In vivostructure probing of RNA inArchaea: Novel insights into the ribosome structure ofMethanosarcina acetivorans

Autor: Allison M. Williams, Elizabeth A. Jolley, Michel Geovanni Santiago-Martínez, Cheong Xin Chan, Robin R. Gutell, James G. Ferry, Philip C. Bevilacqua

Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third dom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f896f7a87ce8fcba82b34e521438e039
https://doi.org/10.1101/2023.04.14.536875

R2DT is a framework for predicting and visualising RNA secondary structure using templates

Autor: Eric P. Nawrocki, Aparna Maddala, Jamie J. Cannone, Robin R. Gutell, Patricia P. Chan, Todd M. Lowe, Blake A. Sweeney, Anton I. Petrov, Caeden D. Meade, David Hoksza, Carlos Eduardo Ribas, Robert D. Finn, Loren Dean Williams, Anton S. Petrov, Fábio Madeira

Publikováno v: Nature Communications
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognis

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d37bfd191b5af38cc3f47593d980d65e
http://europepmc.org/articles/PMC8190129

RNAcentral 2021:Secondary structure integration, improved sequence search and new member databases

Autor: Alex Bateman, Dimitra Karagkouni, Robin R. Gutell, Lina Ma, Ruth C. Lovering, Prita Mani, Artemis G. Hatzigeorgiou, Pieter-Jan Volders, Elspeth A. Bruford, Simon Kay, Kevin J. Peterson, Lauren M. Lui, Steven J Marygold, Todd M. Lowe, Jamie J. Cannone, Anton S. Petrov, Patricia P. Chan, Robert D. Finn, Adam Frankish, Stefan E. Seemann, David Hoksza, Bastian Fromm, Ioanna Kalvari, Maciej Szymanski, Ruth L. Seal, Ruth Barshir, Pieter Mestdagh, Simona Panni, Carlos Eduardo Ribas, Michelle S. Scott, Pablo Porras, Simon Fishilevich, Anton I. Petrov, Sam Griffiths-Jones, Blake A. Sweeney, Zhang Zhang, Jonathan M. Mudge, Zasha Weinberg, Sridhar Ramachandran, Jan Gorodkin, Shuai Weng, Eric P. Nawrocki, Wojciech M. Karlowski, Barbara Kramarz, Philia Bouchard-Bourelle, Gil dos Santos

Publikováno v: Sweeney, B A, Petrov, A I, Ribas, C E, Finn, R D, Bateman, A, Szymanski, M, Karlowski, W M, Seemann, S E, Gorodkin, J, Cannone, J J, Gutell, R R, Kay, S, Marygold, S, Dos Santos, G, Frankish, A, Mudge, J M, Barshir, R, Fishilevich, S, Chan, P P, Lowe, T M, Seal, R, Bruford, E, Panni, S, Porras, P, Karagkouni, D, Hatzigeorgiou, A G, Ma, L, Zhang, Z, Volders, P J, Mestdagh, P, Griffiths-Jones, S, Fromm, B, Peterson, K J, Kalvari, I, Nawrocki, E P, Petrov, A S, Weng, S, Bouchard-Bourelle, P, Scott, M, Lui, L M, Hoksza, D, Lovering, R C, Kramarz, B, Mani, P, Ramachandran, S & Weinberg, Z 2021, ' RNAcentral 2021 : Secondary structure integration, improved sequence search and new member databases ', Nucleic Acids Research, vol. 49, no. D1, pp. D212-D220 . https://doi.org/10.1093/nar/gkaa921
NUCLEIC ACIDS RESEARCH
Nucleic Acids Research

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8e19e03b750a9a147992e2137ae30e05
https://curis.ku.dk/ws/files/259671035/gkaa921.pdf

The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum.

Autor: Jean E Feagin, Maria Isabel Harrell, Jung C Lee, Kevin J Coe, Bryan H Sands, Jamie J Cannone, Germaine Tami, Murray N Schnare, Robin R Gutell

Publikováno v: PLoS ONE, Vol 7, Iss 6, p e38320 (2012)

The mitochondrial genome in the human malaria parasite Plasmodium falciparum is most unusual. Over half the genome is composed of the genes for three classic mitochondrial proteins: cytochrome oxidase subunits I and III and apocytochrome b. The remai

Externí odkaz: https://doaj.org/article/e4730cdfb5f14681b48d38d4787c1a8b

A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions.

Autor: Jung C Lee, Robin R Gutell

Publikováno v: PLoS ONE, Vol 7, Iss 5, p e38203 (2012)

While the majority of the ribosomal RNA structure is conserved in the three major domains of life--archaea, bacteria, and eukaryotes, specific regions of the rRNA structure are unique to at least one of these three primary forms of life. In particula

Externí odkaz: https://doaj.org/article/6d5b60bda2cc40c0a78c505b5eb43627