Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations

참고문헌 (203)

1. Heintzman, N. D., "Histone modifications at human enhancers reflect global cell-type-specific gene expression", Nature, 459, pp.108~112 (2009)
2. Andersson, R., "Determinants of enhancer and promoter activities of regulatory elements", Nat. Rev. Genet, 21, pp.71~87 (2020)
3. Moore, J. E., "Expanded encyclopaedias of DNA elements in the human and mouse genomes", Nature, 583, pp.699~710 (2020)
4. Preissl, S., "Characterizing cis-regulatory elements using single-cell epigenomics", Nat. Rev. Genetm, 24, pp.21~43 (2023)
5. Calderon, D., "Landscape of stimulation-responsive chromatin across diverse human immune cells", Nat. Genetm, 51, pp.1494~1505 (2019)
6. Dao, L. T. M., "Transcriptional regulation by promoters with enhancer function", Transcription, 9, pp.307~314 (2018)
7. Nair, S. J., "Transcriptional enhancers at 40 : evolution of a viral DNA element to nuclear architectural structures", Trends Genet, 38, pp.1019~1047 (2022)
8. Consortium, G., "The GTEx consortium atlas of genetic regulatory effects across human tissues", Science, 369, pp.1318~1330 (2020)
9. Boettiger, A., "Advances in chromatin imaging at kilobase-scale resolution", Trends Genet, 36, pp.273~287 (2020)
10. Friedman, M. J., "Dynamics of viral and Host 3D genome structure upon infection", J. Microbiol. Biotechnol, 32, pp.1515~1526 (2022)
11. Friedman, M. J., "Transcriptional and epigenetic reg ulation of context-dependent plasticity in T-Helper Lineages", Immune Netw, 23, pp.e5~ (2023)
12. Lafontaine, D. L., "Hi-C 3.0: improved protocol for genome-wide chromosome conformation capture", Curr. Protoc, 1, pp.e198~ (2021)
13. Brant, L., "Exploiting native forces to capture chromosome conformation in mammalian cell nuclei", Mol. Syst. Biol, 12, pp.891~ (2016)
14. Rao, S. S., "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping", Cell, 159, pp.1665~1680 (2014)
15. Quinodoz, S. A., "SPRITE : a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding", Nat. Protoc, 17, pp.36~75 (2022)
16. Liu, S., "The toolbox for untangling chromosome architecture in immune cells", Front. Immunol, 12, pp.670884~ (2021)
17. Su, J. H., "Genome-scale imaging of the 3D organization and transcriptional activity of chromatin", Cell, 182, pp.1641~1659 (2020)
18. Nguyen, H. Q., "3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing", Nat. Methods, 17, pp.822~832 (2020)
19. Lu, T., "Spatially resolved epigenomic profiling of single cells in complex tissues", Cell, 185, pp.4448~4464 (2022)
20. Alexander, J. M., "Live-cell imaging reveals enhancer-dependent", Elife, 8 (2019)[DOI]
21. Bartman, C. R., "Enhancer regulation of transcriptional bursting parameters revealed by forced chromatin looping", Mol. Cell, 62, pp.237~247 (2016)
22. Levo, M., "Transcriptional coupling of distant regulatory genes in living embryos", Nature, 605, pp.754~760 (2022)
23. Chen, H., "Dynamic interplay between enhancer-promoter topology and gene activity", Nat. Genet, 50, pp.1296~1303 (2018)
24. Van Tricht, C., "Imaging the unimaginable : leveraging signal generation of CRISPR-Cas for sensitive genome imaging", Trends Biotechnol, 41, pp.769~784 (2023)
25. Bot, J. F., "The double life of CRISPR-Cas13", Curr. Opin. Biotechnol, 78, pp.102789~ (2022)
26. Cao, H., "Progress of CRISPR-Cas13 Mediated Live-Cell RNA imaging and detection of RNA-Protein interactions", Front. Cell Dev. Biol, 10, pp.866820~ (2022)
27. Yang, L. Z., "Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems", Mol. Cell, 76, pp.981~997 (2019)
28. Wang, H., "CRISPR-mediated live imaging of genome editing and tran scription", Science, 365, pp.1301~1305 (2019)
29. Jerkovic, I., "Understanding 3D genome organization by multi disciplinary methods", Nat. Rev. Mol. Cell Biol, 22, pp.511~528 (2021)
30. Ostersehlt, L. M., "DNA-PAINT MINFLUX nanoscopy", Nat. Methods, 19, pp.1072~1075 (2022)
31. Nuñez, J. K., "Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing", Cell, 184, pp.2503~2519 (2021)
32. Carleton, J. B., "Multiplex enhancer interference reveals collaborative control of gene regulation by estrogen receptor α-bound enhancers", Cell Syst, 5, pp.333~344 (2017)
33. Xie, S., "Multiplexed engineering and analysis of combinatorial enhancer activity in single cells", Mol. Cell, 66, pp.285~299 (2017)
34. Nasser, J., "Genome-wide enhancer maps link risk variants to disease genes", Nature, 593, pp.238~243 (2021)
35. Morris, J. A., "Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens", Science, 380, pp.eadh7699~ (2023)
36. Merkenschlager, M., "CTCF and cohesin : linking gene regulatory elements with their targets", Cell, 152, pp.1285~1297 (2013)
37. Higashi, T. L., "SMC complexes: lifting the lid on loop extrusion", Curr. Opin. Cell Biol, 74, pp.13~22 (2022)
38. Davidson, I. F., "Genome folding through loop extrusion by SMC complexes", Nat. Rev. Mol. Cell Biol, 22, pp.445~464 (2021)
39. Schwarzer, W., "Two independent modes of chromatin organization revealed by cohesin removal", Nature, 551, pp.51~56 (2017)
40. Rao, S. S. P., "Cohesin loss eliminates all loop domains", Cell, 171, pp.305~320 (2017)
41. Nora, E. P., "Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization", Cell, 169, pp.930~944 (2017)
42. Ulianov, S. V., "Active chromatin and transcription play a key role in chro mosome partitioning into topologically associating domains", Genome Res, 26, pp.70~84 (2016)
43. Gamliel, A., "Long-distance association of topological boundaries through nuclear condensates", Proc. Natl. Acad. Sci. USA, 119, pp.e2206216119~ (2022)
44. Islam, Z., "Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries", Genome Res, 33, pp.1~17 (2023)
45. Zhang, H., "CTCF and transcription influence chromatin structure re configuration after mitosis", Nat. Commun, 12, pp.5157~ (2021)
46. Hsieh, T. S., "Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1", Nat. Genet, 54, pp.1919~1932 (2022)
47. Hyle, J., "Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping", Nucleic Acids Res, 47, pp.6699~6713 (2019)
48. Luan, J., "Distinct properties and functions of CTCF revealed by a rapidly inducible degron system", Cell Rep, 34, pp.108783~ (2021)
49. Zuin, J., "Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells", Proc. Natl. Acad. Sci. USA, 111, pp.996~1001 (2014)
50. Huang, H., "CTCF mediates dosage-and sequence-context-dependent transcriptional insulation by forming local chromatin domains", Nat. Genet, 53, pp.1064~1074 (2021)
51. Rinzema, N. J., "Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes", Nat. Struct. Mol. Biol, 29, pp.563~574 (2022)
52. Kane, L., "Cohesin is required for long-range enhancer action at the Shh locus", Nat. Struct. Mol. Biol, 29, pp.891~897 (2022)
53. Aljahani, A., "Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF", Nat. Commun, 13, pp.2139~ (2022)
54. Ushiki, A., "Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia", Nat. Commun, 12, pp.2282~ (2021)
55. Franke, M., "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression", Nat. Commun, 12, pp.5415~ (2021)
56. Xu, B., "Acute depletion of CTCF rewires genome-wide chromatin accessi bility", Genome Biol, 22, pp.244~ (2021)
57. Oh, S., "Enhancer release and retargeting activates disease-susceptibility genes", Nature, 595, pp.735~740 (2021)
58. Hansen, A. S., "Distinct classes of chromatin loops revealed by deletion of an RNA-binding region in CTCF", Mol. Cell, 76, pp.395~411 (2019)
59. Saldaña-Meyer, R., "CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53", Genes Dev, 28, pp.723~734 (2014)
60. Saldaña-Meyer, R., "RNA interactions are essential for CTCF-mediated gen ome organization", Mol. Cell, 76, pp.412~422 (2019)
61. Oh, H. J., "Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops", Cell, 184, pp.6157~6173 (2021)
62. He, C., "High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells", Mol. Cell, 64, pp.416~430 (2016)
63. Kuang, S., "Identification and analysis of consensus RNA motifs binding to the genome regulator CTCF", NAR Genom. Bioinform, 2, pp.lqaa031~ (2020)
64. Hansen, A. S., "Guided nuclear exploration increases CTCF target search efficiency", Nat. Chem. Biol, 16, pp.257~266 (2020)
65. Guo, J. K., "Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo", Mol. Cell (2024)[DOI]
66. Yang, F., "Glucocorticoid receptor:megatrans switching mediates the repression of an ERα-regulated transcriptional program", Mol. Cell, 66, pp.321~331 (2017)
67. Johnson, T. A., "Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo", Nucleic Acids Res, 46, pp.203~214 (2018)
68. Warwick, T., "Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor", Nucleic Acids Res, 50, pp.3745~3763 (2022)
69. Rinaldi, L., "The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation", Sci. Adv, 8, pp.eabj8360~ (2022)
70. Tan, Y., "Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes", Nat. Struct. Mol. Biol, 30, pp.148~158 (2023)
71. Nair, S. J., "Phase separation of ligand-activated enhancers licenses coop erative chromosomal enhancer assembly", Nat. Struct. Mol. Biol, 26, pp.193~203 (2019)
72. Le Dily, F., "Hormone-control regions mediate steroid receptor-dependent genome organization", Genome Res, 29, pp.29~39 (2019)
73. El Khattabi, L., "A pliable mediator acts as a functional rather than an architectural bridge between promoters and enhancers", Cell, 178, pp.1145~1158 (2019)
74. Soutourina, J., "Transcription regulation by the mediator complex", Nat. Rev. Mol. Cell Biol, 19, pp.262~274 (2018)
75. André, K. M., "Mediator roles going beyond tran scription", Trends Genet, 37, pp.224~234 (2021)
76. Furlong, E. E. M., "Developmental enhancers and chromosome topology", Science, 361, pp.1341~1345 (2018)
77. Burgess-Beusse, B., "The insulation of genes from external enhancers and silencing chromatin", Proc. Natl. Acad. Sci. USA, 99, pp.16433~16437 (2002)
78. Lewis, A. E., "Identification of nuclear phosphatidylinositol 4,5-bisphosphate interacting proteins by neomycin extraction", Mol. Cell Proteom, 10, pp.M110.003376~ (2011)
79. Benabdallah, N. S., "Decreased enhancer-promoter proximity accompanying enhancer activation", Mol. Cell, 76, pp.473~484 (2019)
80. Williamson, I., "Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity", Development, 143, pp.2994~3001 (2016)
81. Larsson, A. J. M., "Genomic encoding of transcriptional burst kinetics", Nature, 565, pp.251~254 (2019)
82. Donovan, B. T., "Live-cell imaging reveals the interplay between transcrip tion factors, nucleosomes, and bursting", EMBO J, 38 (2019)[DOI]
83. Senecal, A., "Transcription factors modulate c-Fos transcriptional bursts", Cell Rep, 8, pp.75~83 (2014)
84. Bartman, C. R., "Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation", Mol. Cell, 73, pp.519~532 (2019)
85. Fukaya, T., "Enhancer control of transcriptional bursting", Cell, 166, pp.358~368 (2016)
86. Tunnacliffe, E., "What is a transcriptional burst?", Trends Genet, 36, pp.288~297 (2020)
87. Jin, F., "A high-resolution map of the three-dimensional chromatin inter actome in human cells", Nature, 503, pp.290~294 (2013)
88. Panigrahi, A., "Mechanisms of enhancer action : the known and the unknown", Genome Biol, 22, pp.108~ (2021)
89. Panigrahi, A. K., "SRC-3 coactivator governs dynamic estrogen-induced chromatin looping interactions during transcription", Mol. Cell, 70, pp.679~694 (2018)
90. Core, L. J., "Defining the status of RNA polymerase at promoters", Cell Rep, 2, pp.1025~1035 (2012)
91. Baek, I., "Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre initiation complexes", Mol. Cell, 81, pp.3576~3588 (2021)
92. Vernimmen, D., "Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression", EMBO J, 26, pp.2041~2051 (2007)
93. Koch, F., "Transcription initiation platforms and GTF recruitment at tissue specific enhancers and promoters", Nat. Struct. Mol. Biol, 18, pp.956~963 (2011)
94. Kagey, M. H., "Mediator and cohesin connect gene expression and chro matin architecture", Nature, 467, pp.430~435 (2010)
95. Sun, F. H., "HPF1 remodels the active site of PARP1 to enable the serine ADP ribosylation of histones", Nat. Commun, 12, pp.1028~ (2021)
96. Adelman, K., "Promoter-proximal pausing of RNA polymerase II : emerging roles in metazoans", Nat. Rev. Genet, 13, pp.720~731 (2012)
97. Schaukowitch, K., "Emerging epigenetic mechanisms of long non coding RNAs", Neuroscience, 264, pp.25~38 (2014)
98. Chen, F. X., "PAF1 regulation of promoter-proximal pause release via enhancer activation", Science, 357, pp.1294~1298 (2017)
99. Henriques, T., "Widespread transcriptional pausing and elongation control at enhancers", Genes Dev, 32, pp.26~41 (2018)
100. Hnisz, D., "A phase separation model for transcriptional control", Cell, 169, pp.13~23 (2017)
101. Sharp, P. A., "RNA in formation and regulation of transcriptional condensates", RNA, 28, pp.52~57 (2022)
102. Henninger, J. E., "RNA-mediated feedback control of transcriptional con densates", Cell, 184, pp.207~225 (2021)
103. Shrinivas, K., "Enhancer features that drive formation of transcriptional condensates", Mol. Cell, 75, pp.549~561 (2019)
104. Guo, Y. E., "Pol II phosphorylation regulates a switch between transcriptional and splicing condensates", Nature, 572, pp.543~548 (2019)
105. Sabari, B. R., "Coactivator condensation at super-enhancers links phase separation and gene control", Science, 361 (2018)[DOI]
106. Ferrie, J. J., "“Structure”-function relationships in eukaryotic transcription factors: the role of intrinsically disordered regions in gene regulation", Mol. Cell, 82, pp.3970~3984 (2022)
107. Ottoz, D. S. M., "The role of disorder in RNA binding affinity and specificity", Open Biol, 10, pp.200328~ (2020)
108. Bosch, J., "Effects of blood pressure and lipid lowering on cognition : Results from the HOPE-3 study", Neurology, 92, pp.e1435~e1446 (2019)
109. Hnisz, D., "New insights into genome structure : genes of a feather stick together", Mol. Cell, 67, pp.730~731 (2017)
110. Graham, T. G. W., "Detecting molecular interactions in live-cell single-molecule imaging with proximity assisted photoactivation (PAPA)", Elife, 11 (2022)[DOI]
111. Abraham, B. J., "Small genomic insertions form enhancers that misregulate oncogenes", Nat. Commun, 8, pp.14385~ (2017)
112. Claringbould, A., "Enhancers in disease : molecular basis and emerging treatment strategies", Trends Mol. Med, 27, pp.1060~1073 (2021)
113. Chen, H, "A pan-cancer analysis of enhancer expression in nearly 9000patient samples", Cell, 173, pp.386~399 (2018)
114. Deniz, Ö., "Endogenous retroviruses are a source of enhancers with onco genic potential in acute myeloid leukaemia", Nat. Commun, 11, pp.3506~ (2020)
115. Liu, X., "Resurrection of endogenous retroviruses during aging reinforces senescence", Cell, 186, pp.287~304 (2023)
116. Stephens, P. J., "Massive genomic rearrangement acquired in a single cat astrophic event during cancer development", Cell, 144, pp.27~40 (2011)
117. Zhang, Y., "High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations", Nat. Commun, 11, pp.736~ (2020)
118. Katainen, R., "CTCF", cohesin-binding sites are frequently mutated in cancer, 2015, pp.47, 818~821
119. Akdemir, K. C., "Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer", Nat. Genet, 52, pp.294~305 (2020)
120. Cho, S. W., "Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element", Cell, 173, pp.1398~1412 (2018)
121. 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)
122. Shu, C., "ERR-activated GPR35 promotes immune infiltration level of mac rophages in gastric cancer tissues", Cell Death Discov, 8, pp.444~ (2022)
123. 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 (2021)[DOI]
124. Lower, K. M., "Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition", Proc. Natl. Acad. Sci. USA, 106, pp.21771~21776 (2009)
125. Topfer, S. K., "Disrupting the adult globin promoter alleviates promoter competition and reactivates fetal globin gene expression", Blood, 139, pp.2107~2118 (2022)
126. Bateman, J. R., "Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans", Genetics, 222 (2022)[DOI]
127. Nakamura, T., "Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk", Cell Genom, 4, pp.100488~ (2024)
128. Ong, C. T., "CTCF : an architectural protein bridging genome topology and function", Nat. Rev. Genet, 15, pp.234~246 (2014)
129. Zheng, H., "The role of 3D genome organization in development and cell differentiation", Nat. Rev. Mol. Cell Biol, 20, pp.535~550 (2019)
130. Dehingia, B., "CTCF shapes chromatin structure and gene expression in health and disease", EMBO Rep, 23, pp.e55146~ (2022)
131. Kemp, C. J., "CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer", Cell Rep, 7, pp.1020~1029 (2014)
132. Konrad, E. D. H., "CTCF variants in 39 individuals with a variable neurode velopmental disorder broaden the mutational and clinical spectrum", Genet Med, 21, pp.2723~2733 (2019)
133. Davis, L., "The emerging roles for the chromatin structure regulators CTCF and cohesin in neurodevelopment and behavior", Cell Mol. Life Sci, 75, pp.1205~1214 (2018)
134. Filippova, G. N., "Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity", Cancer Res, 62, pp.48~52 (2002)
135. Bailey, C. G., "Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer", Cell Mol. Life Sci, 78, pp.7519~7536 (2021)
136. Poulos, R. C., "Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the Motif", Cell Rep, 17, pp.2865~2872 (2016)
137. Kaiser, V. B., "Mutational biases drive elevated rates of substitution at regulatory sites across cancer types", PLoS Genet, 12, pp.e1006207~ (2016)
138. Guo, Y. A., "Mutation hotspots at CTCF binding sites coupled to chromo somal instability in gastrointestinal cancers", Nat. Commun, 9, pp.1520~ (2018)
139. Cheng, H., "Cohesin subunit RAD21 : from biology to disease", Gene, 758, pp.144966~ (2020)
140. Boudaoud, I., "Connected gene communities underlie transcriptional changes in cornelia de lange syndrome", Genetics, 207, pp.139~151 (2017)
141. Weiss, F. D., "Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin", Nat. Commun, 12, pp.2919~ (2021)
142. Waldman, T., "Emerging themes in cohesin cancer biology", Nat. Rev. Cancer, 20, pp.504~515 (2020)
143. Losada, A., "Cohesin in cancer : chromosome segregation and beyond", Nat. Rev. Cancer, 14, pp.389~393 (2014)
144. Viny, A. D., "Cohesin members Stag1 and Stag2 display distinct roles in chromatin accessibility and topological control of HSC self-renewal and differ entiation", Cell Stem Cell, 25, pp.682~696 (2019)
145. Wutz, G., "ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin", Elife, 9 (2020)[DOI]
146. Cuadrado, A., "Specific contributions of cohesin-SA1 and Cohesin-SA2 to TADs and polycomb domains in embryonic stem cells", Cell Rep, 27, pp.3500~3510 (2019)
147. Pang, D., "A mini-review of the role of condensin in human nervous system diseases", Front. Mol. Neurosci, 15, pp.889796~ (2022)
148. Martin, C. A., "Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis", Genes Dev, 30, pp.2158~2172 (2016)
149. Golfier, S., "Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner", Elife, 9 (2020)[DOI]
150. Cutts, E. E., "Condensin complexes: understanding loop extrusion one conformational change at a time", Biochem. Soc. Trans, 48, pp.2089~2100 (2020)
151. Kakui, Y., "Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage", Genome Biol, 21, pp.272~ (2020)
152. Verheul, T. C. J., "The Why of YY1 : mechanisms of transcriptional regulation by Yin Yang 1", Front. Cell Dev. Biol, 8, pp.592164~ (2020)
153. Dong, X., "YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency", Nucleic Acids Res, 50, pp.12019~12038 (2022)
154. Schug, J., "Promoter features related to tissue specificity as measured by Shannon entropy", Genome Biol, 6, pp.R33~ (2005)
155. Khachigian, L. M., "The Yin and Yang of YY1 in tumor growth and suppression", Int. J. Cancer, 143, pp.460~465 (2018)
156. Pabian-Jewuła, S., "Ying Yang 1 engagement in brain pathology", J. Neurochem, 161, pp.236~253 (2022)
157. Amir, R. E., "Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2", Nat. Genet, 23, pp.185~188 (1999)
158. Tillotson, R., "The molecular basis of MeCP2 function in the brain", J. Mol. Biol, 432, pp.1602~1623 (2020)
159. Horike, S., "Loss of silent chromatin looping and impaired imprinting of DLX5 in Rett syndrome", Nat. Genet, 37, pp.31~40 (2005)
160. Grubert, F., "Landscape of cohesin-mediated chromatin loops in the human genome", Nature, 583, pp.737~743 (2020)
161. van Arensbergen, J., "In search of the determinants of enhancer-promoter interaction specificity", Trends Cell Biol, 24, pp.695~702 (2014)
162. Ahn, J. H., "Phase separation drives aberrant chromatin looping and cancer development", Nature, 595, pp.591~595 (2021)
163. Chen, M., "3D genomics and its applications in precision medicine", Cell Mol. Biol. Lett, 28, pp.19~ (2023)
164. Jia, Q., "Oncogenic super-enhancer formation in tumorigenesis and its molecular mechanisms", Exp. Mol. Med, 52, pp.713~723 (2020)
165. Feehley, T., "Drugging the epigenome in the age of precision medicine", Clin. Epigenet, 15, pp.6~ (2023)
166. Bauer, D. E., "An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level", Science, 342, pp.253~257 (2013)
167. Frangoul, H., "CRISPR-Cas9 gene editing for sickle cell disease and beta Thalassemia", N. Engl. J. Med, 384, pp.252~260 (2021)
168. Erdős, G., "IUPred3 : prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation", Nucleic Acids Res, 49, pp.W297~W303 (2021)
169. Gregor, A., "De novo mutations in the genome organizer CTCF cause intellectual disability", Am. J. Hum. Genet, 93, pp.124~131 (2013)
170. Bastaki, F., "Identification of a novel CTCF mutation responsible for syn dromic intellectual disability-a case report", BMC Med. Genet, 18, pp.68~ (2017)
171. Guo, J., "Novel CTCF mutations in Chinese patients with ovarian endometriosis", Mol. Med. Rep, 18, pp.1031~1036 (2018)
172. Marshall, A. D., "CTCF genetic alterations in endometrial carcinoma are pro tumorigenic", Oncogene, 36, pp.4100~4110 (2017)
173. Chatterjee, S., "Enhancer variants synergistically drive dysfunction of a gene regulatory network in hirschsprung disease", Cell, 167, pp.355~368 (2016)
174. Zhang, M., "Long-range", Proc. Natl. Acad. Sci. USA, 116, pp.22692~22698 (2019)
175. Zhang, Z., "SNP rs4971059 predisposes to breast carcinogenesis and che moresistance via TRIM46-mediated HDAC1 degradation", EMBO J, 40, pp.e107974~ (2021)
176. Gao, P., "Biology and clinical implications of the 19q13 aggressive prostate cancer susceptibility locus", Cell, 174, pp.576~589 (2018)
177. Yu, C. Y., "A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90", Oncogene, 39, pp.1347~1360 (2020)
178. Giorgio, E., "A large genomic deletion leads to enhancer adoption by the lamin B1 gene : a second path to autosomal dominant adult-onset demyeli nating leukodystrophy(ADLD)", Hum. Mol. Genet, 24, pp.3143~3154 (2015)
179. Lupiáñez, D. G., "Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions", Cell, 161, pp.1012~1025 (2015)
180. Lupiáñez, D. G., "Breaking TADs: how alterations of chromatin domains result in disease", Trends Genet, 32, pp.225~237 (2016)
181. Guo, Y., "CRISPR inversion of CTCF sites alters genome topology and enhancer", promoter function, 2015, pp.162, 900~910
182. Flavahan, W. A., "Insulator dysfunction and oncogene activation in IDH mutant gliomas", Nature, 529, pp.110~114 (2016)
183. Hnisz, D., "Activation of proto-oncogenes by disruption of chromosome neighborhoods", Science, 351, pp.1454~1458 (2016)
184. Gröschel, S., "A single oncogenic enhancer rearrangement causes con comitant EVI1 and GATA2 deregulation in leukemia", Cell, 157, pp.369~381 (2014)
185. Northcott, P. A., "Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma", Nature, 511, pp.428~434 (2014)
186. Ji, X., "3D chromosome regulatory landscape of human pluripotent cells", Cell Stem Cell, 18, pp.262~275 (2016)
187. de Bruijn, S. E., "Structural variants create new topological-associated domains and ectopic retinal enhancer-gene contact in dominant retinitis pig mentosa", Am. J. Hum. Genet, 107, pp.802~814 (2020)
188. Laugsch, M., "Modeling the pathological long-range regulatory effects of human structural variation with patient-specific hiPSCs", Cell Stem Cell, 24, pp.736~752 (2019)
189. Vicente-García, C., "Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory ele ments", Genome Biol, 18, pp.106~ (2017)
190. Chai, P., "Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis", Nucleic Acids Res, 48, pp.12135~12150 (2020)
191. Meinel, J. A., "Disruption of the topologically associated domain at Xp21.2 is related to 46,XY gonadal dysgenesis", J. Med. Genet (2022)[DOI]
192. Sun, J. H., "Disease-associated short tandem repeats co-localize with chro matin domain boundaries", Cell, 175, pp.224~238 (2018)
193. Valton, A. L., "TAD disruption as oncogenic driver", Curr. Opin. Genet. Dev, 36, pp.34~40 (2016)
194. Kaiser, V. B., "When TADs go bad : chromatin structure and nuclear organisation in human disease", F1000Res, 6, pp.1~ (2017)[DOI]
195. Anania, C., "Order and disorder : abnormal 3D chromatin organization in human disease", Brief. Funct. Genom, 19, pp.128~138 (2020)
196. Tena, J. J., "Topologically associating domains and reg ulatory landscapes in development, evolution and disease", Front. Cell Dev. Biol, 9, pp.702787~ (2021)
197. Chen, F., "Three additional de novo CTCF mutations in Chinese patients help to define an emerging neurodevelopmental disorder", Am. J. Med. Genet C. Semin. Med. Genet, 181, pp.218~225 (2019)
198. Oh, S., "Functional roles of CTCF in breast cancer", BMB Rep, 50, pp.445~453 (2017)
199. Price, E., "An updated catalog of CTCF variants associated with neurode velopmental disorder phenotypes", Front. Mol. Neurosci, 16, pp.1185796~ (2023)
200. Zhang, B. N., "A cohesin subunit variant identified from a peripheral scler ocornea pedigree", Dis. Markers, 2019, pp.8781524~ (2019)
201. Bonora, E., "Mutations in RAD21 disrupt regulation of APOB in patients with chronic intestinal pseudo-obstruction", Gastroenterology, 148, pp.771~782 (2015)
202. Shah, R. R., "MeCP2 mutations : progress towards understanding and treating Rett syndrome", Genome Med, 9, pp.17~ (2017)
203. Gabriele, M., "YY1 haploinsufficiency causes an intellectual disability syn drome featuring transcriptional and chromatin dysfunction", Am. J. Hum. Genet, 100, pp.907~925 (2017)

관련 논문AI추천