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Cited by 175Genomics and Chromatin DynamicsCancer-related molecular mechanisms researchEpigenetics and DNA Methylation

Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice

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Canzio, Daniele, Nwakeze, Chiamaka L., Horta, Adan, Rajkumar, Sandy M., Coffey, Eliot L., Duffy, Erin E., Duffié, Rachel, Monahan, Kevin +4 more·2019·Cell
DOI 10.1016/j.cell.2019.03.008PMC PMC6823843

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Abstract

Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.

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  • The CTCF sites on the Pcdhα promoters are methylated, preventing CTCF binding and looping.

    “However, the CTCF sites on the promoters are methylated, preventing CTCF binding and looping.”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [141]

    The Introduction (page not supplied) says CTCF sites are hypermethylated in inactive Pcdhα promoters, preventing CTCF/Cohesin binding. It also says promoter–enhancer looping requires that binding. The claim omits the inactive-promoter qualification: the same passage describes active promoters as hypomethylated. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • In the mammalian protocadherin α (Pcdhα) gene cluster, each promoter contains a CTCF binding site capable of looping with a convergent CTCF binding site on the enhancer.

    “In the mammalian protocadherin α (Pcdhα) gene cluster, each promoter contains a CTCF binding site capable of looping with a convergent CTCF binding site on the enhancer.”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [141]

  • Selective demethylation of the CTCF binding site on a particular Pcdhα promoter allows that promoter to establish contact with the enhancer, resulting in activation of the expression of that particular Pcdhα gene.

    “Selective demethylation of the CTCF binding site on a particular promoter allows that promoter to establish contact with the enhancer, resulting in activation of the expression of that particular Pcdhα gene [140,141].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [141]

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Research works printed but not linked: 40

  1. Arab K, Karaulanov E, Musheev M, Trnka P, Schaefer A, Grummt I, and Niehrs C (2019). GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet 51, 217–. 30617255 PMC6420098
  2. Arab K, Park YJ, Lindroth AM, Schafer A, Oakes C, Weichenhan D, Lukanova A, Lundin E, Risch A, Meister M, (2014). Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol. Cell 55, 604– 614. 25087872
  3. Bell AC, and Felsenfeld G (2000). Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482– 485. 10839546
  4. Brown T, Howe FS, Murray SC, Wouters M, Lorenz P, Seward E, Rata S, Angel A, and Mellor J (2018). Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol. Syst. Biol 14, e8007. 29440389 PMC5810148
  5. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, (2015). Highly efficient Cas9-mediated transcriptional programming. Nat Meth 12, 326– 328. PMC4393883 25730490
  6. Colquitt BM, Allen WE, Barnea G, and Lomvardas S (2013). Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity. Proc. Natl. Acad. Sci. U.S.a 110, 14682– 14687. 23969834 PMC3767503
  7. Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, and Simon MD (2015). Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Mol. Cell 59, 858– 866. 26340425 PMC4560836
  8. Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T, Koide T, Kitsukawa T, Hamada S, and Yagi T (2005). Monoallelic yet combinatorial expression of variable exons of the protocadherin-alpha gene cluster in single neurons. Nat Genet 37, 171– 176. 15640798
  9. Fuchs G, Voichek Y, Benjamin S, Gilad S, Amit I, and Oren M (2014). 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol 15, R69. 24887486 PMC4072947
  10. Ghirlando R, and Felsenfeld G (2016). CTCF: making the right connections. Genes & Development 30, 881– 891. 27083996 PMC4840295
  11. Hasegawa S, Hamada S, Kumode Y, Esumi S, Katori S, Fukuda E, Uchiyama Y, Hirabayashi T, Mombaerts P, and Yagi T (2008). The protocadherin-alpha family is involved in axonal coalescence of olfactory sensory neurons into glomeruli of the olfactory bulb in mouse. Mol. Cell. Neurosci 38, 66– 79. 18353676
  12. Hirayama T, Tarusawa E, Yoshimura Y, Galjart N, and Yagi T (2012). CTCF is required for neural development and stochastic expression of clustered Pcdh genes in neurons. Cell Reports 2, 345– 357. 22854024
  13. Jain S, Ba Z, Zhang Y, Dai H-Q, and Alt FW (2018). CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning. Cell. PMC6026039 29804837
  14. Kawaguchi M, Toyama T, Kaneko R, Hirayama T, Kawamura Y, and Yagi T (2008). Relationship between DNA methylation states and transcription of individual isoforms encoded by the protocadherin-alpha gene cluster. Journal of Biological Chemistry 283, 12064– 12075. 18204046
  15. Kehayova P, Monahan K, Chen W, and Maniatis T (2011). Regulatory elements required for the activation and repression of the protocadherin-alpha gene cluster. Proceedings of the National Academy of Sciences 108, 17195– 17200. PMC3193253 21949399
  16. Lefebvre JL, Sanes JR, and Kay JN (2015). Development of Dendritic Form and Function. Annu. Rev. Cell Dev. Biol 31, 741– 777. 26422333
  17. Li X, Yue X, Pastor WA, Lin L, Georges R, Chavez L, Evans SM, and Rao A (2016). Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling. Proc. Natl. Acad. Sci. U.S.a 113, E8267– E8276. 27930333 PMC5187696
  18. Lipovich L, Vanisri RR, Kong SL, Lin C-Y, and Liu ET (2006). Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. J. Mol. Evol 62, 73– 88. 16341467
  19. Magklara A, Yen A, Colquitt BM, Clowney EJ, Magklara A, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, (2011). An epigenetic signature for monoallelic olfactory receptor expression. Cell 145, 555– 570. 21529909 PMC3094500
  20. Maniatis T, and Reed R (2002). An extensive network of coupling among gene expression machines. Nature 416, 499– 506. 11932736
  21. Marina RJ, and Oberdoerffer S (2016). Epigenomics meets splicing through the TETs and CTCF. Cc 15, 1397– 1399. PMC4934062 27104639
  22. Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, and Lomvardas S (2014). Enhancer interaction networks as a means for singular olfactory receptor expression. Cell 159, 543– 557. 25417106 PMC4243057
  23. Monahan K, Horta A, and Lomvardas S (2019). LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Nature 565, 448– 453. 30626972 PMC6436840
  24. Monahan K, Rudnick ND, Kehayova PD, Pauli F, Newberry KM, Myers RM, and Maniatis T (2012). Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc. Natl. Acad. Sci. U.S.a 109, 9125– 9130. 22550178 PMC3384188
  25. Mountoufaris G, Canzio D, Nwakeze CL, Chen WV, and Maniatis T (2018). Writing, Reading, and Translating the Clustered Protocadherin Cell Surface Recognition Code for Neural Circuit Assembly. Annu. Rev. Cell Dev. Biol 34, 471– 493. 30296392
  26. Mountoufaris G, Chen WV, Hirabayashi Y, O’Keeffe S, Chevee M, Nwakeze CL, Polleux F, and Maniatis T (2017). Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. Science 356, 411– 414. 28450637 PMC5529182
  27. Nechaev S, Fargo DC, Santos dos G, Liu L, Gao Y, and Adelman K (2010). Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335– 338. 20007866 PMC3435875
  28. Noonan JP, Li J, Nguyen L, Caoile C, Dickson M, Grimwood J, Schmutz J, Feldman MW, and Myers RM (2003). Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster. Am. J. Hum. Genet 72, 621– 635. 12577201 PMC1180238
  29. Ong C-T, and Corces VG (2014). CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15, 234– 246. 24614316 PMC4610363
  30. Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. 159, 1665– 1680. PMC5635824 25497547
  31. Ribich S, Tasic B, and Maniatis T (2006). Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. Proceedings of the National Academy of Sciences 103, 19719– 19724. PMC1750919 17172445
  32. Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K, (2011). A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature 476, 467– 471. 21832993 PMC3179485
  33. Tasic B, Nabholz CE, Baldwin KK, Kim Y, Rueckert EH, Ribich SA, Cramer P, Wu Q, Axel R, and Maniatis T (2002). Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing. Mol. Cell 10, 21– 33. 12150904
  34. Toyoda S, Okano M, Tarusawa E, Kawaguchi M, Hirabayashi M, Kobayashi T, Toyama T, Oda M, Nakauchi H, Yoshimura Y, (2014). Developmental epigenetic modification regulates stochastic expression of clustered protocadherin genes, generating single neuron diversity. Neuron 82, 94– 108. 24698270
  35. Wang X, Su H, and Bradley A (2002). Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model. Genes & Development 16, 1890– 1905. 12154121 PMC186422
  36. Wu Q, and Maniatis T (1999). A striking organization of a large family of human neural cadherin-like cell adhesion genes. 97, 779– 790. 10380929
  37. Wu X, and Zhang Y (2017). TET-mediated active DNA demethylation: mechanism, function and beyond. Nat Rev Genet 18, 517– 534. 28555658
  38. Zhu Z, Gonzalez F, and Huangfu D (2014). The iCRISPR platform for rapid genome editing in human pluripotent stem cells. Meth. Enzymol 546, 215– 250. 25398343 PMC4418970
  39. Zipursky SL, and Grueber WB (2013). The molecular basis of self-avoidance. Annu. Rev. Neurosci 36, 547– 568. 23841842
  40. Zipursky SL, and Sanes JR (2010). Chemoaffinity revisited: dscams, protocadherins, and neural circuit assembly. 143, 343– 353. 21029858

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Authors
Canzio, D., Nwakeze, C. L., Horta, A., Rajkumar, S. M., Coffey, E. L., Duffy, E. E., Duffié, R., Monahan, K., O’Keeffe, S., Simon, M. D., Lomvardas, S., & Maniatis, T.
Affiliations
  • Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
  • Whitehead Institute for Biomedical Research (US)
  • Yale University (US)
  • Columbia University (US)
  • New York Genome Center (US)
Corresponding author
Maniatis, Tom
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2019-04
Volume
177
Issue
3
Pages
639-653.e15
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2019.03.008
PMC
PMC6823843
OpenAlex
W2932098601
Cited by
175
References
10
Citations by year
2026: 12 · 2025: 19 · 2024: 21 · 2023: 33 · 2022: 18 · 2021: 31 · 2020: 27 · 2019: 14
FWCI
7.53
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • Helen Hay Whitney Foundation
  • National Institutes of Health (1R01MH108579, 5R01NS088476, GM108474, DC016785, R01DC013560, K99/R00 K99GM121815, DP2 HD083992-01)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
antisense long non-coding RNA, DNA demethylation, stochastic gene expression, CTCF binding, enhancer-promoter looping, TET3, olfactory sensory neurons
MeSH terms
DNA Demethylation, CCCTC-Binding Factor, Animals, Binding Sites, Cell Line, Enhancer Elements, Genetic, Exons, Female, Multigene Family, Humans, Mice, Transgenic, Neurons, Promoter Regions, Genetic, RNA Polymerase II, Transcription, Genetic, Cadherins, RNA, Antisense, Mice, RNA, Long Noncoding

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