Supported by
National Natural Science Foundation of China(32372867);National Major Agricultural Science and Technology Project(NK20221001);China Agriculture Research System of MOF and MARA(CARS-41)
全基因组关联分析(genome-wide association study，GWAS)已鉴定出大量与人类疾病和动植物经济性状显著关联的遗传变异。然而，由于多数变异位于基因组的非编码区域，使得从众多变异位点中准确识别具有生物学功能的变异仍面临巨大挑战。进入后GWAS时代，以高通量报告基因分析、CRISPR/Cas9基因编辑技术及表观遗传学分析为代表的高通量解析方法，已成为系统揭示基因组中功能变异的有力工具。这些方法不仅能够有效识别功能性变异，还可以揭示其调控基因表达的机制，从而阐明影响性状或疾病形成的分子基础。本文系统综述了当前用于基因组功能性变异的高通量鉴定方法，总结了其在主要农业动物中的应用进展，并对其未来研究前景进行展望，以期为后续相关领域研究提供参考。
尹心怡, 王守志 . 后GWAS时代基因组功能变异的高通量鉴定方法及其在农业动物中的应用[J]. 遗传, 2026 , 48(5) : 451 -470 . DOI: 10.16288/j.yczz.25-319
Genome-wide association study (GWAS) has identified a large number of genetic variations that are significantly associated with human diseases and animal and plant economic traits. However, the majority of these variants are located in non-coding regions of the genome, which makes it challenging to accurately pinpoint functional variants of biological significance from a vast number of candidate loci. In the post-GWAS era, high-throughput analytical approaches, such as high-throughput reporter gene analysis, CRISPR/Cas9-based gene editing technologies, and epigenetic analyses, have become powerful tools for systematically uncovering functional variants in the genome. These methods not only enable efficient identification of functional variants but also help elucidate the mechanisms through which they regulate gene expression, thereby clarifying the molecular basis underlying trait formation or disease pathogenesis. In this review, we systematically summarize current high-throughput strategies for identifying functional genomic variants, highlight their applications and recent advances in major agricultural animal species, and outline future research directions, with the aim of providing a reference for subsequent studies in related fields.
Key words： agricultural animals; GWAS; functional variant; gene expression regulation
| [1] | Stange M, Barrett RDH, Hendry AP. The importance of genomic variation for biodiversity, ecosystems and people. Nat Rev Genet, 2021, 22(2): 89-105. |
| [2] | Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J. 10 Years of GWAS discovery: biology, function, and translation. Am J Hum Genet, 2017, 101(1): 5-22. |
| [3] | Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature, 2009, 461(7265): 747-753. |
| [4] | Zhu YZ, Tazearslan C, Suh Y. Challenges and progress in interpretation of non-coding genetic variants associated with human disease. Exp Biol Med (Maywood), 2017, 242(13): 1325-1334. |
| [5] | Moore JH, Asselbergs FW, Williams SM. Bioinformatics challenges for genome-wide association studies. Bioinformatics, 2010, 26(4): 445-455. |
| [6] | Tam V, Patel N, Turcotte M, Bossé Y, Paré G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet, 2019, 20(8): 467-484. |
| [7] | Wani N, Raza K. Integrative approaches to reconstruct regulatory networks from multi-omics data: a review of state-of-the-art methods. Comput Biol Chem, 2019, 83: 107120. |
| [8] | Yang WM, Zhang T, Song XM, Dong GC, Xu L, Jiang F. SNP-target genes interaction perturbing the cancer risk in the post-GWAS. Cancers (Basel), 2022, 14(22): 5636. |
| [9] | Bhattacharya S, Ray S. In silico screening and exploration into phenotypic alterations of deleterious oncogenic single nucleotide polymorphisms in HSPB1 gene. Genomics, 2021, 113(4): 2812-2825. |
| [10] | Walsh IM, Bowman MA, Soto Santarriaga IF, Rodriguez A, Clark PL. Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness. Proc Natl Acad Sci USA, 2020, 117(7): 3528-3534. |
| [11] | Shastry BS. SNPs: impact on gene function and phenotype. Methods Mol Biol, 2009, 578: 3-22. |
| [12] | Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol, 2018, 19(10): 621-637. |
| [13] | Wang YN, Gan T, Qu S, Xu LL, Hu Y, Liu LJ, Shi SF, Lv JC, Tsoi LC, Patrick MT, He K, Berthier CC, Xu HJ, Zhou XJ, Zhang H. MTMR3 risk alleles enhance Toll like receptor 9-induced IgA immunity in IgA nephropathy. Kidney Int, 2023, 104(3): 562-576. |
| [14] | Jores T, Tonnies J, Dorrity MW, Cuperus JT, Fields S, Queitsch C. Identification of plant enhancers and their constituent elements by STARR-seq in tobacco leaves. Plant Cell, 2020, 32(7): 2120-2131. |
| [15] | Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang MG, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang LY, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou LL, Elia A, Lupien M, He HH, Murphy DJ, Wang LG, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A noncoding single-nucleotide polymerphism at 8q24 drives IDH1-mutant glioma formation. Science, 2022, 78(6615): 68-78. |
| [16] | Wang K. Characteristic analysis and functional research of silencer CAE in the promoter of mouse cholesterol 7α1-hydroxylase gene[Dissertation]. Henan Agricultural University, 2025. |
| 王轲. 小鼠胆固醇7α1-羟化酶启动子中沉默子CAE的特性分析及功能研究[学位论文]. 河南农业大学, 2025. | |
| [17] | Cui KR, Chen ZJ, Cao YQ, Liu S, Ren G, Hu GQ, Fang DF, Wei DP, Liu CY, Zhu JF, Wu C, Zhao KJ. Restraint of IFN-γ expression through a distal silencer CNS-28 for tissue homeostasis. Immunity, 2023, 56(5): 944-958.e6. |
| [18] | Li YL. Functional and mechanistic studies of noncoding variant rs6048205 in pancreatic differentiation and diabetes susceptibility[Dissertation]. Wuhan University, 2024. |
| 李迎雷. 非编码变异rs6048205影响胰腺分化及糖尿病易感性的机制研究[学位论文]. 武汉大学, 2024. | |
| [19] | Zhang C, Yan YS, Zhou BB, Gao HM, Jin XH, Hui L, Hao SJ, Cao ZF, Ma X. Phenotypic study of humanized mice carrying the PAH deep intronic variant c.1199+502A>T. Orphanet J Rare Dis, 2025, 20(1): 254. |
| [20] | Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol, 2018, 19(3): 158-174. |
| [21] | Mayr C. What are 3' UTRs doing? Cold Spring Harb Perspect Biol, 2019, 11(10): a034728. |
| [22] | French JD, Edwards SL. The role of noncoding variants in heritable disease. Trends Genet, 2020, 36(11): 880-891. |
| [23] | Pan XY, Zhao JR, Zhou ZY, Chen JJ, Yang ZX, Wu YX, Bai MZ, Jiao Y, Yang Y, Hu XY, Cheng TL, Lu QY, Wang B, Li CL, Lu YJ, Diao L, Zhong YQ, Pan J, Zhu JM, Xiao HS, Qiu ZL, Li JS, Wang ZF, Hui JY, Bao L, Zhang X. 5'-UTR SNP of FGF13 causes translational defect and intellectual disability. eLife, 2021, 10: e63021. |
| [24] | Melnikov A, Murugan A, Zhang XL, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG, Kinney JB, Kellis M, Lander ES, Mikkelsen TS. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol, 2012, 30(3): 271-277. |
| [25] | Guo MG, Reynolds DL, Ang CE, Liu YF, Zhao Y, Donohue LKH, Siprashvili Z, Yang X, Yoo Y, Mondal S, Hong A, Kain J, Meservey L, Fabo T, Elfaki I, Kellman LN, Abell NS, Pershad Y, Bayat V, Etminani P, Holodniy M, Geschwind DH, Montgomery SB, Duncan LE, Urban AE, Altman RB, Wernig M, Khavari PA. Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases. Nat Genet, 2023, 55(11): 1876-1891. |
| [26] | McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao NX, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. Cell Genom, 2023, 3(10): 100404. |
| [27] | Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res, 2017, 27(1): 38-52. |
| [28] | Xiao F, Zhang XR, Morton SU, Kim SW, Fan YF, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao YP, Chen J, Hagen J, Liu XJ, Zhou PZ, Richter F, Shen YF, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nat Genet, 2024, 56(3): 420-430. |
| [29] | Wang KY, Meng M, Leng MH, Wang YQ, Ni J, Yuan HY, Zhang XR, Cao YP. Protocol for assessing regulatory elements in murine heart using an AAV9-based massively parallel reporter assay. STAR Protoc, 2025, 6(2): 103782. |
| [30] | Shen SQ, Myers CA, Hughes AEO, Byrne LC, Flannery JG, Corbo JC. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res, 2016, 26(2): 238-255. |
| [31] | Zhao SQ, Hong CKY, Myers CA, Granas DM, White MA, Corbo JC, Cohen BA. A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nat Genet, 2023, 55(2): 346-354. |
| [32] | Brown AR, Fox GA, Kaplow IM, Lawler AJ, Phan BN, Gadey L, Wirthlin ME, Ramamurthy E, May GE, Chen ZH, Su Q, McManus CJ, van de Weerd R, Pfenning AR. An in vivo systemic massively parallel platform for deciphering animal tissue-specific regulatory function. Front Genet, 2025, 16: 1533900. |
| [33] | Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science, 2013, 339(6123): 1074-1077. |
| [34] | Bruner WS, Grant SFA. Translation of genome-wide association study: from genomic signals to biological insights. Front Genet, 2024, 15: 1375481. |
| [35] | Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet, 2023, 39(6): 462-490. |
| [36] | Yuan M, Li H, Wang SH. Massively parallel reporter assay: a novel technique for analyzing the regulation of gene expression. Hereditas(Beijing), 2023, 45(10): 859-873. |
| 袁萌, 李辉, 王守志. 大规模平行报告基因测定:一种分析基因表达调控的新技术. 遗传, 2023, 45(10): 859-873. | |
| [37] | Wang JL, Li Q, Zhan TZ. Principle and application of self-transcribing active regulatory region sequencing in enhancer discovery research. Hereditas(Beijing), 2024, 46(8): 589-602. |
| 王纪龙, 李青, 战廷正. 自转录活性调节区测序技术在增强子发现研究中的应用. 遗传, 2024, 46(8): 589-602. | |
| [38] | Petersen RM, Vockley CM, Lea AJ. Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes. Genome Res, 2025, 35(8): 1781-1793. |
| [39] | Vanhille L, Griffon A, Maqbool MA, Zacarias-Cabeza J, Dao LTM, Fernandez N, Ballester B, Andrau JC, Spicuglia S. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Nat Commun, 2015, 6: 6905. |
| [40] | Penner-Goeke S, Bothe M, Rek N, Kreitmaier P, Pöhlchen D, Kühnel A, Glaser LV, Kaya E, Krontira AC, Röh S, Czamara D, Ködel M, Monteserin-Garcia J, Diener L, Wölfel B, Sauer S, Rummel C, Riesenberg S, Arloth- Knauer J, Ziller M, Labeur M, Meijsing S, Binder EB. High-throughput screening of glucocorticoid- induced enhancer activity reveals mechanisms of stress-related psychiatric disorders. Proc Natl Acad Sci USA, 2023, 120(49): e2305773120. |
| [41] | Hansen TJ, Hodges E. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Genome Res, 2022, 32(8): 1529-1541. |
| [42] | Sheng TT, Ho SWT, Ooi WF, Xu C, Xing MJ, Padmanabhan N, Huang KK, Ma LJ, Ray M, Guo YA, Sim NL, Anene-Nzelu CG, Chang MM, Razavi-Mohseni M, Beer MA, Foo RSY, Sundar R, Chan YH, Tan ALK, Ong X, Skanderup AJ, White KP, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Med, 2021, 13(1): 158. |
| [43] | Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I. Functional dissection of the enhancer repertoire in human embryonic stem cells. Cell Stem Cell, 2018, 23(2): 276-288.e8. |
| [44] | Wang M, Yang XX, Wu QX. High-resolution dissection of human cell type-specific enhancers in cis and trans activities. Genomics, 2025, 117(1): 110985. |
| [45] | Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, Tung J. Genome-wide quantification of the effects of DNA methylation on human gene regulation. eLife, 2018, 7: e37513. |
| [46] | Davidson BSA, Arcila-Galvis JE, Trevisan-Herraz M, Mikulasova A, Brackley CA, Russell LJ, Rico D. Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer. Front Cell Dev Biol, 2024, 12: 1294510. |
| [47] | Zhu XS, Huang L, Wang C, Li GL, Deng B, Kong DS, Wang XX, Chang RR, Gu Y, Wen QH, Kong SY, Liu YW, Zhang YB. Uncovering the whole genome silencers of human cells via Ss-STARR-seq. Nat Commun, 2025, 16(1): 723. |
| [48] | Zhu XS, Huang L, Li GL, Deng B, Wang XX, Yang H, Zhang YY, Wen QH, Wang C, Zhang JS, Zhao YX, Li K, Liu YW. Genome-wide silencer screening reveals key silencer modulating reprogramming efficiency in mouse induced pluripotent stem cells. Adv Sci (Weinh), 2025, 12(18): e2408839. |
| [49] | Chang TY, Waxman DJ. HDI-STARR-seq: condition- specific enhancer discovery in mouse liver in vivo. BMC Genomics, 2024, 25(1): 1240. |
| [50] | Neumayr C, Pagani M, Stark A, Arnold CD. STARR-seq and UMI-STARR-seq: assessing enhancer activities for genome-wide-, high-, and low-complexity candidate libraries. Curr Protoc Mol Biol, 2019, 128(1): e105. |
| [51] | Kalita CA, Brown CD, Freiman A, Isherwood J, Wen XQ, Pique-Regi R, Luca F. High-throughput characterization of genetic effects on DNA-protein binding and gene transcription. Genome Res, 2018, 28(11): 1701-1708. |
| [52] | Jones IR, Ren XJ, Shen Y. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Hum Mol Genet, 2022, 31(R1): R47-R53. |
| [53] | Bendixen L, Jensen TI, Bak RO. CRISPR-Cas-mediated transcriptional modulation: the therapeutic promises of CRISPRa and CRISPRi. Mol Ther, 2023, 31(7): 1920-1937. |
| [54] | Bi JF, Mo WP, Liu M, Song YJ, Xiao Q, Fan SB, Wang WB, Shi TF, Zheng YQ, Lian J, Liu R, Chen BH, Huang XF, Li P, Zhao ZF, Shi JD, Zhang L, Su GS, Zhang N, Lu WG. Systematic decoding of functional enhancer connectomes and risk variants in human glioma. Nat Cell Biol, 2025, 27(10): 1838-1847. |
| [55] | Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES, Engreitz JM. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbbations. Nat Genet, 2019, 51(12): 1664-1669. |
| [56] | Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR- based gene therapies: from preclinical to clinical treatments. Cells, 2024, 13(10): 800. |
| [57] | Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays, 2024, 46(7): e2300210. |
| [58] | Schoger E, Carroll KJ, Iyer LM, McAnally JR, Tan W, Liu N, Noack C, Shomroni O, Salinas G, Groß J, Herzog N, Doroudgar S, Bassel-Duby R, Zimmermann WH, Zelarayán LC. CRISPR-mediated activation of endogenous gene expression in the postnatal heart. Circ Res, 2020, 126(1): 6-24. |
| [59] | Li KL, Liu YX, Cao H, Zhang Y, Gu ZM, Liu X, Yu A, Kaphle P, Dickerson KE, Ni M, Xu J. Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing. Nat Commun, 2020, 11(1): 485. |
| [60] | Dixit A, Parnas O, Li BY, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell, 2016, 167(7): 1853-1866.e17. |
| [61] | Zheng XH, Thompson PC, White CM, Jin X. Massively parallel in vivo Perturb-seq screening. Nat Protoc, 2025, 20(7): 1733-1767. |
| [62] | Shi T, Jin X. Probing neuropsychiatric disorders through in vivo CRISPR screening. Curr Opin Genet Dev, 2025, 96: 102424. |
| [63] | Fair T, Pavlovic BJ, Swope D, Castillo OE, Schaefer NK, Pollen AA. Mapping cis- and trans-regulatory target genes of human-specific deletions. Nat Commun, 2025, 16(1): 11380. |
| [64] | Zhao YH, Wu D, Jiang DL, Zhang XY, Wu T, Cui J, Qian M, Zhao J, Oesterreich S, Sun W, Finkel T, Li G. A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs. Nat Commun, 2020, 11(1): 3340. |
| [65] | Wu T, Li G. An improved EMSA-based method to prioritize candidate cis-REs for further functional validation. Bio Protoc, 2022, 12(8): e4397. |
| [66] | Liu Z, Zhao YH, Song HL, Miao HX, Wang YY, Tu CT, Fu TY, Qin JL, Du B, Qian M, Ren H. Identification and characterization of colorectal-cancer-associated SNPs on the SMAD 7 locus. J Cancer Res Clin Oncol, 2023, 149(18): 16659-16668. |
| [67] | Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet, 2009, 10(10): 669-680. |
| [68] | Yamakawa A, Hojo H, Ohba S. ChIP-seq assays from mammalian cartilage and chondrocytes. Methods Mol Biol, 2021, 2245: 167-178. |
| [69] | Ng NHJ, Ghosh S, Bok CM, Ching C, Low BSJ, Chen JT, Lim E, Miserendino MC, Tan YS, Hoon S, Teo AKK. HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes. Nat Commun, 2024, 15(1): 4288. |
| [70] | Mundade R, Ozer HG, Wei H, Prabhu L, Lu T. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. Cell Cycle, 2014, 13(18): 2847-2852. |
| [71] | Marsolier J, Moutaux E, Grosselin K, Griffiths A, Vallot C. Single-cell epigenomic profiling with high-throughput droplet scChIP-seq. Methods Mol Biol, 2025, 2919: 213-239. |
| [72] | Grosselin K, Durand A, Marsolier J, Poitou A, Marangoni E, Nemati F, Dahmani A, Lameiras S, Reyal F, Frenoy O, Pousse Y, Reichen M, Woolfe A, Brenan C, Griffiths AD, Vallot C, Gérard A. High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer. Nat Genet, 2019, 51(6): 1060-1066. |
| [73] | Emerson FJ, Lee SS. CUT&RUN for chromatin profiling in Caenorhabditis elegans. Curr Protoc, 2022, 2(6): e445. |
| [74] | Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun, 2019, 10(1): 1930. |
| [75] | Yang X, Wang QY, Li TY, Zhou Y, Gao JM, Ma WT, Zhao N, Liu XY, Ai ZH, Cheng SY, Gu YY, Zhao BJ, Yue S, Hu ZB. A splicing variant in EFCAB7 hinders ciliary transport and disrupts cardiac development. J Biol Chem, 2025, 301(3): 108249. |
| [76] | Fu ZJ, Jiang SJ, Sun YW, Zheng SQ, Zong L, Li PP. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics, 2024, 19(1): 2293411. |
| [77] | Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur HS, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene CD, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat Biotechnol, 2021, 39(7): 819-824. |
| [78] | Bartosovic M, Kabbe M, Castelo-Branco G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol, 2021, 39(7): 825-835. |
| [79] | Deng YX, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai ZL, Castelo-Branco G, Fan R. Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level. Science, 2022, 375(6581): 681-686. |
| [80] | Bobadilla LK, Tranel PJ. Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance. Pest Manag Sci, 2024, 80(2): 235-244. |
| [81] | Zhang Y, Wang Y, Zhang YH, Jia XC, Li CX, Zhou ZT, Hu SS, Li ZL. Genome-wide analysis reveals that PhoP regulates pathogenicity in Riemerella anatipestifer. Microbiol Spectr, 2022, 10(5): e0188322. |
| [82] | Qi YC, Xie WF, Zhang RX, Wang FQ, Wen Q, Hu YR, Liu Q, Shen JW. Transcription factor Pofst3 regulates Pleurotus ostreatus development by targeting multiple biological pathways. Fungal Biol, 2024, 128(8 Pt A): 2295-2304. |
| [83] | Bartlett A, O'Malley RC, Huang SSC, Galli M, Nery JR, Gallavotti A, Ecker JR. Mapping genome-wide transcription- factor binding sites using DAP-seq. Nat Protoc, 2017, 12(8): 1659-1672. |
| [84] | Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods, 2009, 48(3): 233-239. |
| [85] | He HH, Meyer CA, Hu SS, Chen MW, Zang CZ, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods, 2014, 11(1): 73-78. |
| [86] | Chereji RV, Bryson TD, Henikoff S. Quantitative MNase-seq accurately maps nucleosome occupancy levels. Genome Biol, 2019, 20(1): 198. |
| [87] | Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc, 2022, 17(6): 1518-1552. |
| [88] | Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun, 2023, 14(1): 346. |
| [89] | Mezger A, Klemm S, Mann I, Brower K, Mir A, Bostick M, Farmer A, Fordyce P, Linnarsson S, Greenleaf W. High-throughput chromatin accessibility profiling at single-cell resolution. Nat Commun, 2018, 9(1): 3647. |
| [90] | Chen X, Miragaia RJ, Natarajan KN, Teichmann SA. A rapid and robust method for single cell chromatin accessibility profiling. Nat Commun, 2018, 9(1): 5345. |
| [91] | Xu K, Zhang WW, Wang C, Hu LF, Wang RT, Wang CZ, Tang L, Zhou GH, Zou BJ, Xie H, Tang JH, Guan XX. Integrative analyses of scRNA-seq and scATAC-seq reveal CXCL 14 as a key regulator of lymph node metastasis in breast cancer. Hum Mol Genet, 2021, 30(5): 370-380. |
| [92] | Friman ET, Flyamer IM, Marenduzzo D, Boyle S, Bickmore WA. Ultra-long-range interactions between active regulatory elements. Genome Res, 2023, 33(8): 1269-1283. |
| [93] | Selvarajan I, Toropainen A, Garske KM, López Rodríguez M, Ko A, Miao Z, Kaminska D, Õunap K, Örd T, Ravindran A, Liu OH, Moreau PR, Jawahar Deen A, Männistö V, Pan C, Levonen AL, Lusis AJ, Heikkinen S, Romanoski CE, Pihlajamäki J, Pajukanta P, Kaikkonen MU. Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease. Am J Hum Genet, 2021, 108(3): 411-430. |
| [94] | Saw AK, Madhok A, Bhattacharya A, Nandi S, Galande S. Integrated promoter-capture Hi-C and Hi-C analysis reveals fine-tuned regulation of the 3D chromatin architecture in colorectal cancer. Front Genet, 2025, 16: 1553469. |
| [95] | Shi CF, Rattray M, Orozco G. HiChIP-Peaks: a HiChIP peak calling algorithm. Bioinformatics, 2020, 36(12): 3625-3631. |
| [96] | Liu T, Wang Z. DeepChIA-PET: accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks. PLoS Comput Biol, 2023, 19(7): e1011307. |
| [97] | Yu M, Juric I, Abnousi A, Hu M, Ren B. Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). Methods Mol Biol, 2021, 2351: 181-199. |
| [98] | Plummer D, Lang XY, Zhang SS, Li Y, Li J, Jin FL. A comprehensive benchmark of single-cell Hi-C embedding tools. Nat Commun, 2025, 16(1): 9119. |
| [99] | Tan LZ, Xing D, Chang CH, Li H, Xie XS. Three-dimensional genome structures of single diploid human cells. Science, 2018, 361(6405): 924-928. |
| [100] | Lee DS, Luo CY, Zhou JT, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat Methods, 2019, 16(10): 999-1006. |
| [101] | Khateb M, Perovanovic J, Ko KD, Jiang K, Feng XS, Acevedo-Luna N, Chal J, Ciuffoli V, Genzor P, Simone J, Haase AD, Pourquié O, Dell'Orso S, Sartorelli V. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep, 2022, 40(7): 111219. |
| [102] | Tian XH. Identification of porcine alveolar macrophages enhancer and its mechanism[Dissertation]. Huazhong Agricultural University, 2021. |
| 田小欢. 猪肺泡巨噬细胞增强子的鉴定及其机制研究[学位论文]. 华中农业大学, 2021. | |
| [103] | Wu YQ, Zhang YD, Liu H, Gao Y, Liu YY, Chen L, Liu L, Irwin DM, Hou CH, Zhou ZY, Zhang YP. Genome- wide identification of functional enhancers and their potential roles in pig breeding. J Anim Sci Biotechnol, 2022, 13(1): 75. |
| [104] | Li RQ, Zeng W, Ma M, Wei ZX, Liu HB, Liu XF, Wang M, Shi X, Zeng JH, Yang LF, Mo DL, Liu XH, Chen YS, He ZY. Precise editing of myostatin signal peptide by CRISPR/Cas 9 increases the muscle mass of liang guang small spotted pigs. Transgenic Res, 2020, 29(1): 149-163. |
| [105] | An YL, Han PY, Zhang C, Yue YQ, Wen CL, Meng YY, Li HR, Li X. The role of NUDT3 in lipid accumulation and its functional variants related to backfat thickness in pigs. Int J Biol Macromol, 2025, 307(Pt 3): 141901. |
| [106] | Zhang S, Wang C, Qin SH, Chen CL, Bao YZ, Zhang YY, Xu LN, Liu QY, Zhao YX, Li K, Tang ZL, Liu YW. Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development. Genome Res, 2024, 34(12): 2190-2202. |
| [107] | Han ZY. Integrated multiomics strategy to mine key genes and regulatory elements for cold resistance in min pigs and enshi black pigs[Dissertation]. Huazhong Agricultural University, 2024. |
| 韩哲宇. 整合多组学策略挖掘民猪和恩施黑猪抗寒关键基因与调控元件[学位论文]. 华中农业大学, 2024. | |
| [108] | Jiang YF, Li HX, Lin Y, Zhang ZH, Wang YF. Three- dimensional genome architecture of porcine white and beige adipocytes. Acta Vet Zootech Sin, 2025, 56(11): 5433-5448. |
| 蒋一帆, 李昊星, 林育, 张治华, 王彦芳. 猪白色与米色脂肪细胞的三维基因组结构解析. 畜牧兽医学报, 2025, 56(11): 5433-5448. [DOI] | |
| [109] | Han JH, Lee HJ, Kim TH. Characterization of transcriptional enhancers in the chicken genome using CRISPR- mediated activation. Front Genome Ed, 2023, 5: 1269115. |
| [110] | Kim J, Han JH, Kim M, Schmidt G, Cho E, Lee JH, Kim TH. From GWAS signal to function: targeted CRISPR activation enables functional characterization of non-coding SNPs in chickens. Front Genome Ed, 2025, 7: 1662152. |
| [111] | Li XQ, Zhang F, Sun YX, Sun DD, Yang FX, Liu YT, Hou ZC. A novel candidate gene CLN8 regulates fat deposition in avian. J Anim Sci Biotechnol, 2023, 14(1): 70. |
| [112] | Mu F, Jing Y, He JR, Hou JJ, Huang JX, Zhang JY, Gao F, Lou M, Yan XH, Wang N. Establishing the super- enhancer landscape in chicken adipose tissue. Poult Sci, 2025, 104(11): 105746. |
| [113] | Li DD, Wei QQ, Kang L, Sun Y, Jiang YL. DHCR7 expression, function and estrogen-induced promoter histone modification changes in chicken granulosa cells of pre-hierarchical follicles. Poult Sci, 2025, 104(11): 105837. |
| [114] | Shen LY, Bai X, Zhao LR, Zhou JM, Chang C, Li XQ, Cao ZP, Li YM, Luan P, Li H, Zhang H. Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens. Nat Commun, 2024, 15(1): 9274. |
| [115] | Zou HY, Yu DW, Yao S, Ding FR, Li JL, Li L, Li X, Zhao SJ, Pang YW, Hao HS, Du WH, Zhao XM, Dai YP, Zhu HB. Efficient editing of the ZBED6-binding site in intron 3 of IGF 2 in a bovine model using the CRISPR/Cas9 System. Genes (Basel), 2022, 13(7): 1132. |
| [116] | Ma XL, Zhang XR, Chen Y, Liang HY, Abdureyimu G, Wang LQ, LIN JP, Li WJ, Wang XG, Wu YS. PDGFD gene editing in Altay sheep embryos. Acta Vet Zootech Sin, 2025, 56(4): 1700-1711. |
| 马秀玲, 张欣如, 陈莹, 梁红艳, 古丽米热·阿布都热依木, 汪立芹, 林嘉鹏, 李伟健, 王旭光, 吴阳升. 阿勒泰羊胚胎PDGFD基因编辑研究. 畜牧兽医学报, 2025, 56(4): 1700-1711. | |
| [117] | Cao XK, Cheng J, Huang YZ, Lan XY, Lei CZ, Chen H. Comparative enhancer map of cattle muscle genome annotated by ATAC-Seq. Front Vet Sci, 2021, 8: 782409. |
| [118] | Mi XY. Differential analysis of mammary cell taxa during different lactation periods in goats and functional mining of lactation super enhancers[Dissertation]. Gansu Agricultural University, 2025. |
| 米晓钰. 奶山羊不同泌乳时期乳腺细胞类群的差异分析及泌乳超级增强子的功能挖掘[学位论文]. 甘肃农业大学, 2025. | |
| [119] | Ge L. Functional study of candidate genes in the 37-38 Mb region of chromosome 6 and association analysis of SNPs in the promotor region with growth and development traits in Suhu sheep breeding population[Dissertation]. Yangzhou University, 2023. |
| 葛玲. 6号染色体37-38 Mb区域候选基因功能研究及其启动子区SNPs与苏湖肉羊选育群生长发育性状关联分析[学位论文]. 扬州大学, 2023. | |
| [120] | D'Elia B, Fuxman Bass J. Applications of high- throughput reporter assays to gene regulation studies. Curr Opin Struct Biol, 2025, 94: 103105. |
| [121] | Javaid D, Ganie SY, Hajam YA, Reshi MS. CRISPR/ Cas9 system: a reliable and facile genome editing tool in modern biology. Mol Biol Rep, 2022, 49(12): 12133-12150. |
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