Table of Contents Table of Contents
Previous Page  98 128 Next Page
Information
Show Menu
Previous Page 98 128 Next Page
Page Background

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