Structural insights of non-canonical U•U pair and Hoogsteen interaction probed with Se atom

Sheng, Jia; Gan, Jianhua; Soares, Alexei S.; Saloň, Jozef; Huang, Zhen

doi:10.1093/nar/gkt799

Cited by 30 publications

(20 citation statements)

References 54 publications

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“…3A, RNA 3) (14). We cannot rule out the possibility that RNA 3 forms a weak hairpin structure through non-canonical U-U base pairing (22)(23)(24)(25). However, such a structure would be much less stable than that formed through canonical base pairing in CCUG repeat RNA 1 (Fig.…”

Section: Resultsmentioning

confidence: 96%

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

deLorimier

Hinman

Copperman

et al. 2017

Journal of Biological Chemistry

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Edited by Ronald C. WekMyotonic dystrophy type 2 is a genetic neuromuscular disease caused by the expression of expanded CCUG repeat RNAs from the non-coding region of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. These CCUG repeats bind and sequester a family of RNA-binding proteins known as Muscleblind-like 1, 2, and 3 (MBNL1, MBNL2, and MBNL3), and sequestration plays a significant role in pathogenicity. MBNL proteins are alternative splicing regulators that bind to the consensus RNA sequence YGCY (Y ‫؍‬ pyrimidine). This consensus sequence is found in the toxic RNAs (CCUG repeats) and in cellular RNA substrates that MBNL proteins have been shown to bind. Replacing the uridine in CCUG repeats with pseudouridine (⌿) resulted in a modest reduction of MBNL1 binding. Interestingly, ⌿ modification of a minimally structured RNA containing YGCY motifs resulted in more robust inhibition of MBNL1 binding. The different levels of inhibition between CCUG repeat and minimally structured RNA binding appear to be due to the ability to modify both pyrimidines in the YGCY motif, which is not possible in the CCUG repeats. Molecular dynamic studies of unmodified and pseudouridylated minimally structured RNAs suggest that reducing the flexibility of the minimally structured RNA leads to reduced binding by MBNL1. Myotonic dystrophy type 1 (DM1)3 is a genetic neuromuscular disease caused by expression of expanded CUG repeats in the 3Ј UTR of the dystrophia myotonica protein kinase (DMPK) gene. Similar to DM1, myotonic dystrophy type 2 (DM2) is caused by expression of expanded CCUG repeats in an intron of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. DM1 and DM2 occur when the CUG/CCUG repeats are expanded beyond 100 repeats, and patients can have up to thousands of CUG/CCUG repeats (1, 2). A primary component of the currently accepted DM1 and DM2 disease mechanism is that expanded CUG/CCUG repeats sequester RNAbinding proteins (primarily the Muscleblind-like family), which prevents these proteins from performing their functions in cells (3, 4).The members of the Muscleblind-like family of proteins (MBNL1, MBNL2, and MBNL3) bind RNA and regulate several RNA processing pathways, including alternative splicing, premiRNA biogenesis, mRNA localization, alternative polyadenylation, and circular RNA generation (5-9). MBNL proteins bind to the consensus YGCY RNA sequence (6, 10). CUG and CCUG repeats are composed of YGCY motifs creating hundreds or thousands of perfect MBNL-binding sites resulting in large numbers of MBNL proteins binding to the repeats and forming nuclear foci (11). When MBNL proteins are sequestered, they are unable to regulate RNA processing events, and consequently, many DM1 and DM2 symptoms are caused by misregulated alternative splicing and potentially the loss of other MBNL activities (12). It is therefore important to understand how MBNL proteins bind to their toxic and cellular RNA substrates to develop mechanisms to alleviate MBNL sequestration in DM1 and DM2.MBNL pro...

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Section: Resultsmentioning

confidence: 96%

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

deLorimier

Hinman

Copperman

et al. 2017

Journal of Biological Chemistry

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“…For example, in the presence of U1-C the oligonucleotides with +3U or +4U, which introduce U–U mismatches, compete better with the wild type than they do in the absence of U1-C. Different types of U–U basepair have been reported ( Lietzke et al, 1996 ; Leontis et al, 2002 ; Kiliszek et al, 2009 ; Sheng et al, 2013 ). Our crystal structure showed that U1-C forms hydrogen bonds exclusively with sugar-phosphate backbone between −2 to +3 positions of pre-mRNA and at C9 and G11 of U1 snRNA ( Figure 4B–C ).…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

Kondo

Oubridge

Roon

et al. 2015

eLife

230

292

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U1 snRNP binds to the 5′ exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein–protein and RNA-protein interactions within U1 snRNP, and show how the 5′ splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5′-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5′-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5′-splice sites.DOI: http://dx.doi.org/10.7554/eLife.04986.001

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“…This was done by Sheng et al, where they successfully crystallized 4-Seuridine-derivatized RNA (5 0 -rU-Se U-CGCG-3 0 ) (PDB: 3HGA) using a 21.2 Â 250-mm Zorbax RX-C8 column. [21] Prep Cell RNA Purification: A Denaturing and Non-Denaturing PAGE Alternative…”

Section: Denaturing Polyacrylamide Gel Electrophoresis (Page)mentioning

confidence: 99%

RNA and RNA–Protein Complex Crystallography and its Challenges

Flores¹,

Walshe²,

Ataide³

2014

Aust. J. Chem.

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RNA biology has changed completely in the past decade with the discovery of non-coding RNAs. Unfortunately, obtaining mechanistic information about these RNAs alone or in cellular complexes with proteins has been a major problem. X-ray crystallography of RNA and RNA–protein complexes has suffered from the major problems encountered in preparing and purifying them in large quantity. Here, we review the available techniques and methods in vitro and in vivo used to prepare and purify RNA and RNA–protein complex for crystallographic studies. We also discuss the future directions necessary to explore the vast number of RNA species waiting for their atomic-resolution structure to be determined.

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Structural insights of non-canonical U•U pair and Hoogsteen interaction probed with Se atom

Cited by 30 publications

References 54 publications

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

RNA and RNA–Protein Complex Crystallography and its Challenges

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