153
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Intergenic and Intronic DNA Hypomethylated Regions as Putative Regulators of Imprinted Domains

, , &
Pages 445-461 | Received 02 Oct 2017, Accepted 04 Dec 2017, Published online: 23 Mar 2018

References

  • Barlow DP , BartolomeiMS . Genomic imprinting in mammals . Cold Spring Harb. Perspect. Biol.6 ( 2 ), pii:a018382 ( 2014 ).
  • Kim J , BretzCL , LeeS . Epigenetic instability of imprinted genes in human cancers . Nucleic Acids Res.43 ( 22 ), 10689 – 10699 ( 2015 ).
  • Bretz CL , LangohrIM , LeeS , KimJ . Epigenetic instability at imprinting control regions in a Kras(G12D)-induced T-cell neoplasm . Epigenetics10 ( 12 ), 1111 – 1120 ( 2015 ).
  • Kelsey G , BartolomeiMS . Imprinted genes … and the number is?PLoS Genet.8 ( 3 ), e1002601 ( 2012 ).
  • He H , KimJ . Regulation and function of the Peg3 imprinted domain . Genomics Inform.12 ( 3 ), 105 – 113 ( 2014 ).
  • Su AI , WiltshireT , BatalovSet al. A gene atlas of the mouse and human protein-encoding transcriptomes . Proc. Natl Acad. Sci. USA101 ( 16 ), 6062 – 6067 ( 2004 ).
  • Barlow DP . Genomic imprinting: a mammalian epigenetic discovery model . Annu. Rev. Genet.45 , 379 – 403 ( 2011 ).
  • Kim J , YeA . Phylogenetic and epigenetic footprinting of the putative enhancers of the Peg3 domain . PLoS ONE11 ( 4 ), e0154216 ( 2016 ).
  • Thiaville MM , KimH , FreyWD , KimJ . Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain . PLoS ONE8 ( 9 ), e75417 ( 2013 ).
  • Rogers ED , RamalieJR , McMurrayEN , SchmidtJV . Localizing transcriptional regulatory elements at the mouse Dlk1 locus . PLoS ONE7 ( 5 ), e36483 ( 2012 ).
  • Schlesinger F , SmithAD , GingerasTR , HannonGJ , HodgesE . De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements . Genome Res.23 ( 10 ), 1601 – 1614 ( 2013 ).
  • Li Y , HuangW , NiuL , UmbachDM , CovoS , LiL . Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes . BMC Genomics14 , 553 ( 2013 ).
  • Perera BP , KimJ . Alternative promoters of Peg3 with maternal specificity . Sci. Rep.6 , 24438 ( 2016 ).
  • Luo Z , LinC , WoodfinARet al. Regulation of the imprinted Dlk1-Dio3 locus by allele-specific enhancer activity . Genes Dev.30 ( 1 ), 92 – 101 ( 2016 ).
  • Nordin M , BergmanD , HaljeM , EngstromW , WardA . Epigenetic regulation of the Igf2/H19 gene cluster . Cell Prolif.47 ( 3 ), 189 – 199 ( 2014 ).
  • Court F , BaniolM , HagegeHet al. Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA . Nucleic Acids Res.39 ( 14 ), 5893 – 5906 ( 2011 ).
  • Nativio R , SparagoA , ItoY , WeksbergR , RiccioA , MurrellA . Disruption of genomic neighbourhood at the imprinted IGF2-H19 locus in Beckwith–Wiedemann syndrome and Silver–Russell syndrome . Hum. Mol. Genet.20 ( 7 ), 1363 – 1374 ( 2011 ).
  • Charalambous M , MenheniottTR , BennettWRet al. An enhancer element at the Igf2/H19 locus drives gene expression in both imprinted and non-imprinted tissues . Dev. Biol.271 ( 2 ), 488 – 497 ( 2004 ).
  • Stadler MB , MurrR , BurgerLet al. DNA-binding factors shape the mouse methylome at distal regulatory regions . Nature480 ( 7378 ), 490 – 495 ( 2011 ).
  • Hon GC , RajagopalN , ShenYet al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues . Nat. Genet.45 ( 10 ), 1198 – 1206 ( 2013 ).
  • Pollard KS , HubiszMJ , RosenbloomKR , SiepelA . Detection of nonneutral substitution rates on mammalian phylogenies . Genome Res.20 ( 1 ), 110 – 121 ( 2010 ).
  • Blanchette M , KentWJ , RiemerCet al. Aligning multiple genomic sequences with the threaded blockset aligner . Genome Res.14 ( 4 ), 708 – 715 ( 2004 ).
  • Stamatoyannopoulos JA , SnyderM , HardisonRet al. An encyclopedia of mouse DNA elements (mouse ENCODE) . Genome Biol.13 ( 8 ), 418 ( 2012 ).
  • Gerstein MB , KundajeA , HariharanMet al. Architecture of the human regulatory network derived from ENCODE data . Nature489 ( 7414 ), 91 – 100 ( 2012 ).
  • Wang J , ZhuangJ , IyerSet al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors . Genome Res.22 ( 9 ), 1798 – 1812 ( 2012 ).
  • Wang J , ZhuangJ , IyerSet al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium . Nucleic Acids Res.41 , D171 – D176 ( 2013 ).
  • Ovcharenko I , LootsGG , GiardineBMet al. Mulan: multiple-sequence local alignment and visualization for studying function and evolution . Genome Res.15 ( 1 ), 184 – 194 ( 2005 ).
  • Ye A , HeH , KimJ . Paternally expressed Peg3 controls maternally expressed Zim1 as a trans factor . PLoS ONE9 ( 9 ), e108596 ( 2014 ).
  • Winer J , JungCK , ShackelI , WilliamsPM . Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro . Anal. Biochem.270 ( 1 ), 41 – 49 ( 1999 ).
  • Creyghton MP , ChengAW , WelsteadGGet al. Histone H3K27ac separates active from poised enhancers and predicts developmental state . Proc. Natl Acad. Sci. USA107 ( 50 ), 21931 – 21936 ( 2010 ).
  • Clark SJ , HarrisonJ , PaulCL , FrommerM . High sensitivity mapping of methylated cytosines . Nucleic Acids Res.22 ( 15 ), 2990 – 2997 ( 1994 ).
  • Andersson R , GebhardC , Miguel-EscaladaIet al. An atlas of active enhancers across human cell types and tissues . Nature507 ( 7493 ), 455 – 461 ( 2014 ).
  • Huang J , LiuX , LiDet al. Dynamic control of enhancer repertoires drives lineage and stage-specific transcription during hematopoiesis . Dev. Cell36 ( 1 ), 9 – 23 ( 2016 ).
  • Faisal M , KimH , KimJ . Sexual differences of imprinted genes’ expression levels . Gene533 ( 1 ), 434 – 438 ( 2014 ).
  • Ferron SR , CharalambousM , RadfordEet al. Postnatal loss of Dlk1 imprinting in stem cells and niche astrocytes regulates neurogenesis . Nature475 ( 7356 ), 381 – 385 ( 2011 ).
  • Surmacz B , NoisaP , Risner-JaniczekJRet al. DLK1 promotes neurogenesis of human and mouse pluripotent stem cell-derived neural progenitors via modulating Notch and BMP signalling . Stem Cell Rev.8 ( 2 ), 459 – 471 ( 2012 ).
  • Andersson R . Promoter or enhancer, what’s the difference? Deconstruction of established distinctions and presentation of a unifying model . BioEssays37 ( 3 ), 314 – 323 ( 2015 ).
  • Kim TK , ShiekhattarR . Architectural and functional commonalities between enhancers and promoters . Cell162 ( 5 ), 948 – 959 ( 2015 ).
  • Kuroiwa Y , Kaneko-IshinoT , KagitaniFet al. Peg3 imprinted gene on proximal chromosome 7 encodes for a zinc finger protein . Nat. Genet.12 ( 2 ), 186 – 190 ( 1996 ).
  • Kim J , LuX , StubbsL . Zim1, a maternally expressed mouse Kruppel-type zinc-finger gene located in proximal chromosome 7 . Hum. Mol. Genet.8 ( 5 ), 847 – 854 ( 1999 ).
  • Kim J , BergmannA , LucasS , StoneR , StubbsL . Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2 . Genomics84 ( 1 ), 47 – 58 ( 2004 ).
  • Kim J , BergmannA , WehriE , LuX , StubbsL . Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain . Genomics77 ( 1–2 ), 91 – 98 ( 2001 ).
  • Relaix F , WengX , MarazziGet al. Pw1, a novel zinc finger gene implicated in the myogenic and neuronal lineages . Dev. Biol.177 ( 2 ), 383 – 396 ( 1996 ).
  • Bartolomei MS , ZemelS , TilghmanSM . Parental imprinting of the mouse H19 gene . Nature351 ( 6322 ), 153 – 155 ( 1991 ).
  • Dechiara TM , RobertsonEJ , EfstratiadisA . Parental imprinting of the mouse insulin-like growth factor II gene . Cell64 ( 4 ), 849 – 859 ( 1991 ).
  • Yevtodiyenko A , SchmidtJV . Dlk1 expression marks developing endothelium and sites of branching morphogenesis in the mouse embryo and placenta . Dev. Dyn.235 ( 4 ), 1115 – 1123 ( 2006 ).
  • Qu C , JiangT , LiYet al. Gene expression and IG-DMR hypomethylation of maternally expressed gene 3 in developing corticospinal neurons . Gene Expr. Patterns13 ( 1–2 ), 51 – 56 ( 2013 ).
  • Perera BP , KimJ . Sex and tissue specificity of Peg3 promoters . PLoS ONE11 ( 10 ), e0164158 ( 2016 ).
  • Jones S . An overview of the basic helix-loop-helix proteins . Genome Biol.5 ( 6 ), 226 ( 2004 ).
  • Vietri Rudan M , BarringtonC , HendersonSet al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture . Cell Rep.10 ( 8 ), 1297 – 1309 ( 2015 ).
  • Chen WK , KuoWW , HsiehDJet al. CREB negatively regulates IGF2R gene expression and downstream pathways to inhibit hypoxia-induced H9c2 cardiomyoblast cell death . Int. J. Mol. Sci.16 ( 11 ), 27921 – 27930 ( 2015 ).
  • Bretz CL , KimJ . Transcription-driven DNA methylation setting on the mouse Peg3 locus . Epigenetics12 ( 11 ), 945 – 952 ( 2017 ).
  • Kemp CJ , MooreJM , MoserRet al. CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer . Cell Rep.7 ( 4 ), 1020 – 1029 ( 2014 ).
  • Cai C , QinX , WuZet al. Inhibitory effect of MyoD on the proliferation of breast cancer cells . Oncol. Lett.11 ( 6 ), 3589 – 3596 ( 2016 ).
  • Gabay M , LiY , FelsherDW . MYC activation is a hallmark of cancer initiation and maintenance . Cold Spring Harb. Perspect. Med.4 ( 6 ), pii:a014241 ( 2014 ).
  • Kappelmann M , BosserhoffA , KuphalS . AP-1/c-Jun transcription factors: regulation and function in malignant melanoma . Eur. J. Cell Biol.93 ( 1–2 ), 76 – 81 ( 2014 ).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.