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Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation.

Majumder M, Bosmeny MS, Gupta R.

RNA. 2016 Oct;22(10):1604-19. doi: 10.1261/rna.057547.116.


NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.

Hao Y, Wu W, Li H, Yuan J, Luo J, Zhao Y, Chen R.

Database (Oxford). 2016 Apr 17;2016. pii: baw057. doi: 10.1093/database/baw057.


Direct and site-specific quantification of RNA 2'-O-methylation by PCR with an engineered DNA polymerase.

Aschenbrenner J, Marx A.

Nucleic Acids Res. 2016 May 5;44(8):3495-502. doi: 10.1093/nar/gkw200.


Cajal bodies are linked to genome conformation.

Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M.

Nat Commun. 2016 Mar 21;7:10966. doi: 10.1038/ncomms10966.


Nucleic Acid Modifications in Regulation of Gene Expression.

Chen K, Zhao BS, He C.

Cell Chem Biol. 2016 Jan 21;23(1):74-85. doi: 10.1016/j.chembiol.2015.11.007. Review.


A mass spectrometry-based method for direct determination of pseudouridine in RNA.

Yamauchi Y, Nobe Y, Izumikawa K, Higo D, Yamagishi Y, Takahashi N, Nakayama H, Isobe T, Taoka M.

Nucleic Acids Res. 2016 Apr 7;44(6):e59. doi: 10.1093/nar/gkv1462.


Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and -independent pseudouridine synthase Cbf5.

Tillault AS, Fourmann JB, Loegler C, Wieden HJ, Kothe U, Charpentier B.

RNA. 2015 Jul;21(7):1233-9. doi: 10.1261/rna.051425.115.


Pseudouridine: still mysterious, but never a fake (uridine)!

Spenkuch F, Motorin Y, Helm M.

RNA Biol. 2014;11(12):1540-54. doi: 10.4161/15476286.2014.992278. Review.


Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation.

Adachi H, Yu YT.

World J Biol Chem. 2014 Nov 26;5(4):398-408. doi: 10.4331/wjbc.v5.i4.398. Review.


Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review).

Karijolich J, Yu YT.

Int J Mol Med. 2014 Aug;34(2):355-62. doi: 10.3892/ijmm.2014.1809. Review.


Targeting vertebrate intron-encoded box C/D 2'-O-methylation guide RNAs into the Cajal body.

Marnef A, Richard P, Pinzón N, Kiss T.

Nucleic Acids Res. 2014 Jun;42(10):6616-29. doi: 10.1093/nar/gku287.


Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex.

Karunatilaka KS, Rueda D.

RNA. 2014 Jan;20(1):16-23. doi: 10.1261/rna.041806.113.


Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function.

Deryusheva S, Gall JG.

RNA. 2013 Dec;19(12):1802-14. doi: 10.1261/rna.042028.113.


Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10.

Joardar A, Jana S, Fitzek E, Gurha P, Majumder M, Chatterjee K, Geisler M, Gupta R.

RNA. 2013 Sep;19(9):1279-94. doi: 10.1261/rna.039230.113.


mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.

Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q.

RNA Biol. 2013 Jul;10(7):1087-92. doi: 10.4161/rna.25193.


Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.

Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M.

Genome Biol. 2013 May 26;14(5):R45. doi: 10.1186/gb-2013-14-5-r45.


Alternative processing of the U2 small nuclear RNA produces a 19-22nt fragment with relevance for the detection of non-small cell lung cancer in human serum.

Mazières J, Catherinne C, Delfour O, Gouin S, Rouquette I, Delisle MB, Prévot G, Escamilla R, Didier A, Persing DH, Bates M, Michot B.

PLoS One. 2013;8(3):e60134. doi: 10.1371/journal.pone.0060134.


Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia.

Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG.

Nucleic Acids Res. 2012 Nov;40(21):10995-1008. doi: 10.1093/nar/gks887.


The development and application of small molecule modulators of SF3b as therapeutic agents for cancer.

Webb TR, Joyner AS, Potter PM.

Drug Discov Today. 2013 Jan;18(1-2):43-9. doi: 10.1016/j.drudis.2012.07.013. Review.


Comprehensive survey and geometric classification of base triples in RNA structures.

Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB.

Nucleic Acids Res. 2012 Feb;40(4):1407-23. doi: 10.1093/nar/gkr810.

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