Mapping In Vivo RNA Structures and Interactions.

RNA folds to form diverse secondary and tertiary structures and often interacts with other biomolecules to function in cells. The technologies developed to map in vivo RNA structures and interactions can be broadly classified into four categories.

Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches.

Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level of gene function and regulation. Thus, characterizing the structures and interactions of lncRNAs is essential for understanding their mechanistic roles in cells. Through a combination of (bio)chemical approaches and automated capillary and high-throughput sequencing (HTS), the complexity and diversity of RNA structures and interactions has been revealed in the transcriptomes of multiple species. These methods have uncovered important biological insights into the mechanistic and functional roles of lncRNA in gene expression and RNA metabolism, as well as in development and disease. In this review, we summarize the latest sequencing strategies to reveal RNA structure, RNA-RNA, RNA-DNA, and RNA-protein interactions, and highlight the recent applications of these approaches to map functional lncRNAs. We discuss the advantages and limitations of these strategies, and provide recommendations to further advance methodologies capable of mapping RNA structure and interactions in order to discover new biology of lncRNAs and decipher their molecular mechanisms and implication in diseases.

Structure of the voltage-gated calcium channel Ca(v)1.1 at 3.6 Å resolution.

The voltage-gated calcium (Cav) channels convert membrane electrical signals to intracellular Ca2+-mediated events. Among the ten subtypes of Cav channel in mammals, Cav1.1 is specified for the excitation-contraction coupling of skeletal muscles. Here we present the cryo-electron microscopy structure of the rabbit Cav1.1 complex at a nominal resolution of 3.6 Å. The inner gate of the ion-conducting α1-subunit is closed and all four voltage-sensing domains adopt an 'up' conformation, suggesting a potentially inactivated state. The extended extracellular loops of the pore domain, which are stabilized by multiple disulfide bonds, form a windowed dome above the selectivity filter. One side of the dome provides the docking site for the α2δ-1-subunit, while the other side may attract cations through its negative surface potential. The intracellular I-II and III-IV linker helices interact with the ß1a-subunit and the carboxy-terminal domain of α1, respectively. Classification of the particles yielded two additional reconstructions that reveal pronounced displacement of ß1a and adjacent elements in α1. The atomic model of the Cav1.1 complex establishes a foundation for mechanistic understanding of excitation-contraction coupling and provides a three-dimensional template for molecular interpretations of the functions and disease mechanisms of Cav and Nav channels.

Morphological Description and Potential Geographic Distribution of the Genus Dolichopus Latreille (Diptera, Dolichopodidae, Dolichopodinae) in Inner Mongolia, China.

Eight species of Dolichopus Latreille were previously recorded in Inner Mongolia. However, there have been only a few studies on their potential distribution. Here, three newly discovered species from Inner Mongolia are described, namely Dolichopus (Dolichopus) apicimaculatus sp. nov., Dolichopus (Dolichopus) jiufengensis sp. nov., and Dolichopus (Dolichopus) luae sp. nov. There were also twelve known Dolichopus species that were newly recorded in Inner Mongolia, including the newly recorded subgenus Hygroceleuthus. A key to the Dolichopus species from Inner Mongolia and the potential geographic distribution of Dolichopus in Inner Mongolia were provided. Potential geographic distribution of the genus in Inner Mongolia were determined as well.

The genus Hercostomus Loew (Diptera, Dolichopodidae, Dolichopodinae) from Inner Mongolia, China, with the description of two new species.

Previously, only two species of Hercostomus Loew were known to occur in Inner Mongolia. Here two species from Inner Mongolia are described as new to science, namely Hercostomuschifengensis sp. nov. and Hercostomustriangulatus sp. nov. Three new records of Hercostomus in Inner Mongolia are added. A key to the species of Hercostomus in Inner Mongolia is provided.

Two new Geranomyia Haliday (Diptera, Limoniidae) crane flies from Mount Jiulong in China, with an updated key to Chinese species.

The genus Geranomyia Haliday, 1833 is globally distributed, with 351 known species, of which 26 occur in China. Herein, an overview of the genus Geranomyia from Mount Jiulong, Zhejiang, China, is presented. Two new species are described and illustrated. Geranomyia jiulongensis sp. nov. and G. subablusa sp. nov. are distinguished from other Geranomyia species by the characters of the thorax and male genitalia. An updated key to the Geranomyia of China is presented.

The complete mitochondrial genome and phylogenetic analysis of Tipula (Yamatotipula) nova Walker, 1848 (Diptera, Tipulidae) from Qingdao, Shandong, China.

The genus Tipula Linnaeus, 1758 is a large group of crane flies with more than 2400 known species from 41 subgenera. In this study, we report the first complete mitochondrial (mt) genome sequence of the subgenus Tipula (Yamatotipula), which is a circular molecule of 15,668 bp with an AT content of 77.2%. The mt genome contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a long non-coding region. Three conserved overlapping regions, 8 bp between tRNATrp and tRNACys , 7 bp between ATP8 and ATP6, and 7 bp between ND4 and ND4L, are found. Phylogenetic analysis reveals that the Tipulomorpha includes the family Trichoceridae and the Trichoceridae is sister-group to the remaining Tipulomorpha.