Delta-like 4 mRNA is regulated by adjacent natural antisense transcripts

Vascular Cell

Volumn 7, Issue 1, 2015, Pages

  Li, Keguo ^a   Chowdhury, Tamjid ^a   Vakeel, Padmanabhan ^a   Koceja, Christopher ^a   Sampath, Venkatesh ^a   Ramchandran, Ramani ^a  

^a MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

Delta like4; Hemangiomas; Non coding RNA; Vascular

Indexed keywords

COMPLEMENTARY DNA; DELTA LIKE 4; LIGAND; MESSENGER RNA; UNCLASSIFIED DRUG;

ANGIOGENESIS; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL DENSITY; CELL MIGRATION; CELL PROLIFERATION; CELLULAR DISTRIBUTION; DOWN REGULATION; ENDOTHELIUM CELL; GENE LOCUS; HUMAN; HUMAN CELL; IN VITRO STUDY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN LOCALIZATION; REAL TIME POLYMERASE CHAIN REACTION;

MURINAE;

EID: 84928338548     PISSN: 2045824X     EISSN: 2045824X     Source Type: Journal    
DOI: 10.1186/s13221-015-0028-9     Document Type: Article

References (32)

1. Li K, Blum Y, Verma A, Liu Z, Pramanik K, Leigh NR, et al. A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. Blood. 2010;115:133-9.
2. Michalik KM, You X, Manavski Y, Doddaballapur A, Zornig M, Braun T, et al. Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ Res. 2014;114:1389-97.
3. Bell RD, Long X, Lin M, Bergmann JH, Nanda V, Cowan SL, et al. Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arterioscler Thromb Vasc Biol. 2014;34:1249-59.
4. Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 2013;154:240-51.
5. Prasanth KV, Spector DL. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 2007;21:11-42.
6. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science. 2008;322:1855-7.
7. Rosok O, Sioud M. Systematic identification of sense-antisense transcripts in mammalian cells. Nat Biotechnol. 2004;22:104-8.
8. Coultas L, Chawengsaksophak K, Rossant J. Endothelial cells and VEGF in vascular development. Nature. 2005;438:937-45.
9. Gale NW, Dominguez MG, Noguera I, Pan L, Hughes V, Valenzuela DM, et al. Haploinsufficiency of delta-like 4 ligand results in embryonic lethality due to major defects in arterial and vascular development. Proc Natl Acad Sci U S A. 2004;101:15949-54.
10. Shutter JR, Scully S, Fan W, Richards WG, Kitajewski J, Deblandre GA, et al. Dll4, a novel Notch ligand expressed in arterial endothelium. Genes Dev. 2000;14:1313-8.
11. Benedito R, Duarte A. Expression of Dll4 during mouse embryogenesis suggests multiple developmental roles. Gene Expr Patterns. 2005;5:750-5.
12. Pollet I, Opina CJ, Zimmerman C, Leong KG, Wong F, Karsan A. Bacterial lipopolysaccharide directly induces angiogenesis through TRAF6-mediated activation of NF-kappaB and c-Jun N-terminal kinase. Blood. 2003;102:1740-2.
13. Kim MY, Park JH, Mo JS, Ann EJ, Han SO, Baek SH, et al. Downregulation by lipopolysaccharide of Notch signaling, via nitric oxide. J Cell Sci. 2008;121:1466-76.
14. Jakobsson L, Franco CA, Bentley K, Collins RT, Ponsioen B, Aspalter IM, et al. Endothelial cells dynamically compete for the tip cell position during angiogenic sprouting. Nat Cell Biol. 2010;12:943-53.
15. ZhuGe QZM, Zheng W, Yang GY, Mao X, Xie L, Chen G, et al. Notch-1 signalling is activated in brain arteriovenous malformations in humans. Brain. 2009;132:11.
16. Noguera-Troise I, Daly C, Papadopoulos NJ, Coetzee S, Boland P, Gale NW, et al. Blockade of Dll4 inhibits tumour growth by promoting non-productive angiogenesis. Nature. 2006;444:1032-7.
17. Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet. 2014;15:423-37.
18. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23:1494-504.
19. Liu ZJ, Shirakawa T, Li Y, Soma A, Oka M, Dotto GP, et al. Regulation of Notch1 and Dll4 by vascular endothelial growth factor in arterial endothelial cells: implications for modulating arteriogenesis and angiogenesis. Mol Cell Biol. 2003;23:14-25.
20. Uesaka M, Nishimura O, Go Y, Nakashima K, Agata K, Imamura T. Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. BMC Genomics. 2014;15:35.
21. Ebralidze AK, Guibal FC, Steidl U, Zhang P, Lee S, Bartholdy B, et al. PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Dev. 2008;22:2085-92.
22. Tomikawa J, Shimokawa H, Uesaka M, Yamamoto N, Mori Y, Tsukamura H, et al. Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. J Biol Chem. 2011;286:34788-99.
23. Sacilotto N, Monteiro R, Fritzsche M, Becker PW, Sanchez-Del-Campo L, Liu K, et al. Analysis of Dll4 regulation reveals a combinatorial role for Sox and Notch in arterial development. Proc Natl Acad Sci U S A. 2013;110:11893-8.
24. Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322:1845-8.
25. Schmidt C, Fischer G, Kadner H, Genersch E, Kuhn K, Poschl E. Differential effects of DNA-binding proteins on bidirectional transcription from the common promoter region of human collagen type IV genes COL4A1 and COL4A2. Biochim Biophys Acta. 1993;1174:1-10.
26. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM. An abundance of bidirectional promoters in the human genome. Genome Res. 2004;14:62-6.
27. van Noort V, Snel B, Huynen MA. Predicting gene function by conserved co-expression. Trends Genet. 2003;19:238-42.
28. Li YY, Yu H, Guo ZM, Guo TQ, Tu K, Li YX. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol. 2006;2:e74.
29. Battistoni A, Guarguaglini G, Degrassi F, Pittoggi C, Palena A, Di Matteo G, et al. Deregulated expression of the RanBP1 gene alters cell cycle progression in murine fibroblasts. J Cell Sci. 1997;110(Pt 19):2345-57.
30. Hansen JJ, Bross P, Westergaard M, Nielsen MN, Eiberg H, Borglum AD, et al. Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter. Hum Genet. 2003;112:71-7.
31. Heikkila P, Soininen R, Tryggvason K. Directional regulatory activity of cis-acting elements in the bidirectional alpha 1(IV) and alpha 2(IV) collagen gene promoter. J Biol Chem. 1993;268:24677-82.
32. Siekmann AF, Lawson ND. Notch signalling limits angiogenic cell behaviour in developing zebrafish arteries. Nature. 2007;445:781-4.