pages tagged ribosome

in progress

The ITSx software detects ITS sequences from larger rDNA fragments by matching HMMS representing the tail of the 18S, the whole 5.8S and the head of the 28S (?10.1111 2041-210X.12073).

RSS Atom

Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., De Wit, P., Sánchez-García, M., Ebersberger, I., de Sousa, F., Amend, A., Jumpponen, A., Unterseher, M., Kristiansson, E., Abarenkov, K., Bertrand, Y.J.K., Sanli, K., Eriksson, K.M., Vik, U., Veldre, V. and Nilsson, R.H.

Methods Ecol Evol, 4: 914-919. 2013

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data.

Fungal HMMs were computed for a 45-base-pair region of the immediate 3′ end of SSU, the 5′ and 3′ ends of 5.8S, and the 5′ end of LSU [...] The SSU is extracted as everything from the 5′ end of the query sequence to the 3′ end of SSU as indicated by the HMM match; the ITS1 is extracted 1 bp downstream from the end of SSU and 1 bp upstream of the start of 5.8S; and so on. [...] we evaluated the proportion of false positives by generating one million random sequences of 550 bp [...] Zero false-positive ‘ITS’ sequences were detected among the random sequences [...] The extractor cannot identify sequences of SSU, 5.8S or LSU shorter than c. 20 bp (25 bp for consistent performance)

Schlötterer C, Hauser MT, von Haeseler A, Tautz D.

Mol Biol Evol. 1994 May;11(3):513-22. doi:10.1093/oxfordjournals.molbev.a040131

Comparative evolutionary analysis of rDNA ITS regions in Drosophila.

Average substitution rate of 1.2% per million year.

Wolf M, Chen S, Song J, Ankenbrand M, Müller T.

PLoS One. 2013 Jun 24;8(6):e66726. doi:10.1371/journal.pone.0066726

Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept.

The CBC Species Concept

Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K.

Nature. 2020 Sep;585(7824):298-302. doi: 10.1038/s41586-020-2497-0

Nucleolar RNA polymerase II drives ribosome biogenesis.

Active (S2p) Pol II is enriched at InterGenic Spacer (IGS) regions. Pol II inhibition with α-amanitin (AMN) or flavopiridol for 30 min was sufficient to disrupt rRNA processing. IGS noncoding RNAs (ncRNAs) decreased in abundance following Pol I inhibition and increased with Pol II inhibition. Double inhibition decreased their abundance. Pol I transcribed sense intergenic ncRNAs (sincRNAs) and Pol II antisense intergenic ncRNAs (asincRNAs).