Terminal loop-mediated regulation of miRNA biogenesis: selectivity and mechanisms

Castilla-Llorente, Virginia; Nicastro, Giuseppe; Ramos, Andrés

doi:10.1042/bst20130058

Cited by 33 publications

(35 citation statements)

References 50 publications

(62 reference statements)

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“…Since the spatial orientation of RRM1 and RRM2 are also antiparallel, the TAG elements maintain a 5′-3′ polarity relative to the beta sheet surface as the chain transverses the dimer interface 7 . The UP1-DNA structures have provided valuable insights into features of sequence specific nucleic acid recognition; however, they do not explain how hnRNP A1 interacts with its RNA targets that do not typically exist as linear strands but instead adopt complex secondary and tertiary structures 8; 9; 10; 11; 12; 13 .…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, hnRNP A1 binds stable RNA stem loop structures to mediate cap independent translation 14; 15; 16 , microRNA biogenesis 9; 10; 11; 12; 13 and alternative splice site selection 8; 17; 18; 19 . RNA chemical protection studies of hnRNP A1 bound to pri-miRNA-18a and HIV splicing silencers show discrete protection patterns, unlike the binding interface observed in UP1-DNA crystal structures 17; 19; 20 .…”

Section: Introductionmentioning

confidence: 99%

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The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein

Morgan

Meagher

Levengood

et al. 2015

Journal of Molecular Biology

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The hnRNP A1 protein is a multifunctional RNA binding protein implicated in a wide range of biological functions. Mechanisms and putative hnRNP A1-RNA interactions have been inferred primarily from the crystal structure of its UP1 domain bound to ssDNA. RNA stem loops represent an important class of known hnRNP A1 targets, yet little is known about the structural basis of hnRNP A1-RNA recognition. Here, we report the first high-resolution structure (1.92 Å) of UP1 bound to a 5′-AGU-3′ trinucleotide that resembles sequence elements of several native hnRNP A1 RNA stem loop targets. UP1 interacts specifically with the AG dinucleotide sequence via a “nucleobase pocket” formed by the beta sheet surface of RRM1 and the inter-RRM linker; RRM2 does not contact the RNA. The inter-RRM linker forms the lid of the nucleobase pocket and we show using structure-guided mutagenesis that the conserved salt bridge interactions (R75:D155 and R88:D157) on the alpha helical side of the RNA binding surface stabilize the linker in a geometry poised to bind RNA. We further investigated the structural basis of UP1 binding HIV SL3ESS3 by determining a SAXS-scored structural model of the complex. UP1 docks on the apical loop of SL3ESS3 using its RRM1 domain and inter-RRM linker only. The biophysical implications of the structural model were tested by measuring kinetic binding parameters, where mutations introduced within the apical loop reduce binding affinities by slowing down the rate of complex formation. Collectively, the data presented here provide the first insights into hnRNP A1-RNA interactions.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein

Morgan

Meagher

Levengood

et al. 2015

Journal of Molecular Biology

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“…Even those clustered on the same primary transcript can be differentially processed in a tissue-specific manner 3-5 . Over the past decade, it has been shown that specific sequences and structures of primary and precursor miRNAs can be recognized by processing machineries and protein factors for regulation [16][17][18][19][20][21][22][23][24][25][26] . For example, pri-miRNAs…”

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confidence: 99%

Visualizing a protonated RNA state that modulates microRNA-21 maturation

Baisden

Boyer

Zhao

et al. 2019

Preprint

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MicroRNAs are evolutionarily conserved small, non-coding RNAs that regulate diverse biological processes. Due to their essential regulatory roles, microRNA biogenesis is tightly regulated, where protein factors are often found to interact with specific primary and precursor microRNAs for regulation. Here, using NMR relaxation dispersion spectroscopy and mutagenesis, we reveal that the precursor of oncogenic microRNA-21 exists as a pH-dependent ensemble that spontaneously reshuffles the secondary structure of the entire apical stem-loop region, including the Dicer cleavage site. We show that the alternative excited conformation transiently sequesters the bulged adenine into a non-canonical protonated A + -G mismatch, conferring a two-fold enhancement in Dicer processing over its ground conformational state. These results indicate that microRNA maturation efficiency may be encoded in the intrinsic dynamic ensemble of primary and precursor microRNAs, providing potential means of regulating microRNA biogenesis in response to environmental and cellular stimuli. Page 3 MicroRNAs (miRNAs) are highly conserved, small noncoding RNAs that regulate more than 60% of protein coding genes at the post-transcriptional level 1-5 . Most miRNAs are initially transcribed by RNA polymerase II as introns of protein-coding genes or from independent coding genes into long primary transcripts (pri-miRNAs) that feature 5'-end 7-methylguanosine caps and 3'-end poly-A tails 6,7 . In the canonical biogenesis pathway, pri-miRNAs are subsequently processed into ~70 nucleotide precursor hairpins (pre-miRNAs) by the Microprocessor complex, consisting of one RNase III family enzyme, Drosha, and two DiGeorge critical region 8 proteins (DGCR8) 8,9 . Pre-miRNAs are then exported from the nucleus to the cytoplasm by Exportin-5 (Ref. 10) and further processed into ~20 base-pair miRNA/miRNA* duplexes by another RNase III family enzyme, Dicer, in complex with transactivation-responsive RNA binding protein (TRBP) 11,12 . The resulting single-stranded mature miRNA is incorporated into the miRNA-inducing silencing complex (miRISC), which regulates protein expression by repressing translation, promoting deadenylation, and/or cleaving target mRNA 13 .Due to their essential regulatory roles, miRNA biogenesis is tightly regulated to ensure proper gene expression 3-5 , and abnormal miRNA regulation has often been associated with cancer, neurological disorders, cardiovascular diseases and others 14,15 .Remarkably, despite sharing the same set of enzymes in the canonical biogenesis pathway, individual miRNAs exhibit cell-type and cell-state specific expressions. Even those clustered on the same primary transcript can be differentially processed in a tissue-specific manner 3-5 . Over the past decade, it has been shown that specific sequences and structures of primary and precursor miRNAs can be recognized by processing machineries and protein factors for regulation [16][17][18][19][20][21][22][23][24][25][26] . For example, pri-miRNAs

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“…hnRNP A1 can also act as a negative regulator of let-7a processing, by competing with the activator protein KSRP for binding to the pri-let-7a terminal loop 36,37 . In addition to hnRNP A1, several other RBPs recognize the terminal loop of miRNA precursors and influence either positively or negatively their biogenesis at the post-transcriptional level 38 . It was proposed that binding of Lin28 to the terminal loop of pre-let-7 leads to partial melting in the upper part of the stem, which can inhibit processing by both Drosha and Dicer 39 .…”

Section: Discussionmentioning

confidence: 99%

Structural basis for terminal loop recognition and processing of pri-miRNA-18a by hnRNP A1

Kooshapur

Choudhury

Simon³

et al. 2017

Preprint

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Running title: Terminal loop control of miRNA biogenesis not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/178855 doi: bioRxiv preprint first posted online Aug. 23, 2017; 2 Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic and structural basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously described a role for hnRNP A1, an RBP implicated in many aspects of RNA processing, as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, we reveal the mechanistic basis for this stimulatory role of hnRNP A1 by combining integrative structural biology with biochemical and functional assays. We demonstrate that hnRNP A1 forms a 1:1 complex with pri-mir-18a that involves binding of both RNA recognition motifs (RRMs) to cognate RNA sequence motifs in the conserved terminal loop of pri-mir-18a.Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its down-stream processing. Our results highlight terminal loop RNA recognition by RNA-binding proteins as a general principle of miRNA biogenesis and regulation.Keywords: microRNA biogenesis; miR-18a, miR-17-92 cluster; hnRNP A1; nuclear magnetic resonance (NMR); X-ray crystallography; small angle X-ray/neutron scattering (SAXS/SANS); RNA recognition motif (RRM)not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/178855 doi: bioRxiv preprint first posted online Aug. 23, 2017; 3 MicroRNAs (miRNAs, miRs) are a class of highly conserved small non-coding RNAs that play a crucial role in the regulation of gene expression. They are involved in a variety of biological processes including cell growth, proliferation and differentiation 1 . Mature miRNAs are generated by two RNA cleavage steps involving nuclear and cytoplasmic RNase III enzymes (Drosha and Dicer, respectively). Primary miRNA (pri-miRNA or pri-mir) transcripts are cropped by the Microprocessor complex (comprising Drosha and DGCR8) in the nucleus forming ~70 nucleotide (nt) stem-loop precursor miRNAs (pre-miRNAs or pre-mir), which, following export to the cytoplasm, are further processed by Dicer into mature miRNAs (reviewed in 2 ). Many miRNA genes in higher organisms are transcribed together as a cluster 3 . A prototypical example is the miR-17-92 cluster that is encoded as an intronic polycistron on chromosome 13 in humans. This cluster encodes six individual miRNAs that are highly conserved in vertebrates (miR-17, miR-18a, miR-19a, miR-20a, miR-19b-1, miR-92a-1, reviewed in 4 ). The miR-17-92 cluster is frequently amplified a...

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Terminal loop-mediated regulation of miRNA biogenesis: selectivity and mechanisms

Cited by 33 publications

References 50 publications

The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein

The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein

Visualizing a protonated RNA state that modulates microRNA-21 maturation

Structural basis for terminal loop recognition and processing of pri-miRNA-18a by hnRNP A1

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