DNA regulatory element cooperation and competition in transcription

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참고문헌 (110)

1. Wienert B, "Wake-up sleepy gene : reactivating fetal globin for -hemoglobinopathies", Trends Genet, 34, pp.927~940 (2018)
2. Bauer DE, "An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level", Science, 342, pp.253~257 (2013)
3. Frangoul H, "CRISPR-Cas9 gene editing for sickle cell disease and -thalassemia", N Engl J Med, 384, pp.252~260 (2021)
4. Friedman MJ, "Transcriptional and epigenetic regulation of context-dependent plasticity in T-helper lineages", Immune Netw, 23, pp.e5~ (2023)
5. Schoenfelder S, "Long-range enhancerpromoter contacts in gene expression control", Nat Rev Genet, 20, pp.437~455 (2019)
6. Zhang D, "Engineering threedimensional genome folding", Nat Genet, 53, pp.602~611 (2021)
7. Friedman MJ, "Dynamics of viral and host 3D genome structure upon infection", J Microbiol Biotechnol, 32, pp.1515~1526 (2022)
8. Benabdallah NS, "Decreased enhancer-promoter proximity accompanying enhancer activation", Mol Cell, 76, pp.473~484 (2019)
9. Alexander JM, "Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity", Elife, 8, pp.41769~ (2019)
10. Wang H, "Engineering 3D genome organization", Nat Rev Genet, 22, pp.343~360 (2021)
11. Deng W, "Controlling longrange genomic interactions at a native locus by targeted tethering of a looping factor", Cell, 149, pp.1233~1244 (2012)
12. Deng W, "Reactivation of developmentally silenced globin genes by forced chromatin looping", Cell, 158, pp.849~860 (2014)
13. Breda L, "Forced chromatin looping raises fetal hemoglobin in adult sickle cells to higher levels than pharmacologic inducers", Blood, 128, pp.1139~1143 (2016)
14. Hao N, "Programmable DNA looping using engineered bivalent dCas9 complexes", Nat Commun, 8, pp.1628~ (2017)
15. Morgan SL, "Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping", Nat Commun, 8, pp.15993~ (2017)
16. Kim JH, "LADL : light-activated dynamic looping for endogenous gene expression control", Nat Methods, 16, pp.633~639 (2019)
17. Qin G, "Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry", Proc Natl Acad Sci U S A, 119, pp.e2204725119~ (2022)
18. Panigrahi AK, "Enhancer-promoter entanglement explains their transcriptional interdependence", Proc Natl Acad Sci U S A, 120, pp.e2216436120~ (2023)
19. Zhang Y, "Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations", Nature, 504, pp.306~310 (2013)
20. Szutorisz H, "The role of enhancers as centres for general transcription factor recruitment", Trends Biochem Sci, 30, pp.593~599 (2005)
21. Panigrahi A, "Mechanisms of enhancer action : the known and the unknown", Genome Biol, 22, pp.108~ (2021)
22. Baek I, "Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II preinitiation complexes", Mol Cell, 81, pp.3576~3588 (2021)
23. Gorbea Colón JJ, "Structural basis of a transcription pre-initiation complex on a divergent promoter", Mol Cell, 83, pp.574~588 (2023)
24. Oh S, "Enhancer release and retargeting activates disease-susceptibility genes", Nature, 595, pp.735~740 (2021)
25. Chen Q, "Enhancer RNAs in transcriptional regulation : recent insights", Front Cell DevBiol, 11, pp.1205540~ (2023)
26. Kim TK, "Widespread transcription at neuronal activity-regulated enhancers", Nature, 465, pp.182~187 (2010)
27. Li W, "Enhancers as non-coding RNA transcription units : recent insights and future perspectives", Nat Rev Genet, 17, pp.207~223 (2016)
28. Hou TY, "Spirits in the material world : enhancer RNAs in transcriptional regulation", Trends Biochem Sci, 46, pp.138~153 (2021)
29. Li W, "Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation", Nature, 498, pp.516~520 (2013)
30. Park A, "Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs", Proc Natl Acad Sci U S A, 117, pp.21618~21627 (2020)
31. Xiang JF, "Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus", Cell Res, 24, pp.513~531 (2014)
32. Hsieh CL, "Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation", Proc Natl Acad Sci U S A, 111, pp.7319~7324 (2014)
33. Tan SH, "The enhancer RNA", Blood, 134, pp.239~251 (2019)
34. Sigova AA, "Transcription factor trapping by RNA in gene regulatory elements", Science, 350, pp.978~981 (2015)
35. Rahnamoun H, "RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation", Nat Struct Mol Biol, 25, pp.687~697 (2018)
36. Bose DA, "RNA binding to CBP stimulates histone acetylation and transcription", Cell, 168, pp.135~149 (2017)
37. Hou TY, "Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression", Cell Rep, 39, pp.110944~ (2022)
38. Schaukowitch K, "Enhancer RNA facilitates NELF release from immediate early genes", Mol Cell, 56, pp.29~42 (2014)
39. Gorbovytska V, "Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF", Nat Commun, 13, pp.2429~ (2022)
40. Tsai PF, "A muscle-specific enhancer RNA mediates cohesin recruitment and regulates transcription in trans", Mol Cell, 71, pp.129~141 (2018)
41. Alvarez-Dominguez JR, "Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis", Blood, 130, pp.1965~1975 (2017)
42. Nair SJ, "Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly", Nat Struct Mol Biol, 26, pp.193~203 (2019)
43. Lee JH, "Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation", Mol Cell, 81, pp.3368~3385 (2021)
44. Li Y, "N(6)-methyladenosine cotranscriptionally directs the demethylation of histone H3K9me2", Nat Genet, 52, pp.870~877 (2020)
45. Liu J, "N(6)-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription", Science, 367, pp.580~586 (2020)
46. Deng S, "RNA m(6)A regulates transcription via DNA demethylation and chromatin accessibility", Nat Genet, 54, pp.1427~1437 (2022)
47. Lin Y, "Toxic PR polydipeptides encoded by the C9orf72 repeat expansion target LC domain polymers", Cell, 167, pp.789~802 (2016)
48. Gamliel A, "Long-distance association of topological boundaries through nuclear condensates", Proc Natl Acad Sci U S A, 119, pp.e2206216119~ (2022)
49. Wang B, "Liquid-liquid phase separation in human health and diseases", Signal Transduct Target Ther, 6, pp.290~ (2021)
50. Dignon GL, "Temperature-controlled liquid-liquid phase separation of disordered proteins", ACS Cent Sci, 5, pp.821~830 (2019)
51. Harami GM, "Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions", Proc Natl Acad Sci U S A, 117, pp.26206~26217 (2020)
52. Last MGF, "pH-controlled coacervate-membrane interactions within liposomes", ACS Nano, 14, pp.4487~4498 (2020)
53. Shakya A, "DNA local-flexibilitydependent assembly of phase-separated liquid droplets", Biophys J, 115, pp.1840~1847 (2018)
54. Boija A, "Transcription factors activate genes through the phase-separation capacity of their activation domains", Cell, 175, pp.1842~1855 (2018)
55. Khong A, "The stress granule transcriptome reveals principles of mRNA accumulation in stress granules", Mol Cell, 68, pp.808~820 (2017)
56. Somasundaram K, "LncRNAs divide and rule : the master regulators of phase separation", Front Genet, 13, pp.930792~ (2022)
57. Sartorelli V, "Enhancer RNAs are an important regulatory layer of the epigenome", Nat Struct Mol Biol, 27, pp.521~528 (2020)
58. Deng S, "RNA m(6)A regulates transcription via DNA demethylation and chromatin accessibility", Nat Genet, 54, pp.1427~1437 (2022)
59. Henninger JE, "RNAmediated feedback control of transcriptional condensates", Cell, 184, pp.207~225 (2021)
60. Blobel GA, "Testing the super-enhancer concept", Nat Rev Genet, 22, pp.749~755 (2021)
61. Xu J, "Transcriptional silencing of {gamma}-globin by BCL11A involves longrange interactions and cooperation with SOX6", GenesDev, 24, pp.783~798 (2010)
62. Stamatoyannopoulos G, "Control of globin gene expression during development and erythroid differentiation", Exp Hematol, 33, pp.259~271 (2005)
63. Kim Y, "The distinctive roles of erythroid specific activator GATA-1 and NF-E2in transcription of the human fetal gamma-globin genes", Nucleic Acids Res, 39, pp.6944~6955 (2011)
64. Fraser P, "Each hypersensitive site of the human beta-globin locus control region confers a different developmental pattern of expression on the globin genes", Genes Dev, 7, pp.106~113 (1993)
65. Kim J, "The human -globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites", FASEB J, 35, pp.e21669~ (2021)
66. Nieto JM, "Heterozygosity for deletion of hypersensitive site 3 in the human locus control region has an unexpected minor effect on red cell phenotype", J Hum Genet, 59, pp.585~587 (2014)
67. Navas PA, "The 5’HS4 core element of the human beta-globin locus control region is required for high-level globin gene expression in definitive but not in primitive erythropoiesis", J Mol Biol, 312, pp.17~26 (2001)
68. Bender MA, "Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region", Mol Cell, 5, pp.387~393 (2000)
69. Grosveld F, "Transcriptional regulation by(super)enhancers : from discovery to mechanisms", Annu Rev Genomics Hum Genet, 22, pp.127~146 (2021)
70. Whyte WA, "Master transcription factors and mediator establish super-enhancers at key cell identity genes", Cell, 153, pp.307~319 (2013)
71. Parker SC, "Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants", Proc Natl Acad Sci U S A, 110, pp.17921~17926 (2013)
72. Zhou RW, "Etiology of super-enhancer reprogramming and activation in cancer", Epigenetics Chromatin, 16, pp.29~ (2023)
73. Pott S, "What are super-enhancers?", Nat Genet, 47, pp.8~12 (2015)
74. Tu YH, "Identification of cell states using super-enhancer RNA", BMC Genomics, 22, pp.787~ (2021)
75. Sabari BR, "Coactivator condensation at super-enhancers links phase separation and gene control", Science, 361, pp.3958~ (2018)
76. Hnisz D, "Super-enhancers in the control of cell identity and disease", Cell, 155, pp.934~947 (2013)
77. Shin HY, "Targeting Super-enhancers for disease treatment and diagnosis", Mol Cells, 41, pp.506~514 (2018)
78. Tang F, "Super-enhancer function and its application in cancer targeted therapy", NPJ Precis Oncol, 4, pp.2~ (2020)
79. Blayney JW, "Super-enhancers include classical enhancers and facilitators to fully activate gene expression", Cell, 186, pp.5826~5839 (2023)
80. Hsieh TS, "Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1", Nat Genet, 54, pp.1919~1932 (2022)
81. Conte C, "Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons", EMBO J, 21, pp.3908~3916 (2002)
82. Dixon JR, "Topological domains in mammalian genomes identified by analysis of chromatin interactions", Nature, 485, pp.376~380 (2012)
83. Choi OR, "Developmental regulation of beta-globin gene switching", Cell, 55, pp.17~26 (1988)
84. Ohtsuki S, "Different core promoters possess distinct regulatory activities in the Drosophila embryo", Genes Dev, 12, pp.547~556 (1998)
85. Sharpe J, "Selectivity, sharing and competitive interactions in the regulation of Hoxb genes", EMBO J, 17, pp.1788~1798 (1998)
86. Cho SW, "Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element", Cell, 173, pp.1398~1412 (2018)
87. Fu B, "CRISPR-Cas9-mediated gene editing of the BCL11A enhancer for pediatric ", Nat Med, 28, pp.1573~1580 (2022)
88. Topfer SK, "Disrupting the adult globin promoter alleviates promoter competition and reactivates fetal globin gene expression", Blood, 139, pp.2107~2118 (2022)
89. Voon HP, "Controlling alpha-globin : a review of alpha-globin expression and its impact on beta-thalassemia", Haematologica, 93, pp.1868~1876 (2008)
90. De Gobbi M, "A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter", Science, 312, pp.1215~1217 (2006)
91. Lower KM, "Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition", Proc Natl Acad Sci U S A, 106, pp.21771~21776 (2009)
92. Jin EH, "Association between promoter polymorphisms of TFF1, TFF2, and TFF3 and the risk of gastric and diffuse gastric cancers in a Korean population", J Korean Med Sci, 30, pp.1035~1041 (2015)
93. Leeman-Neill RJ, "Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression", Nat Genet, 55, pp.2160~2174 (2023)
94. Kimura S, "Enhancer retargeting of CDX2 and UBTF : : ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia", Blood, 139, pp.3519~3531 (2022)
95. Yang M, "13q12. 2deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking", Blood, 136, pp.946~956 (2020)
96. Shu C, "ERR-activated GPR35 promotes immune infiltration level of macrophages in gastric cancer tissues", Cell Death Discov, 8, pp.444~ (2022)
97. Ajima R, "Formal proof of the requirement of MESP1 and MESP2 in mesoderm specification and their transcriptional control via specific enhancers in mice", Development, 148, pp.194613~ (2021)
98. Nakamura T, "Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk", Cell Genom, 4, pp.100488~ (2024)
99. Bai F, "A distal enhancer guides the negative selection of toxic glycoalkaloids during tomato domestication", Nat Commun, 15, pp.2894~ (2024)
100. Bateman JR, "Altering enhancerpromoter linear distance impacts promoter competition in cis and in trans", Genetics, 222, pp.98~ (2022)
101. Carleton JB, "Multiplex enhancer interference reveals collaborative control of gene regulation by estrogen receptor -bound enhancers", Cell Syst, 5, pp.333~344 (2017)
102. Xie S, "Multiplexed engineering and analysis of combinatorial enhancer activity in single cells", Mol Cell, 66, pp.285~299 (2017)
103. Morris JA, "Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens", Science, 380, pp.7699~ (2023)
104. Friedman MJ, "Enhancer-promoter specificity in gene transcription : molecular mechanisms and disease associations", Exp Mol Med, 56, pp.772~787 (2024)
105. Feehley T, "Drugging the epigenome in the age of precision medicine", Clin Epigenetics, 15, pp.6~ (2023)
106. Cappelluti MA, "Durable and efficient gene silencing in vivo by hit-andrun epigenome editing", Nature, 627, pp.416~423 (2024)
107. Pachano T, "Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness", Nat Genet, 53, pp.1036~1049 (2021)
108. Amabile A, "Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing", Cell, 167, pp.219~232 (2016)
109. Gourisankar S, "Rewiring cancer drivers to activate apoptosis", Nature, 620, pp.417~425 (2023)
110. Wan L, "Inflammatory immune-associated eRNA : mechanisms, functions and therapeutic prospects", Front Immunol, 13, pp.849451~ (2022)

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