MBNL1–RNA Recognition: Contributions of MBNL1 Sequence and RNA Conformation

Fu, Yuan; Ramisetty, Sreenivasa Rao; Hussain, Nejmun; Baranger, Anne M.

doi:10.1002/cbic.201100487

Cited by 34 publications

(50 citation statements)

References 55 publications

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“…5E). The disparity in binding affinity that we observed between the ZF1-2 and ZF3-4 domains echoes recent binding studies conducted with structured RNAs (11).…”

Section: Resultssupporting

confidence: 87%

Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Regulatory Events

Purcell

Oddo

Wang

et al. 2012

Molecular and Cellular Biology

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The RNA binding protein and alternative splicing factor Muscleblind-like 1 (MBNL1) has been a topic of intense study due to its role in myotonic dystrophy (DM) pathogenesis. MBNL1 contains four zinc finger (ZF) RNA binding domains arranged in two pairs. Through combinatorial mutagenesis of the ZF domains, we demonstrate that the pairs of ZFs have differential affinity for RNA and subsequently differential splicing activities. We evaluated splicing and binding activity for six MBNL1-mediated splicing events and found that the splicing activity profiles for the ZF mutants vary among transcripts. Clustering analysis of splicing profiles revealed that two distinct classes of MBNL1 pre-mRNA substrates exist. For some of the RNA transcripts tested, binding and splicing activity of the ZF mutants correlated. However, for some transcripts it appears that MBNL1 exerts robust splicing activity in the absence of RNA binding. We demonstrate that functionally distinct classes of MBNL1-mediated splicing events exist as defined by requirements for ZF-RNA interactions.A lternative splicing is a cellular mechanism that is used to create proteomic diversity from a limited number of genes. Although the mechanisms that govern the regulation of alternative splicing are vast, the overarching mechanistic theme is that alternative splicing results from a careful balance between positive and negative splicing signals in the pre-mRNA and the relative concentrations of the many proteins involved in recognizing these signals (reviewed in references 2, 16, 20, 49, and 51).Muscleblind-like 1, or MBNL1, is an alternative splicing factor that has been the focus of intense study over the last decade due to its involvement in myotonic dystrophy (DM) pathogenesis (10, 23). DM is a debilitating, multisystemic disease that is caused by the expansion of certain noncoding, CTG-and CCTG-containing repeats within the genome (3,26,30). Once transcribed into RNA, the CUG-or CCUG-containing expansions form stable structures that are capable of aberrantly sequestering RNA binding proteins, including MBNL1, in structures referred to as foci (8,9,31). Once sequestered to the toxic RNA, MBNL1 is no longer able to perform its normal cellular role in the regulation of key splicing events, leading to missplicing and ultimately disease symptoms (36, 38). Many disease-associated and MBNL1-dependent splicing events have been defined (7, 35); however, mechanistic insights into how MBNL1 regulates splicing are limited. An important step toward a comprehensive understanding of the regulatory mechanisms governed by MBNL1 is a thorough understanding of how MBNL1 recognizes its cellular targets. To this end, the following study was conducted to evaluate the consequences of MBNL1 mutagenesis on splicing function and RNA binding.The architecture of MBNL1 is seemingly very simple. MBNL1 contains four zinc fingers (ZFs) of the CX 7 CX 4 -6 CX 3 H-type (1, 32). The four ZF domains are the only known RNA binding domains of MBNL1. The ZFs are commonly referred to as ZF1, ZF2, Z...

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“…5E). The disparity in binding affinity that we observed between the ZF1-2 and ZF3-4 domains echoes recent binding studies conducted with structured RNAs (11).…”

Section: Resultssupporting

confidence: 87%

Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Regulatory Events

Purcell

Oddo

Wang

et al. 2012

Molecular and Cellular Biology

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“…15 This unique sequence-dependent feature is essential for the co-transcriptional biogenesis of circRNAs, because the production rate and the balance between splicing and circularization are also determined by the intronic sequences. 16,17 The rate can be elevated by binding to muscle blind-like (MBL/MBNL1) protein, an RNA binding protein (RBP) that stimulates circRNA biogenesis, or by binding to several specific repeated RNA sequences such as poly (CUG) and poly (CCUG).Taking the Alu repeats as an example, they are found throughout the genome and thought to actively participate in circRNAs genesis. Such repeats retro-transpose by hijacking a reverse transcriptase and an endonuclease from autonomous retro-transposons for re-insertion into the genome.…”

Section: Biogenesis and Functionmentioning

confidence: 99%

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

2016

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Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear premRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the "microRNA sponge" function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.

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“…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 proteins have two sets of zinc finger domains that are proposed to bind to RNA on opposing faces of the domain (13,14). Teplova and Patel (15) published a crystal structure of one of the zinc finger domains of MBNL1 in complex with a YGCYcontaining RNA, showing that MBNL1 interacts with the Watson-Crick face of the GC dinucleotide.…”

mentioning

confidence: 99%

“…MBNL proteins have two sets of zinc finger domains that are proposed to bind to RNA on opposing faces of the domain (13,14). Teplova and Patel (15) published a crystal structure of one of the zinc finger domains of MBNL1 in complex with a YGCYcontaining RNA, showing that MBNL1 interacts with the Watson-Crick face of the GC dinucleotide.…”

mentioning

confidence: 99%

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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MBNL1–RNA Recognition: Contributions of MBNL1 Sequence and RNA Conformation

Cited by 34 publications

References 55 publications

Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Regulatory Events

Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Regulatory Events

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

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

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