17. Liu P, Yang H, Zhang J, Peng X, Lu Z,
Tong W, Chen J (2017) The lncRNA
MALAT1 acts as a competing endogenous
RNA to regulate KRAS expression by sponging
miR-217 in pancreatic ductal adenocarcinoma.
Sci Rep 7:5186
18. Ariel F, Jegu T, Latrasse D, Romero-Barrios N,
Christ A, Benhame M, Crespi M (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven
chromatin loop. Mol Cell 55:343–504
19. Bardou F, Ariel F, Simpson CG, RomeroBarrios N, Laporte P, Balzergue S, Brown JW,
Crespi M (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176
20. Franco-Zorrilla JM, Valli A, Todesco M,
Mateos I, Puga MI, Rubio-Somoza I,
Leyva A, Weigel D, Garcı ´a JA, Paz-Ares J
(2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat
Genet 39:1033–1037
21. Heo JB, Sung S (2011) Vernalizationmediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79
22. Yang W, Li D, Wang G, Zhang C, Zhang M,
Zhang W, Li S (2017) Three intronic lncRNAs
with monoallelic expression derived from the
MEG8 gene in cattle. Anim Genet 48:272–277
23. Lee JT, Lu N (1999) Targeted mutagenesis of
Tsix leads to nonrandom X inactivation. Cell
99:47–57
24. Mohammad F, Mondal T, Guseva N, Pandey
GK, Kanduri C (2010) Kcnq1ot1 noncoding
RNA mediates transcriptional gene silencing by
interacting with Dnmt1. Development
137:2493–2499
25. Lyle R, Watanabe D, te Vruchte D,
Lerchner W, Smrzka OW, Wutz A,
Schageman J, Hahner L, Davies C, Barlow
DP (2000) The imprinted antisense RNA at
the Igf2r locus overlaps but does not imprint
Mas1. Nat Genet 25:19–21
26. Csorba T, Questa JI, Sun Q, Dean C (2014)
Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC
during vernalization. Proc Natl Acad Sci U S
A 111:16160–16165
27. Wierzbicki AT, Haag JR, Pikaard CS (2008)
Noncoding transcription by RNA polymerase
Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell
135:635–648
28. Kambiz M, Zare H, Dell’Orso S, Grontved L,
Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V (2013) eRNAs Promote Transcription
by Establishing Chromatin Accessibility at
Defined Genomic. Mol Cell 51:606–617
29. Juntawong P, Girke T, Bazin J, Bailey-Serres J
(2014) Translational dynamics revealed by
genome-wide profiling of ribosome footprints
in Arabidopsis. Proc Natl Acad Sci U S A 111:
E203–E212
30. Jiao Y, Meyerowitz EM (2010) Cell-type specific analysis of translating RNAs in developing
flowers reveals new levels of control. Mol Syst
Biol 6:419
31. Zanetti ME, Chang IF, Gong F, Galbraith DW,
Bailey-Serres J (2005) Immunopurification of
polyribosomal complexes of Arabidopsis for
global analysis of gene expression. Plant
Physiol 138:624–635
32. Doyle JP, Dougherty JD, Heiman M, Schmidt
EF, Stevens TR, Ma G, Bupp S, Shrestha P,
Shah RD, Doughty ML, Gong S,
Greengard P, Heintz N (2008) Application of
a translational profiling approach for the comparative analysis of CNS cell types. Cell
135:749–762
33. Heiman M, Schaefer A, Gong S, Peterson JD,
Day M, Ramsey KE, Sua ´rez-Farin ˜as M,
Schwarz C, Stephan DA, Surmeier DJ,
Greengard P, Heintz N (2008) A translational
profiling approach for the molecular characterization of CNS cell types. Cell 135:738–748
34. Sanz E, Yang L, Su T, Morris DR, McKnight
GS, Amieux PS (2009) Cell type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci U S A
106:13939–13944
35. Thomas A, Lee PJ, Dalton JE, Nomie KJ,
Stoica L, Costa-Mattioli M, Chang P,
Nuzhdin S, Arbeitman MN, Dierick HA
(2012) A versatile method for cell-specific
profiling of translated mRNAs in Drosophila.
PLoS One 7:e40276
36. Chen X, Dickman D (2017) Development of a
tissue-specific ribosome profiling approach in
Drosophila enables genome-wide evaluation
of translational adaptations. PLoS Genet 13:
e1007117
37. Tryon RC, Pisat N, Johnson SL, Dougherty JD
(2013) Development of translating ribosome
affinity purification for zebrafish. Genesis
51:187–192
38. Watson FL, Mills EA, Wang X, Guo C, Chen
DF, Marsh-Armstrong N (2012) Cell typespecific translational profiling in the Xenopus
laevis retina. Dev Dyn 241:1960–1972
39. Mustroph A, Zanetti ME, Jang CJ, Holtan
HE, Repetti PP, Galbraith DW, Girke T,
Bailey-Serres J (2009) Profiling translatomes
of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.
Proc Natl Acad Sci U S A 106:18843–18848
TRAP-SEQ Analysis of Long Noncoding RNAs
471
Tong W, Chen J (2017) The lncRNA
MALAT1 acts as a competing endogenous
RNA to regulate KRAS expression by sponging
miR-217 in pancreatic ductal adenocarcinoma.
Sci Rep 7:5186
18. Ariel F, Jegu T, Latrasse D, Romero-Barrios N,
Christ A, Benhame M, Crespi M (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven
chromatin loop. Mol Cell 55:343–504
19. Bardou F, Ariel F, Simpson CG, RomeroBarrios N, Laporte P, Balzergue S, Brown JW,
Crespi M (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176
20. Franco-Zorrilla JM, Valli A, Todesco M,
Mateos I, Puga MI, Rubio-Somoza I,
Leyva A, Weigel D, Garcı ´a JA, Paz-Ares J
(2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat
Genet 39:1033–1037
21. Heo JB, Sung S (2011) Vernalizationmediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79
22. Yang W, Li D, Wang G, Zhang C, Zhang M,
Zhang W, Li S (2017) Three intronic lncRNAs
with monoallelic expression derived from the
MEG8 gene in cattle. Anim Genet 48:272–277
23. Lee JT, Lu N (1999) Targeted mutagenesis of
Tsix leads to nonrandom X inactivation. Cell
99:47–57
24. Mohammad F, Mondal T, Guseva N, Pandey
GK, Kanduri C (2010) Kcnq1ot1 noncoding
RNA mediates transcriptional gene silencing by
interacting with Dnmt1. Development
137:2493–2499
25. Lyle R, Watanabe D, te Vruchte D,
Lerchner W, Smrzka OW, Wutz A,
Schageman J, Hahner L, Davies C, Barlow
DP (2000) The imprinted antisense RNA at
the Igf2r locus overlaps but does not imprint
Mas1. Nat Genet 25:19–21
26. Csorba T, Questa JI, Sun Q, Dean C (2014)
Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC
during vernalization. Proc Natl Acad Sci U S
A 111:16160–16165
27. Wierzbicki AT, Haag JR, Pikaard CS (2008)
Noncoding transcription by RNA polymerase
Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell
135:635–648
28. Kambiz M, Zare H, Dell’Orso S, Grontved L,
Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V (2013) eRNAs Promote Transcription
by Establishing Chromatin Accessibility at
Defined Genomic. Mol Cell 51:606–617
29. Juntawong P, Girke T, Bazin J, Bailey-Serres J
(2014) Translational dynamics revealed by
genome-wide profiling of ribosome footprints
in Arabidopsis. Proc Natl Acad Sci U S A 111:
E203–E212
30. Jiao Y, Meyerowitz EM (2010) Cell-type specific analysis of translating RNAs in developing
flowers reveals new levels of control. Mol Syst
Biol 6:419
31. Zanetti ME, Chang IF, Gong F, Galbraith DW,
Bailey-Serres J (2005) Immunopurification of
polyribosomal complexes of Arabidopsis for
global analysis of gene expression. Plant
Physiol 138:624–635
32. Doyle JP, Dougherty JD, Heiman M, Schmidt
EF, Stevens TR, Ma G, Bupp S, Shrestha P,
Shah RD, Doughty ML, Gong S,
Greengard P, Heintz N (2008) Application of
a translational profiling approach for the comparative analysis of CNS cell types. Cell
135:749–762
33. Heiman M, Schaefer A, Gong S, Peterson JD,
Day M, Ramsey KE, Sua ´rez-Farin ˜as M,
Schwarz C, Stephan DA, Surmeier DJ,
Greengard P, Heintz N (2008) A translational
profiling approach for the molecular characterization of CNS cell types. Cell 135:738–748
34. Sanz E, Yang L, Su T, Morris DR, McKnight
GS, Amieux PS (2009) Cell type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci U S A
106:13939–13944
35. Thomas A, Lee PJ, Dalton JE, Nomie KJ,
Stoica L, Costa-Mattioli M, Chang P,
Nuzhdin S, Arbeitman MN, Dierick HA
(2012) A versatile method for cell-specific
profiling of translated mRNAs in Drosophila.
PLoS One 7:e40276
36. Chen X, Dickman D (2017) Development of a
tissue-specific ribosome profiling approach in
Drosophila enables genome-wide evaluation
of translational adaptations. PLoS Genet 13:
e1007117
37. Tryon RC, Pisat N, Johnson SL, Dougherty JD
(2013) Development of translating ribosome
affinity purification for zebrafish. Genesis
51:187–192
38. Watson FL, Mills EA, Wang X, Guo C, Chen
DF, Marsh-Armstrong N (2012) Cell typespecific translational profiling in the Xenopus
laevis retina. Dev Dyn 241:1960–1972
39. Mustroph A, Zanetti ME, Jang CJ, Holtan
HE, Repetti PP, Galbraith DW, Girke T,
Bailey-Serres J (2009) Profiling translatomes
of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.
Proc Natl Acad Sci U S A 106:18843–18848
TRAP-SEQ Analysis of Long Noncoding RNAs
471