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Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships.

ABSTRACT: Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is an abundant nuclear-localized long noncoding RNA (lncRNA) that has significant roles in cancer. While the interacting partners and evolutionary sequence conservation of MALAT1 have been examined, much of the structure of MALAT1 is unknown. Here, we propose a hypothetical secondary structural model for 8425 nucleotides of human MALAT1 using three experimental datasets that probed RNA structures in vitro and in various human cell lines. Our model indicates that approximately half of human MALAT1 is structured, forming 194 helices, 13 pseudoknots, five structured tetraloops, nine structured internal loops, and 13 intramolecular long-range interactions that give rise to several multiway junctions. Evolutionary conservation and covariation analyses support 153 of 194 helices in 51 mammalian MALAT1 homologs and 42 of 194 helices in 53 vertebrate MALAT1 homologs, thereby identifying an evolutionarily conserved core that likely has important functional roles in mammals and vertebrates. Data mining revealed that RNA modifications, somatic cancer-associated mutations, and single-nucleotide polymorphisms may induce structural rearrangements that sequester or expose binding sites for several cancer-associated microRNAs. Our findings reveal new mechanistic leads into the roles of MALAT1 by identifying several intriguing structure-function relationships in which the dynamic structure of MALAT1 underlies its biological functions.

SUBMITTER: McCown PJ

PROVIDER: S-EPMC6888369 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships.

McCown Phillip J PJ Wang Matthew C MC Jaeger Luc L Brown Jessica A JA

International journal of molecular sciences 20191109 22

Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is an abundant nuclear-localized long noncoding RNA (lncRNA) that has significant roles in cancer. While the interacting partners and evolutionary sequence conservation of MALAT1 have been examined, much of the structure of MALAT1 is unknown. Here, we propose a hypothetical secondary structural model for 8425 nucleotides of human MALAT1 using three experimental datasets that probed RNA structures in vitro and in various human ...[more]

PMID: 31717552

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Project description:BackgroundAlthough deformation and fracture of the vertebral endplate have been implicated in spinal conditions such as vertebral fracture and disc degeneration, few biomechanical studies of this structure are available. The goal of this study was to quantify the mechanical behavior of the vertebral endplate.MethodsEight-five rectangular specimens were dissected from the superior and/or inferior central endplates of human lumbar spine segments L1 to L4. Micro-computed tomography (μCT) imaging, four-point-bend testing, and ashing were performed to quantify the apparent elastic modulus and yield stress (modulus and yield stress, respectively, of the porous vertebral endplate), tissue yield stress (yield stress of the tissue of the vertebral endplate, excluding pores), ultimate strain, fracture strain, bone volume fraction (BV/TV), bone mineral density (BMD), and various measures of tissue density and composition (tissue mineral density, ash fraction, and ash density). Regression was used to assess the dependence of mechanical properties on density and composition.ResultsWide variations in elastic and failure properties, and in density and tissue composition, were observed. BMD and BV/TV were good predictors of many of the apparent-level mechanical properties, including modulus, yield stress, and in the case of the inferior vertebral endplate, failure strains. Similar values of the mechanical properties were noted between superior and inferior vertebral endplates. In contrast to the dependence of apparent stiffness and strength on BMD and BV/TV, none of the mechanical properties depended on any of the tissue-level density measurements.ConclusionThe dependence of many of the mechanical properties of the vertebral endplate on BV/TV and BMD suggests possibilities for noninvasive assessment of how this region of the spine behaves during habitual and injurious loading. Further study of the nonmineral components of the endplate tissue is required to understand how the composition of this tissue may influence the overall mechanical behavior of the vertebral endplate.

Dataset Information

Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships.

Publications

Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships.

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