Acknowledgments
We thank Julia Bailey-Serres, Kaisa Kajala, and others that have
contributed to improving the TRAP-SEQ technology. We also
thank Claudio Rivero for discussion and advice on RNA-SEQ
analysis. This work has been financially supported by grants from
ANPCyT, Argentina, funded to M.E.Z. (PICT 2016-0582, PICT
2017-0581), F.A.B. (PICT 2016-0333), and M.A.R. (PICT 20172272). M.E.Z., F.A.B., and M.A.R. are members of CONICET.
S.T. is a fellow of the same institution and has been awarded a
Fulbright Scholarship.
References
1. Farazi TA, Juranek SA, Tuschl T (2008) The
growing catalog of small RNAs and their association with distinct Argonaute/Piwi family
members. Development 135:1201–1214
2. Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant
Biol 64:137–159
3. Kung JT, Colognori D, Lee JT (2013) Long
noncoding RNAs: past, present, and future.
Genetics 193:651–669
4. Ariel F, Romero-Barrios N, Jegu T,
Benhamed M, Crespi M (2015) Battles and
hijacks: noncoding transcription in plants.
Trends Plant Sci 20:362–371
5. Booy EP, McRae EK, Koul A, Lin F, McKenna
SA (2017) The long non-coding RNA BC200
(BCYRN1) is critical for cancer cell survival and
proliferation. Mol Cancer 16:109
6. Shin H, Lee J, Kim Y, Jang S, Lee Y, Kim S, Lee
Y (2017) Knockdown of BC200 RNA expression reduces cell migration and invasion by
destabilizing mRNA for calcium-binding protein S100A11. RNA Biol 14:1418–1143
7. Kondrashov AV, Kiefmann M, Ebnet K,
Khanam T, Muddashetty RS, Brosius J (2005)
Inhibitory effect of naked neural BC1 RNA or
BC200 RNA on eukaryotic in vitro translation
systems is reversed by poly(A)-binding protein
(PABP). J Mol Biol 353:88–103
8. Wang H, Iacoangeli A, Popp S, Muslimov IA,
Imataka H, Sonenberg N, Lomakin IB, Tiedge
H (2002) Dendritic BC1 RNA: functional role
in regulation of translation initiation. J Neurosci 22:10232–10241
9. Yoon JH, Abdelmohsen K, Srikantan S,
Yang X, Martindale JL, De S, Huarte M,
Zhan M, Becker KG, Gorospe M (2012)
LincRNA-p21 suppresses target mRNA translation. Mol Cell 47:648–655
10. Carrieri C, Cimatti L, Biagioli M, Beugnet A,
Zucchelli S, Fedele S, Pesce E, Ferrer I,
Collavin L, Santoro C, Forrest AR,
Carninci P, Biffo S, Stupka E, Gustincich S
(2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded
SINEB2 repeat. Nature 491:454–457
11. Tran NT, Su H, Khodadadi-Jamayran A, Lin S,
Zhang L, Zhou D, Pawlik KM, Townes TM,
Chen Y, Mulloy JC, Zhao X (2016) The
AS-RBM15 lncRNA enhances RBM15 protein
translation during megakaryocyte differentiation. EMBO Rep 17:887–900
12. Jabnoune M, Secco D, Lecampion C,
Robaglia C, Shu Q, Poirier Y (2013) A rice
cis-natural antisense RNA acts as a translational
enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25:4166–4182
13. Bazin J, Baerenfaller K, Gosai SJ, Gregory BD,
Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs
unveils new modes of translational regulation.
Proc Natl Acad Sci U S A 114:
E10018–E10027
14. Deforges J, Reis RS, Jacquet P, Sheppard S,
Gadekar VP, Hart-Smith G, Tanzer A,
Hofacker IL, Iseli C, Xenarios I, Poirier Y
(2019) Control of cognate sense mRNA translation by cis-natural antisense RNAs. Plant
Physiol 180:305–322
15. Brown CJ, Hendrich BD, Rupert JL, Lafrenie ´re RG, Xing Y, Lawrence JP, Willard HF
(1992) The human XIST gene: analysis of a
17 kb inactive X-specific RNA that contains
conserved repeats and is highly localized within
the nucleus. Cell 71:527–542
16. Rinn JL, Kertesz M, Wang JK, Squazzo SL,
Xu X, Brugmann SA, Goodnough LH, Helms
JA, Farnham PJ, Segal E, Chang HY (2007)
Functional demarcation of active and silent
chromatin domains in human HOX loci by
noncoding RNAs. Cell 129:1311–1323
470
Soledad Traubenik et al.
We thank Julia Bailey-Serres, Kaisa Kajala, and others that have
contributed to improving the TRAP-SEQ technology. We also
thank Claudio Rivero for discussion and advice on RNA-SEQ
analysis. This work has been financially supported by grants from
ANPCyT, Argentina, funded to M.E.Z. (PICT 2016-0582, PICT
2017-0581), F.A.B. (PICT 2016-0333), and M.A.R. (PICT 20172272). M.E.Z., F.A.B., and M.A.R. are members of CONICET.
S.T. is a fellow of the same institution and has been awarded a
Fulbright Scholarship.
References
1. Farazi TA, Juranek SA, Tuschl T (2008) The
growing catalog of small RNAs and their association with distinct Argonaute/Piwi family
members. Development 135:1201–1214
2. Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant
Biol 64:137–159
3. Kung JT, Colognori D, Lee JT (2013) Long
noncoding RNAs: past, present, and future.
Genetics 193:651–669
4. Ariel F, Romero-Barrios N, Jegu T,
Benhamed M, Crespi M (2015) Battles and
hijacks: noncoding transcription in plants.
Trends Plant Sci 20:362–371
5. Booy EP, McRae EK, Koul A, Lin F, McKenna
SA (2017) The long non-coding RNA BC200
(BCYRN1) is critical for cancer cell survival and
proliferation. Mol Cancer 16:109
6. Shin H, Lee J, Kim Y, Jang S, Lee Y, Kim S, Lee
Y (2017) Knockdown of BC200 RNA expression reduces cell migration and invasion by
destabilizing mRNA for calcium-binding protein S100A11. RNA Biol 14:1418–1143
7. Kondrashov AV, Kiefmann M, Ebnet K,
Khanam T, Muddashetty RS, Brosius J (2005)
Inhibitory effect of naked neural BC1 RNA or
BC200 RNA on eukaryotic in vitro translation
systems is reversed by poly(A)-binding protein
(PABP). J Mol Biol 353:88–103
8. Wang H, Iacoangeli A, Popp S, Muslimov IA,
Imataka H, Sonenberg N, Lomakin IB, Tiedge
H (2002) Dendritic BC1 RNA: functional role
in regulation of translation initiation. J Neurosci 22:10232–10241
9. Yoon JH, Abdelmohsen K, Srikantan S,
Yang X, Martindale JL, De S, Huarte M,
Zhan M, Becker KG, Gorospe M (2012)
LincRNA-p21 suppresses target mRNA translation. Mol Cell 47:648–655
10. Carrieri C, Cimatti L, Biagioli M, Beugnet A,
Zucchelli S, Fedele S, Pesce E, Ferrer I,
Collavin L, Santoro C, Forrest AR,
Carninci P, Biffo S, Stupka E, Gustincich S
(2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded
SINEB2 repeat. Nature 491:454–457
11. Tran NT, Su H, Khodadadi-Jamayran A, Lin S,
Zhang L, Zhou D, Pawlik KM, Townes TM,
Chen Y, Mulloy JC, Zhao X (2016) The
AS-RBM15 lncRNA enhances RBM15 protein
translation during megakaryocyte differentiation. EMBO Rep 17:887–900
12. Jabnoune M, Secco D, Lecampion C,
Robaglia C, Shu Q, Poirier Y (2013) A rice
cis-natural antisense RNA acts as a translational
enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25:4166–4182
13. Bazin J, Baerenfaller K, Gosai SJ, Gregory BD,
Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs
unveils new modes of translational regulation.
Proc Natl Acad Sci U S A 114:
E10018–E10027
14. Deforges J, Reis RS, Jacquet P, Sheppard S,
Gadekar VP, Hart-Smith G, Tanzer A,
Hofacker IL, Iseli C, Xenarios I, Poirier Y
(2019) Control of cognate sense mRNA translation by cis-natural antisense RNAs. Plant
Physiol 180:305–322
15. Brown CJ, Hendrich BD, Rupert JL, Lafrenie ´re RG, Xing Y, Lawrence JP, Willard HF
(1992) The human XIST gene: analysis of a
17 kb inactive X-specific RNA that contains
conserved repeats and is highly localized within
the nucleus. Cell 71:527–542
16. Rinn JL, Kertesz M, Wang JK, Squazzo SL,
Xu X, Brugmann SA, Goodnough LH, Helms
JA, Farnham PJ, Segal E, Chang HY (2007)
Functional demarcation of active and silent
chromatin domains in human HOX loci by
noncoding RNAs. Cell 129:1311–1323
470
Soledad Traubenik et al.