Insulated neighborhood

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Multiple levels of mammalian genome organization. Chromosomes occupy discrete territories in the nucleus (left). Topologically associating domains (TADs) are regions of the genome with locally high interaction frequency (center). Insulated neighborhoods are loops formed by the interaction of CTCF/cohesin-bound anchors containing genes and their regulatory elements.

In mammalian biology, insulated neighborhoods are chromosomal loop structures formed by the physical interaction of two DNA loci bound by the transcription factor CTCF and co-occupied by cohesin.[1] Insulated neighborhoods are thought to be structural and functional units of gene control because their integrity is important for normal gene regulation. Current evidence suggests that these structures form the mechanistic underpinnings of higher-order chromosome structures, including topologically associating domains (TADs). Insulated neighborhoods are functionally important in understanding gene regulation in normal cells and dysregulated gene expression in disease.

Enhancer-gene targeting[edit]

Mammalian gene transcription is generally controlled by enhancers.[2][3][4][5][6] Enhancers can regulate transcription of genes at large distances by looping to physically contact their target genes. This property of enhancers makes it difficult to identify an enhancer’s target gene(s). Insulators, another type of DNA regulatory element, limit an enhancer’s ability to target distal genes when the insulator is located between an enhancer and a potential target.[7][8][9][10] In mammals, insulators are bound by CTCF,[11] but only a minority of CTCF-bound sites function as insulators.[12] CTCF molecules can form homodimers on DNA, which can be co-bound by cohesin; this chromatin loop structure helps constrain the ability of enhancers within the loop to target genes outside the loop. Loops with CTCF and cohesin at the start and end of the loop that restrict enhancer-gene targeting are “insulated neighborhoods.”


Insulated neighborhoods are defined as chromosome loops that are formed by CTCF homodimers, co-bound with cohesin, and containing at least one gene.[13][14] The CTCF/cohesin-bound regions delimiting an insulated neighborhood are called “anchors.” One study in human Embryonic stem cells identified ~13,000 insulated neighborhoods that, on average, each contained three genes and was about 90kb in size.[15] Two lines of evidence argue that the boundaries of insulated neighborhoods are insulating: 1) the vast majority (~90-97%) of enhancer-gene interactions are contained within insulated neighborhoods and 2) genetic perturbation of CTCF/cohesin-bound insulated neighborhood anchors leads to local gene dysregulation due to novel interactions outside of the neighborhood.

The majority of insulated neighborhoods appear to be maintained during development because CTCF binding and CTCF-CTCF loop structures are very similar across human cell types.[16][17] While the location of many insulated neighborhood structures are maintained across different cell types, the enhancer-gene interactions occurring within them are cell-type specific, consistent with the cell type-specific activity of enhancers.[18][19]

Association with TADs[edit]

Topologically associating domains (TADs) are megabase-size regions of relatively high DNA interaction frequencies.[20][21] Mechanistic studies indicate TADs are single insulated neighborhoods or collections of insulated neighborhoods.[22]

Relevance to human disease[edit]

Genetic and epigenetic variation of insulated neighborhood anchors have been linked to several human diseases. One study of a genetic variant linked to asthma disrupts CTCF binding and insulated neighborhood formation.[23] Studies of imprinted loci showed DNA methylation controls CTCF-anchored loops regulating gene expression. Individuals with methylation aberrations at an imprinted CTCF-binding site near IGF2/H19 form aberrant Insulated Neighborhoods and develop Beckwith-Wiedemann syndrome (when both alleles have the paternal type of insulated neighborhood) or Silver-Russell syndrome (when both alleles have the maternal type of insulated neighborhood).[24]

Insulated neighborhoods aid in identifying the target genes of disease-associated enhancer variants. The majority of disease-linked DNA variants identified from genome-wide association studies occur in enhancers.[25][26][27][28] Identifying target genes of enhancers with disease-linked variants has been difficult because enhancers may act over long distances, but the constraint on enhancer-gene targeting by insulated neighborhoods refines the prediction of target genes. For example, a DNA variant associated with type 2 diabetes occurs within an enhancer located between the CDC123 and CAMK1D genes but only affects CAMK1D because this gene and the enhancer are within the same insulated neighborhood, while CDC123 lies outside the neighborhood.[29][30]

Somatic mutations that alter insulated neighborhood anchors can contribute to tumorigenesis. Chromosomal alterations such as translocations, deletions and tandem duplications intersecting with insulated neighborhood anchor sites can activate oncogenes.[31][32][33] Epigenetic dysregulation can also contribute to tumorigenesis by altering insulated neighborhoods. IDH-mutant gliomas display altered DNA methylation patterns, so CTCF binding, which is DNA methylation-dependent, is also altered.[34] Altered CTCF-binding disrupts insulated neighborhoods and can lead to oncogene misregulation.


  1. ^ Hnisz, D; Day, DS; Young, RA (17 November 2016). "Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control". Cell. 167 (5): 1188–1200. doi:10.1016/j.cell.2016.10.024. PMC 5125522. PMID 27863240.
  2. ^ Buecker, C; Wysocka, J (June 2012). "Enhancers as information integration hubs in development: lessons from genomics". Trends in Genetics. 28 (6): 276–284. doi:10.1016/j.tig.2012.02.008. PMC 5064438. PMID 22487374.
  3. ^ Heinz, S; Romanoski, CE; Benner, C; Glass, CK (March 2015). "The selection and function of cell type-specific enhancers". Nature Reviews Molecular Cell Biology. 16 (3): 144–154. doi:10.1038/nrm3949. PMC 4517609. PMID 25650801.
  4. ^ Levine, M; Cattoglio, C; Tjian, R (27 March 2014). "Looping back to leap forward: transcription enters a new era". Cell. 157 (1): 13–25. doi:10.1016/j.cell.2014.02.009. PMC 4059561. PMID 24679523.
  5. ^ Ong, CT; Corces, VG (April 2011). "Enhancer function: new insights into the regulation of tissue-specific gene expression". Nature Reviews Genetics. 12 (4): 283–293. doi:10.1038/nrg2957. PMC 3175006. PMID 21358745.
  6. ^ Ren, B; Yue, F (2015). "Transcriptional Enhancers: Bridging the Genome and Phenome". Cold Spring Harbor Symposia on Quantitative Biology. 80: 17–26. doi:10.1101/sqb.2015.80.027219. PMID 26582789.
  7. ^ Chung, JH; Whiteley, M; Felsenfeld, G (13 August 1993). "A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila". Cell. 74 (3): 505–514. doi:10.1016/0092-8674(93)80052-g. PMID 8348617. S2CID 45876439.
  8. ^ Geyer, PK; Corces, VG (October 1992). "DNA position-specific repression of transcription by a Drosophila zinc finger protein". Genes & Development. 6 (10): 1865–1873. doi:10.1101/gad.6.10.1865. PMID 1327958.
  9. ^ Kellum, R; Schedl, P (8 March 1991). "A position-effect assay for boundaries of higher order chromosomal domains". Cell. 64 (5): 941–950. doi:10.1016/0092-8674(91)90318-s. PMID 1848159. S2CID 43485905.
  10. ^ Udvardy, A; Maine, E; Schedl, P (20 September 1985). "The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains". Journal of Molecular Biology. 185 (2): 341–358. doi:10.1016/0022-2836(85)90408-5. PMID 2997449.
  11. ^ Bell, AC; West, AG; Felsenfeld, G (6 August 1999). "The protein CTCF is required for the enhancer blocking activity of vertebrate insulators". Cell. 98 (3): 387–396. doi:10.1016/s0092-8674(00)81967-4. PMID 10458613.
  12. ^ Liu, M; Maurano, MT; Wang, H; Qi, H; Song, CZ; Navas, PA; Emery, DW; Stamatoyannopoulos, JA; Stamatoyannopoulos, G (February 2015). "Genomic discovery of potent chromatin insulators for human gene therapy". Nature Biotechnology. 33 (2): 198–203. doi:10.1038/nbt.3062. PMID 25580597. S2CID 19587760.
  13. ^ Dowen, JM; Fan, ZP; Hnisz, D; Ren, G; Abraham, BJ; Zhang, LN; Weintraub, AS; Schuijers, J; Lee, TI; Zhao, K; Young, RA (9 October 2014). "Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes". Cell. 159 (2): 374–387. doi:10.1016/j.cell.2014.09.030. PMC 4197132. PMID 25303531.
  14. ^ Ji, X; Dadon, DB; Powell, BE; Fan, ZP; Borges-Rivera, D; Shachar, S; Weintraub, AS; Hnisz, D; Pegoraro, G; Lee, TI; Misteli, T; Jaenisch, R; Young, RA (4 February 2016). "3D Chromosome Regulatory Landscape of Human Pluripotent Cells". Cell Stem Cell. 18 (2): 262–275. doi:10.1016/j.stem.2015.11.007. PMC 4848748. PMID 26686465.
  15. ^ Ji, X; Dadon, DB; Powell, BE; Fan, ZP; Borges-Rivera, D; Shachar, S; Weintraub, AS; Hnisz, D; Pegoraro, G; Lee, TI; Misteli, T; Jaenisch, R; Young, RA (4 February 2016). "3D Chromosome Regulatory Landscape of Human Pluripotent Cells". Cell Stem Cell. 18 (2): 262–75. doi:10.1016/j.stem.2015.11.007. PMC 4848748. PMID 26686465.
  16. ^ Ji, X; Dadon, DB; Powell, BE; Fan, ZP; Borges-Rivera, D; Shachar, S; Weintraub, AS; Hnisz, D; Pegoraro, G; Lee, TI; Misteli, T; Jaenisch, R; Young, RA (4 February 2016). "3D Chromosome Regulatory Landscape of Human Pluripotent Cells". Cell Stem Cell. 18 (2): 262–75. doi:10.1016/j.stem.2015.11.007. PMC 4848748. PMID 26686465.
  17. ^ Cuddapah, S; Jothi, R; Schones, DE; Roh, TY; Cui, K; Zhao, K (January 2009). "Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains". Genome Research. 19 (1): 24–32. doi:10.1101/gr.082800.108. PMC 2612964. PMID 19056695.
  18. ^ Ji, X; Dadon, DB; Powell, BE; Fan, ZP; Borges-Rivera, D; Shachar, S; Weintraub, AS; Hnisz, D; Pegoraro, G; Lee, TI; Misteli, T; Jaenisch, R; Young, RA (4 February 2016). "3D Chromosome Regulatory Landscape of Human Pluripotent Cells". Cell Stem Cell. 18 (2): 262–75. doi:10.1016/j.stem.2015.11.007. PMC 4848748. PMID 26686465.
  19. ^ Smith, EM; Lajoie, BR; Jain, G; Dekker, J (7 January 2016). "Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus". American Journal of Human Genetics. 98 (1): 185–201. doi:10.1016/j.ajhg.2015.12.002. PMC 4716690. PMID 26748519.
  20. ^ Dixon, JR; Selvaraj, S; Yue, F; Kim, A; Li, Y; Shen, Y; Hu, M; Liu, JS; Ren, B (11 April 2012). "Topological domains in mammalian genomes identified by analysis of chromatin interactions". Nature. 485 (7398): 376–80. Bibcode:2012Natur.485..376D. doi:10.1038/nature11082. PMC 3356448. PMID 22495300.
  21. ^ Nora, EP; Lajoie, BR; Schulz, EG; Giorgetti, L; Okamoto, I; Servant, N; Piolot, T; van Berkum, NL; Meisig, J; Sedat, J; Gribnau, J; Barillot, E; Blüthgen, N; Dekker, J; Heard, E (11 April 2012). "Spatial partitioning of the regulatory landscape of the X-inactivation centre". Nature. 485 (7398): 381–5. Bibcode:2012Natur.485..381N. doi:10.1038/nature11049. PMC 3555144. PMID 22495304.
  22. ^ Ji, X; Dadon, DB; Powell, BE; Fan, ZP; Borges-Rivera, D; Shachar, S; Weintraub, AS; Hnisz, D; Pegoraro, G; Lee, TI; Misteli, T; Jaenisch, R; Young, RA (4 February 2016). "3D Chromosome Regulatory Landscape of Human Pluripotent Cells". Cell Stem Cell. 18 (2): 262–75. doi:10.1016/j.stem.2015.11.007. PMC 4848748. PMID 26686465.
  23. ^ Tang, Z; Luo, OJ; Li, X; Zheng, M; Zhu, JJ; Szalaj, P; Trzaskoma, P; Magalska, A; Wlodarczyk, J; Ruszczycki, B; Michalski, P; Piecuch, E; Wang, P; Wang, D; Tian, SZ; Penrad-Mobayed, M; Sachs, LM; Ruan, X; Wei, CL; Liu, ET; Wilczynski, GM; Plewczynski, D; Li, G; Ruan, Y (17 December 2015). "CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription". Cell. 163 (7): 1611–27. doi:10.1016/j.cell.2015.11.024. PMC 4734140. PMID 26686651.
  24. ^ Nativio, R; Sparago, A; Ito, Y; Weksberg, R; Riccio, A; Murrell, A (1 April 2011). "Disruption of genomic neighbourhood at the imprinted IGF2-H19 locus in Beckwith-Wiedemann syndrome and Silver-Russell syndrome". Human Molecular Genetics. 20 (7): 1363–74. doi:10.1093/hmg/ddr018. PMC 3049359. PMID 21282187.
  25. ^ Ernst, J; Kheradpour, P; Mikkelsen, TS; Shoresh, N; Ward, LD; Epstein, CB; Zhang, X; Wang, L; Issner, R; Coyne, M; Ku, M; Durham, T; Kellis, M; Bernstein, BE (5 May 2011). "Mapping and analysis of chromatin state dynamics in nine human cell types". Nature. 473 (7345): 43–9. Bibcode:2011Natur.473...43E. doi:10.1038/nature09906. PMC 3088773. PMID 21441907.
  26. ^ Farh, KK; Marson, A; Zhu, J; Kleinewietfeld, M; Housley, WJ; Beik, S; Shoresh, N; Whitton, H; Ryan, RJ; Shishkin, AA; Hatan, M; Carrasco-Alfonso, MJ; Mayer, D; Luckey, CJ; Patsopoulos, NA; De Jager, PL; Kuchroo, VK; Epstein, CB; Daly, MJ; Hafler, DA; Bernstein, BE (19 February 2015). "Genetic and epigenetic fine mapping of causal autoimmune disease variants". Nature. 518 (7539): 337–43. Bibcode:2015Natur.518..337F. doi:10.1038/nature13835. PMC 4336207. PMID 25363779.
  27. ^ Hnisz, D; Abraham, BJ; Lee, TI; Lau, A; Saint-André, V; Sigova, AA; Hoke, HA; Young, RA (7 November 2013). "Super-enhancers in the control of cell identity and disease". Cell. 155 (4): 934–47. doi:10.1016/j.cell.2013.09.053. PMC 3841062. PMID 24119843.
  28. ^ Maurano, MT; Humbert, R; Rynes, E; Thurman, RE; Haugen, E; Wang, H; Reynolds, AP; Sandstrom, R; Qu, H; Brody, J; Shafer, A; Neri, F; Lee, K; Kutyavin, T; Stehling-Sun, S; Johnson, AK; Canfield, TK; Giste, E; Diegel, M; Bates, D; Hansen, RS; Neph, S; Sabo, PJ; Heimfeld, S; Raubitschek, A; Ziegler, S; Cotsapas, C; Sotoodehnia, N; Glass, I; Sunyaev, SR; Kaul, R; Stamatoyannopoulos, JA (7 September 2012). "Systematic localization of common disease-associated variation in regulatory DNA". Science. 337 (6099): 1190–5. Bibcode:2012Sci...337.1190M. doi:10.1126/science.1222794. PMC 3771521. PMID 22955828.
  29. ^ Fogarty, MP; Cannon, ME; Vadlamudi, S; Gaulton, KJ; Mohlke, KL (11 September 2014). "Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus". PLOS Genetics. 10 (9): e1004633. doi:10.1371/journal.pgen.1004633. PMC 4161327. PMID 25211022.
  30. ^ GTEx, Consortium. (8 May 2015). "Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans". Science. 348 (6235): 648–60. Bibcode:2015Sci...348..648.. doi:10.1126/science.1262110. PMC 4547484. PMID 25954001.
  31. ^ Gröschel, S; Sanders, MA; Hoogenboezem, R; de Wit, E; Bouwman, BA; Erpelinck, C; van der Velden, VH; Havermans, M; Avellino, R; van Lom, K; Rombouts, EJ; van Duin, M; Döhner, K; Beverloo, HB; Bradner, JE; Döhner, H; Löwenberg, B; Valk, PJ; Bindels, EM; de Laat, W; Delwel, R (10 April 2014). "A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia". Cell. 157 (2): 369–81. doi:10.1016/j.cell.2014.02.019. PMID 24703711.
  32. ^ Hnisz, D; Weintraub, AS; Day, DS; Valton, AL; Bak, RO; Li, CH; Goldmann, J; Lajoie, BR; Fan, ZP; Sigova, AA; Reddy, J; Borges-Rivera, D; Lee, TI; Jaenisch, R; Porteus, MH; Dekker, J; Young, RA (25 March 2016). "Activation of proto-oncogenes by disruption of chromosome neighborhoods". Science. 351 (6280): 1454–8. Bibcode:2016Sci...351.1454H. doi:10.1126/science.aad9024. PMC 4884612. PMID 26940867.
  33. ^ Weischenfeldt, Joachim; Dubash, Taronish; Drainas, Alexandros P.; Mardin, Balca R.; Chen, Yuanyuan; Stütz, Adrian M.; Waszak, Sebsatian M.; Bosco, Graziella; Halvorsen, Ann R.; Raeder, Benjamin; Efthymiopoulos, Theocharis; Erkek, Serap; Siegl, Christine; Brenner, Hermann; Brustugun, Odd T.; Dieter, Sebastian M; Northcott, Paul A.; Petersen, Iver; Pfister, Stefan M.; Schneider, Martin; Solberg, Steinar K.; Thunissen, Erik; Weichert, Wilko; Zichner, Thomas; Thomas, Roman; Peifer, Martin; Helland, Aslaug; Ball, Claudia R.; Jechlinger, Martin; Sotillo, Rocio; Glimm, Hanno; Korbel, Jan O. (2016). "Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking". Nature Genetics. 49 (1): 65–74. doi:10.1038/ng.3722. PMC 5791882. PMID 27869826.
  34. ^ Flavahan, WA; Drier, Y; Liau, BB; Gillespie, SM; Venteicher, AS; Stemmer-Rachamimov, AO; Suvà, ML; Bernstein, BE (7 January 2016). "Insulator dysfunction and oncogene activation in IDH mutant gliomas" (PDF). Nature. 529 (7584): 110–4. Bibcode:2016Natur.529..110F. doi:10.1038/nature16490. PMC 4831574. PMID 26700815.