RNA structures determines

Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo.

16p vialfrednobel 29-01-2022 14 0   Download

Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined.

27p viarchimedes 26-01-2022 4 0   Download

The accurate determination of the genomic coordinates for a given gene – its gene model – is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currentlyavailable methods of computational gene prediction, while on the whole successful, frequently disagree on the model for a given predicted gene, with some or all of the variant gene models often failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq.

18p vibeauty 23-10-2021 7 1   Download

The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development and sex determination have not been comprehensively studied and the lack of complete structure of mRNA transcripts limits further research.

14p visilicon2711 20-08-2021 15 1   Download

Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these parasites, biotrophy is determined by the presence of haustoria, which are specialized structures of parasitism developed by these fungi for the acquisition of nutrients and the delivery of effectors.

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Little is known why proteins and RNAs exhibit half-lives varying over several magnitudes. Despite many efforts, a conclusive link between half-lives and gene function could not be established suggesting that other determinants may influence these molecular attributes.

13p viansan2711 30-07-2021 10 1   Download

RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in the structure, as in the case of riboswitches, and thus the analysis of RNA folding kinetics is crucial for their study.

13p vikentucky2711 26-11-2020 22 1   Download

Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features.

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The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible nonpseudoknotted RNA structures for RNA sequences.

12p viconnecticut2711 29-10-2020 10 2   Download

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov’s classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses.

16p viconnecticut2711 29-10-2020 6 1   Download

RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs.

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RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particular, RNA secondary structures, is critical for elucidating biological functions.

11p vijisoo2711 27-10-2020 9 1   Download

Tomato is widely consumed vegetable in the world. It is used as raw and processed form. Tomato flowers are self as well as controlled pollinated. The crop has more than thirteen species including cultivated and wild types with huge diversity and is susceptible to diverse stress conditions. Recent advances in the biotic and abiotic stress in tomato transcriptomics have been reviewed here. Transcriptome is a particular set of RNA expressed during a stress, developmental stages or a condition in a group of cells.

31p caygaocaolon4 04-04-2020 11 1   Download

The intrachloroplastic localization of post-transcriptional gene expression steps represents one key determinant for the regulation of chloroplast development. We have character-ized an RNA binding protein of 63kDa (RBP63) from Chlamydomonas reinhardtiichloroplasts, which cofraction-ates with stromal thylakoid membranes. Solubility proper-ties suggest that RBP63is a peripheral membrane protein.

8p research12 23-04-2013 32 1   Download

Escherichia coliproteinY (pY) binds to the small ribosomal subunit and stabilizes ribosomes against dissociation when bacteria experience environmental stress. pY inhibits trans-lationin vitro,most probably by interferingwith the binding of the aminoacyl-tRNA to the ribosomal A site. Such a translational arrest may mediate overall adaptation of cells to environmental conditions. We have determined the 3D solution structure of a 112-residue pY and have studied its backbone dynamic by NMRspectroscopy. ...

10p tumor12 22-04-2013 31 1   Download

Rio1 is the founding member of the RIO family of atypical serine kinases that are universally present in all organisms from archaea to mammals. Activity of Rio1 was shown to be absolutely essential inSaccharomyces cerevisiaefor the processing of 18S ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. We determined high-resolution crystal structures ofArchaeoglobus fulgidusRio1 in the presence and absence of bound nucleotides.

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Messenger RNA trafficking, which provides a mechanism for local protein synthesis, is dependent on cis-acting sequences in the 3¢ untranslated regions (3¢UTRs) of the mRNAs concerned acting together withtrans-act-ing proteins. The C-MYC transcription factor is a proto-oncogene product involved in cell proliferation, differentiation and apoptosis. Localization of c-myc mRNA to the perinuclear cytoplasm and its association with the cytoskeleton is determined by a signal in the 3¢UTR.

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DnaG is the primase that lays down RNA primers on single-stranded DNA during bacterial DNA replication. The solution structure of the DnaB-helicase-binding C-terminal domain ofEscherichia coliDnaG was determined by NMR spectroscopy at near-neutral pH. The structure is a rare fold that, besides occurring in DnaG C-terminal domains, has been described only for the N-terminal domain of DnaB.

13p inspiron33 23-03-2013 47 3   Download

In the first half of the talk, the current state of our ongoing structure-function analysis of the mRNA transcription cycle will be dis-cussed. The crystallographic structures of the complete 12-subunit RNA polymerase II in free form and with bound DNA and RNA have been determined as atomic models. The structure of the complete Pol II elongation complex bound by the transcript cleavage factor TFIIS explained how Pol II uses a single tunable active site for both RNA synthesis and RNA cleavage.

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Symposia Lectures Monday Monday, July 9, 2007 A2-L1 J. Diffley No abstract available. A2-L2 Molecular bioimaging of gene transcription P. Cramer Gene Center, Munich, GERMANY In the first half of the talk, the current state of our ongoing structure-function analysis of the mRNA transcription cycle will be discussed. The crystallographic structures of the complete 12-subunit RNA polymerase II in free form and with bound DNA and RNA have been determined as atomic models.

13p galaxyss3 19-03-2013 36 1   Download