

Mondrago´ n, A. (2013). Structural studies of RNase P. Annu. Rev. Biophys.
42
,
537–557.
Mozdy, A.D., and Cech, T.R. (2006). Low abundance of telomerase in yeast:
implications for telomerase haploinsufficiency. RNA
12
, 1721–1737.
Nie, J., Jiang, M., Zhang, X., Tang, H., Jin, H., Huang, X., Yuan, B., Zhang, C.,
Lai, J.C., Nagamine, Y., et al. (2015). Post-transcriptional regulation of Nkx2-5
by RHAU in heart development. Cell Rep.
13
, 723–732.
Noller, H.F. (1984). Structure of ribosomal RNA. Annu. Rev. Biochem.
53
,
119–162.
Novikova, I.V., Hennelly, S.P., and Sanbonmatsu, K.Y. (2012). Structural archi-
tecture of the human long non-coding RNA, steroid receptor RNA activator.
Nucleic Acids Res.
40
, 5034–5051.
Novikova, I.V., Dharap, A., Hennelly, S.P., and Sanbonmatsu, K.Y. (2013). 3S:
shotgun secondary structure determination of long non-coding RNAs.
Methods
63
, 170–177.
O’Leary, V.B., Ovsepian, S.V., Carrascosa, L.G., Buske, F.A., Radulovic, V.,
Niyazi, M., Moertl, S., Trau, M., Atkinson, M.J., and Anastasov, N. (2015).
PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation
in response to low-dose irradiation. Cell Rep.
11
, 474–485.
Parsch, J., Braverman, J.M., and Stephan, W. (2000). Comparative sequence
analysis and patterns of covariation in RNA secondary structures. Genetics
154
, 909–921.
Ponting, C.P., Oliver, P.L., and Reik, W. (2009). Evolution and functions of long
noncoding RNAs. Cell
136
, 629–641.
Qiu, J., Chen, S., Su, L., Liu, J., Xiao, N., Ou, T.M., Tan, J.H., Gu, L.Q., Huang,
Z.S., and Li, D. (2014). Cellular nucleic acid binding protein suppresses tumor
cell metastasis and induces tumor cell death by downregulating heteroge-
neous ribonucleoprotein K in fibrosarcoma cells. Biochim. Biophys. Acta
1840
, 2244–2252.
Quinn, J.J., and Chang, H.Y. (2016). Unique features of long non-coding RNA
biogenesis and function. Nat. Rev. Genet.
17
, 47–62.
Ran, F.A., Hsu, P.D., Wright, J., Agarwala, V., Scott, D.A., and Zhang, F. (2013).
Genome engineering using the CRISPR-Cas9 system. Nat. Protoc.
8
, 2281–
2308.
Ren, A., Vusurovic, N., Gebetsberger, J., Gao, P., Juen, M., Kreutz, C., Micura,
R., and Patel, D.J. (2016). Pistol ribozyme adopts a pseudoknot fold facilitating
site-specific in-line cleavage. Nat. Chem. Biol.
http://dx.doi.org/10.1038/ nchembio.2125.Reznik, B., Clement, S.L., and Lykke-Andersen, J. (2014). hnRNP F complexes
with tristetraprolin and stimulates ARE-mRNA decay. PLoS ONE
9
, e100992.
Rhodes, D., and Lipps, H.J. (2015). G-quadruplexes and their regulatory roles
in biology. Nucleic Acids Res.
43
, 8627–8637.
Rinn, J.L., and Chang, H.Y. (2012). Genome regulation by long noncoding
RNAs. Annu. Rev. Biochem.
81
, 145–166.
Rizki, G., and Boyer, L.A. (2015). Lncing epigenetic control of transcription to
cardiovascular development and disease. Circ. Res.
117
, 192–206.
Rouskin, S., Zubradt, M., Washietl, S., Kellis, M., and Weissman, J.S. (2014).
Genome-wide probing of RNA structure reveals active unfolding of mRNA
structures in vivo. Nature
505
, 701–705.
Sanbonmatsu, K.Y. (2016). Towards structural classification of long non-cod-
ing RNAs. Biochim. Biophys. Acta
1859
, 41–45.
Schmitz, K.M., Mayer, C., Postepska, A., and Grummt, I. (2010). Interaction of
noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and
silencing of rRNA genes. Genes Dev.
24
, 2264–2269.
Serganov, A., and Patel, D.J. (2007). Ribozymes, riboswitches and beyond:
regulation of gene expression without proteins. Nat. Rev. Genet.
8
, 776–790.
Siprashvili, Z., Webster, D.E., Kretz, M., Johnston, D., Rinn, J.L., Chang, H.Y.,
and Khavari, P.A. (2012). Identification of proteins binding coding and non-
coding human RNAs using protein microarrays. BMC Genomics
13
, 633.
Somarowthu, S., Legiewicz, M., Chillo´ n, I., Marcia, M., Liu, F., and Pyle, A.M.
(2015). HOTAIR forms an intricate and modular secondary structure. Mol. Cell
58
, 353–361.
Spitale, R.C., Crisalli, P., Flynn, R.A., Torre, E.A., Kool, E.T., and Chang, H.Y.
(2013). RNA SHAPE analysis in living cells. Nat. Chem. Biol.
9
, 18–20.
Spitale, R.C., Flynn, R.A., Zhang, Q.C., Crisalli, P., Lee, B., Jung, J.W.,
Kuchelmeister, H.Y., Batista, P.J., Torre, E.A., Kool, E.T., and Chang, H.Y.
(2015). Structural imprints in vivo decode RNA regulatory mechanisms.
Nature
519
, 486–490.
Tan, E., Wilson, T.J., Nahas, M.K., Clegg, R.M., Lilley, D.M., and Ha, T. (2003).
A four-way junction accelerates hairpin ribozyme folding via a discrete inter-
mediate. Proc. Natl. Acad. Sci. USA
100
, 9308–9313.
Tijerina, P., Mohr, S., and Russell, R. (2007). DMS footprinting of structured
RNAs and RNA-protein complexes. Nat. Protoc.
2
, 2608–2623.
Ulitsky, I., and Bartel, D.P. (2013). lincRNAs: genomics, evolution, and mech-
anisms. Cell
154
, 26–46.
Wamstad, J.A., Alexander, J.M., Truty, R.M., Shrikumar, A., Li, F., Eilertson,
K.E., Ding, H., Wylie, J.N., Pico, A.R., Capra, J.A., et al. (2012). Dynamic and
coordinated epigenetic regulation of developmental transitions in the cardiac
lineage. Cell
151
, 206–220.
Wang, Y., Ma, M., Xiao, X., and Wang, Z. (2012). Intronic splicing enhancers,
cognate splicing factors and context-dependent regulation rules. Nat.
Struct. Mol. Biol.
19
, 1044–1052.
Weeks, K.M. (2010). Advances in RNA structure analysis by chemical probing.
Curr. Opin. Struct. Biol.
20
, 295–304.
Weiner, A.M., Allende, M.L., Becker, T.S., and Calcaterra, N.B. (2007). CNBP
mediates neural crest cell expansion by controlling cell proliferation and cell
survival during rostral head development. J. Cell. Biochem.
102
, 1553–1570.
Weiner, A.M., Sdrigotti, M.A., Kelsh, R.N., and Calcaterra, N.B. (2011).
Deciphering the cellular and molecular roles of cellular nucleic acid binding
protein during cranial neural crest development. Dev. Growth Differ.
53
,
934–947.
Yadav, V.K., Abraham, J.K., Mani, P., Kulshrestha, R., and Chowdhury, S.
(2008). QuadBase: genome-wide database of G4 DNA–occurrence and con-
servation in human, chimpanzee, mouse and rat promoters and 146 microbes.
Nucleic Acids Res.
36
, D381–D385.
Zappulla, D.C., and Cech, T.R. (2004). Yeast telomerase RNA: a flexible scaf-
fold for protein subunits. Proc. Natl. Acad. Sci. USA
101
, 10024–10029.
Zhang, R., Lin, Y., and Zhang, C.T. (2008). Greglist: a database listing potential
G-quadruplex regulated genes. Nucleic Acids Res.
36
, D372–D376.
50
Molecular Cell
64
, 37–50, October 6, 2016