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Cited by 43Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related molecular mechanisms research

Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters

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Sarda, Shrutii, Das, Avinash, Vinson, Charles, Hannenhalli, Sridhar·2017·Genome Research
DOI 10.1101/gr.212050.116PMC PMC5378174
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Abstract

DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI is unmethylated but remain silenced otherwise. Based on CAGE and Pol II localization data, we found strong evidence of transcription initiation at the upstream CGI and a lack thereof at the methylated proximal promoter itself. Consistent with their alternative promoter activity, CGI-initiated transcripts are associated with signals of stable elongation and splicing that extend into the gene body, as evidenced by tissue-specific RNA-seq and other DNA-encoded splice signals. Furthermore, based on both inter- and intra-species analyses, such CGIs were found to be under greater purifying selection relative to CGIs upstream of silenced genes. Overall, our study describes a hitherto unreported conserved mechanism of transcription of genes with methylated proximal promoters in a tissue-specific fashion. Importantly, this phenomenon explains the aberrant expression patterns of some cancer driver genes, potentially due to aberrant hypomethylation of distal CGIs, despite methylation at proximal promoters.

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  • Depletion of HCC alternative promoters from intragenic CGIs is notably different than alternative promoters usage from intragenic CGIs during developmental stages or gene upstream CGIs in adult tissues.

    “Depletion of HCC alternative promoters from intragenic CGIs is notably different than alternative promoters usage from intragenic CGIs during developmental stages36 or gene upstream CGIs61 in adult tissues”

    From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [61]

    The Discussion reports widespread use of upstream CpG islands as alternative promoters by genes with silenced proximal promoters. The Results and Methods describe analyses of primary human tissues and cell lines, but our copy does not identify the tissues as adult; it also does not assess the citing authors’ HCC comparison. (LLM, conf=0.81)

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Research works printed but not linked: 70

  1. The 1000 Genomes Project Consortium. 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56– 65. 23128226 PMC3498066
  2. Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. 2013 Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499: 360– 363. 23792564 PMC3720719
  3. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Arthur L, Ecker JR, 2010 The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28: 1045– 1048. 20944595 PMC3607281
  4. Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. 1985 A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40: 91– 99. 2981636
  5. Brandeis M, Frank D, Keshet I, Siegfried Z, Mendelsohn M, Nemes A, Temper V, Razin A, Cedar H. 1994 Sp1 elements protect a CpG island from de novo methylation. Nature 371: 435– 438. 8090226
  6. Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. 2016 The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res 26: 301– 314. 26728716 PMC4772013
  7. Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. 2014 Analysis of transcription start sites from nascent RNA supports a unified architecture of mammalian promoters and enhancers. Nat Genet 46: 1311– 1320. 25383968 PMC4254663
  8. Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Gordon Robertson A, Chu A, Beroukhim R, Cibulskis K, Signoretti S, 2013 Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499: 43– 49. 23792563 PMC3771322
  9. Deaton A, Bird A. 2011 CpG islands and the regulation of transcription. Genes Dev 25: 1010– 1022. 21576262 PMC3093116
  10. Deaton AM, Webb S, Kerr ARW, Illingworth RS, Guy J, Andrews R, Bird A. 2011 Cell type–specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 21: 1074– 1086. 21628449 PMC3129250
  11. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003 DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3. 12734009
  12. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, 2012 Landscape of transcription in human cells. Nature 489: 101– 108. 22955620 PMC3684276
  13. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013 STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15– 21. 23104886 PMC3530905
  14. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, 2006 DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378– 1385. 17072317 PMC3082778
  15. Elango N, Yi SV. 2008 DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 25: 1602– 1608. 18469331
  16. The FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014 A promoter-level mammalian expression atlas. Nature 507: 462– 470. 24670764 PMC4529748
  17. Feng D, DuMontier C, Pollak MR. 2015 The role of α-actinin-4 in human kidney disease. Cell Biosci 5: 44. 26301083 PMC4545552
  18. Guillaumet-Adkins A, Richter J, Odero MD, Sandoval J, Agirre X, Catala A, Esteller M, Prósper F, Calasanz M, Buño I, 2014 Hypermethylation of the alternative AWT1 promoter in hematological malignancies is a highly specific marker for acute myeloid leukemias despite high expression levels. J Hematol Oncol 7: 4. 24405639 PMC3900738
  19. Han H, Cortez CC, Yang X, Nichols PW, Jones PA, Liang G. 2011 DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet 20: 4299– 4310. 21835883 PMC3196883
  20. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, 2012 GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22: 1760– 1774. 22955987 PMC3431492
  21. Hoivik EA, Witsoe SL, Bergheim IR, Xu Y, Jakobsson I, Tengholm A, Doskeland SO, Bakke M. 2013 DNA methylation of alternative promoters directs tissue specific expression of Epac2 isoforms. PLoS One 8: e67925. 23861833 PMC3701594
  22. Hon GC, Hawkins RD, Ren B. 2009 Predictive chromatin signatures in the mammalian genome. Hum Mol Genet 18: R195– R201. 19808796 PMC2912651
  23. Illingworth RS, Bird AP. 2009 CpG islands—“a rough guide”. FEBS Lett 583: 1713– 1720. 19376112
  24. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP. 2010 Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6: e1001134. 20885785 PMC2944787
  25. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, 2009a The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178– 186. 19151715 PMC2729128
  26. Irizarry RA, Wu H, Feinberg AP. 2009b A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome 20: 674– 680. 19777308 PMC2962567
  27. Jones PA. 2012 Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484– 492. 22641018
  28. Jones PA, Baylin SB. 2007 The epigenomics of cancer. Cell 128: 683– 692. 17320506 PMC3894624
  29. Jonkers I, Lis JT. 2015 Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 16: 11– 13. PMC4782187 25693130
  30. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, Fulton LL, Dooling DJ, Ding L, Mardis ER, 2012 Comprehensive molecular portraits of human breast tumours. Nature 490: 61– 70. 23000897 PMC3465532
  31. Kouzarides T. 2007 Chromatin modifications and their function. Cell 128: 693– 705. 17320507
  32. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, 2015 Integrative analysis of 111 reference human epigenomes. Nature 518: 317– 330. 25693563 PMC4530010
  33. Larsen F, Gundersen G, Lopez R, Prydz H. 1992 CpG islands as gene markers in the human genome. Genomics 13: 1095– 1107. 1505946
  34. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, 2010 Dynamic changes in the human methylome during differentiation. Genome Res 20: 320– 331. 20133333 PMC2840979
  35. Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. 2015 The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res 25: 467– 477. 25747664 PMC4381519
  36. Levy S, Hannenhalli S. 2002 Identification of transcription factor binding sites in the human genome sequence. Mamm Genome 13: 510– 514. 12370781
  37. Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D. 2011 Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet 43: 1091– 1097. 21964573
  38. Linehan W, Srinivasan R, Schmidt L. 2010 The genetic basis of kidney cancer: a metabolic disease. Nat Rev Urol 7: 277– 285. 20448661 PMC2929006
  39. Liu H, Liu Y, Zhang J-T. 2008 A new mechanism of drug resistance in breast cancer cells: fatty acid synthase overexpression-mediated palmitate overproduction. Mol Cancer Ther 7: 263– 270. 18281512
  40. Mancini-DiNardo D, Steele SJS, Ingram RS, Tilghman SM. 2003 A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum Mol Genet 12: 283– 294. 12554682
  41. Martino D, Saffery R. 2015 Characteristics of DNA methylation and gene expression in regulatory features on the Infinium 450k Beadchip. bioRxiv 10.1101/032862. · DOI · Paper page
  42. Masuda H, Zhang D, Bartholomeusz C, Doihara H, Hortobagyi GN, Ueno NT. 2012 Role of epidermal growth factor receptor in breast cancer. Breast Cancer Res Treat 136: 331– 345. 23073759 PMC3832208
  43. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, 2006 TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108– D110. 16381825 PMC1347505
  44. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, 2010 Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253– 257. 20613842 PMC3998662
  45. Menafra R, Brinkman AB, Matarese F, Franci G, Bartels SJJ, Nguyen L, Shimbo T, Wade PA, Hubner NC, Stunnenberg HG. 2014 Genome-wide binding of MBD2 reveals strong preference for highly methylated loci. PLoS One 9: e99603. 24927503 PMC4057170
  46. Mendizabal I, Yi SV. 2015 Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Hum Mol Genet 25: 69– 82. 26512062 PMC4690492
  47. Moarii M, Boeva V, Vert J-P, Reyal F. 2015 Changes in correlation between promoter methylation and gene expression in cancer. BMC Genomics 16: 873. 26510534 PMC4625954
  48. Nagarajan RP, Zhang B, Bell RJA, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, 2014 Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res 24: 761– 774. 24709822 PMC4009606
  49. Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, 2013 Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol 20: 923– 928. 23851456
  50. Phatnani HP, Greenleaf AL. 2006 Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev 20: 2922– 2936. 17079683
  51. Pollard SM, Stricker SH, Beck S. 2009 A shore sign of reprogramming. Cell Stem Cell 5: 571– 572. 19951682
  52. Quinlan AR, Hall IM. 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841– 842. 20110278 PMC2832824
  53. Rantala JK, Edgren H, Lehtinen L, Wolf M, Kleivi K, Vollan HKM, Aaltola A-R, Laasola P, Kilpinen S, Saviranta P, 2010 Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2. Neoplasia 12: 877– 888. 21082043 PMC2981730
  54. Saxonov S, Berg P, Brutlag DL. 2006 A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci 103: 1412– 1417. 16432200 PMC1345710
  55. Schwalb B, Michel M, Zacher B, Fruhauf K, Demel C, Tresch A, Gagneur J, Cramer P. 2016 TT-seq maps the human transient transcriptome. Science 352: 1225– 1228. 27257258
  56. Schwarz LJ, Fox EM, Balko JM, Garrett JT, Kuba MG, Estrada MV, González-Angulo AM, Mills GB, Red-Brewer M, Mayer IA, 2014 LYN-activating mutations mediate antiestrogen resistance in estrogen receptor–positive breast cancer. J Clin Invest 124: 5490– 5502. 25401474 PMC4348968
  57. Shilpa V, Bhagat R, Premalata CS, Pallavi VR, Ramesh G, Krishnamoorthy L. 2014 Relationship between promoter methylation & tissue expression of MGMT gene in ovarian cancer. Indian J Med Res 140: 616– 623. 25579142 PMC4311314
  58. Sinha AU, Meller J. 2007 Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 8: 82. 17343765 PMC1821339
  59. Smith Z, Chan M, Mikkelsen T, Gu H. 2012 A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484: 339– 344. 22456710 PMC3331945
  60. Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH. 2011 Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci 108: 4364– 4369. 21368160 PMC3060255
  61. Sproul D, Kitchen RR, Nestor CE, Dixon JM, Sims AH, Harrison DJ, Ramsahoye BH, Meehan RR. 2012 Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol 13: R84. 23034185 PMC3491412
  62. van Eijk KR, de Jong S, Boks MPM, Langeveld T, Colas F, Veldink JH, de Kovel CGF, Janson E, Strengman E, Langfelder P, 2012 Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics 13: 636. 23157493 PMC3583143
  63. Van Vlodrop IJH, Niessen HEC, Derks S, Baldewijns MMLL, Van Criekinge W, Herman JG, Van Engeland M. 2011 Analysis of promoter CpG island hypermethylation in cancer: location, location, location! Clin Cancer Res 17: 4225– 4231. 21558408
  64. Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. 2011 Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol 28: 2615– 2627. 21478372 PMC3203547
  65. Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M. 2014 The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol 15: R37. 24555846 PMC4053980
  66. Wan J, Oliver VF, Wang G, Zhu H, Zack DJ, Merbs SL, Qian J. 2015 Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics 16: 49. 25652663 PMC4331481
  67. Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, 2014 The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database (Oxford) 2014: bau093. 25267794 PMC4178372
  68. Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. 2010 Redefining CpG islands using hidden Markov models. Biostatistics 11: 499– 514. 20212320 PMC2883304
  69. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, 2005 Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650– 659. 15388519
  70. Zhu J, He F, Hu S, Yu J. 2008 On the nature of human housekeeping genes. Trends Genet 24: 481– 484. 18786740

Cited by

Sorted by citations

Authors
Sarda, S., Das, A., Vinson, C., & Hannenhalli, S.
Affiliations
  • University of Maryland, College Park (US)
  • National Institutes of Health (US)
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2017-02-21
Volume
27
Issue
4
Pages
553-566
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.212050.116
PMC
PMC5378174
OpenAlex
W2591030978
Cited by
43
References
7
Citations by year
2026: 3 · 2025: 2 · 2024: 5 · 2023: 3 · 2022: 4 · 2021: 4 · 2020: 7 · 2019: 8 · 2018: 4 · 2017: 2 · 2016: 1
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
NIH (R01GM100335)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • 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
Keywords
alternative promoters, promoter methylation, gene silencing, transcription initiation, DNA methylation, tissue-specific gene expression, purifying selection, cancer driver genes, hypomethylation, CAGE
MeSH terms
Cell Line, Humans, Promoter Regions, Genetic, CpG Islands, DNA Methylation, Gene Silencing, Transcriptome, Transcription Initiation, Genetic

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