The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.

/pdf/rnammer-consistent-and-rapid-annotation-of-ribosomal-rna-q2a3v6i83t.pdf

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

Evolution and functions of long noncoding RNAs

http://bio.gsnu.ac.kr/research/miRNA/RNAss/Mfold/miRNAss_JMB_1999_Mathews.pdf

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.

https://science.sciencemag.org/content/sci/289/5481/905.full.pdf

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

The lin-4 and let-7 antisense RNAs are temporal regulators that control the timing of developmental events in Caenorhabditis elegans by inhibiting translation of target mRNAs. let-7 RNA is conserved among bilaterian animals, suggesting that this class of small RNAs [microRNAs (miRNAs)] is evolutionarily ancient. Using bioinformatics and cDNA cloning, we found 15 new miRNA genes in C. elegans. Several of these genes express small transcripts that vary in abundance during C. elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse.

https://science.sciencemag.org/content/sci/294/5543/862.full.pdf

An Extensive Class of Small RNAs in Caenorhabditis elegans

Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals It is thought to enhance protein synthesis by stabilization of a ribosome structure This paper presents the updated database of 5S rRNA and their genes (5S rDNA) Its short characteristics are presented in the Introduction The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences The database is available on line through the World Wide Web at http://biobasesibchpoznanpl/5SData/

5S Ribosomal RNA Database

The non-coding RNAs database (http:// biobases.ibch.poznan.pl/ncRNA/) contains currently available data on RNAs, which do not have long open reading frames and act as riboregulators. Noncoding RNAs are involved in the specific recognition of cellular nucleic acid targets through complementary base pairing to control cell growth and differentiation. Some of them are connected with several well known developmental and neurobehavioral disorders. We have divided them into four groups. This paper is a short introduction to the database and presents its latest, updated edition.

/pdf/the-non-coding-rnas-as-riboregulators-1r3mgmse7j.pdf

The non-coding RNAs as riboregulators

http://rna-informatics.uga.edu/Readings/universal/ncRNANewFrontierMolMed.pdf

A new frontier for molecular medicine: noncoding RNAs.

BACKGROUND Hypertension is a common disease of the cardiovascular system and one of the main causes of mortality in the world. Its etiopathogenesis and molecular mechanisms are unknown. Epigenetic changes may play a role in its development. Therefore the level of 5-methylcytosine (5mC), a well-known epigenetic marker, was analyzed in DNA from the blood of essential hypertension patients. MATERIAL/METHODS TLC chromatographic analysis of the DNA nucleotide composition was used to determine 5mC levels in blood DNA samples from 60 patients suffering from essential hypertension (30 with stage 1 and 30 with stage 2 hypertension) and 30 control subjects. RESULTS The mean levels of 5mC were 1.80 + or - 0.69 in the healthy subjects, 1.14 + or - 0.48 in all the patients with essential hypertension, 1.29 + or - 0.50 in those with stage 1, and 0.99 + or - 0.42 in those with stage 2 of hypertension. Statistically significant differences in 5mC amount in DNA were observed between the control group and the whole patient group, the control group and each subgroup of patients, and the groups of patients with stage 1 and stage 2 of hypertension. The level of 5mC in the DNA of the essential hypertension patients was independent of clinical and biochemical factors. CONCLUSIONS The level of 5mC in the DNA of patients suffering from essential hypertension is lower than in healthy people and depends of the progression of hypertension.

Global DNA methylation changes in blood of patients with essential hypertension.

Recent analyses of the human genome and available data about the other higher eukaryotic genomes have revealed that, in contrast to Eubacteria and Archaea, only a small fraction of the genetic material (ca 1.5%) codes for proteins. Most of genomic DNA and its RNA transcripts are involved in regulation of gene expression, which can be exerted at either the transcriptional level, controlling whether a gene is transcribed and to what extent, or at the post-translational level, regulating the fate of the transcribed RNA molecules, including their stability, efficiency of their translation and subcellular localization. Noncoding RNA genes produce functional RNA molecules (ncRNAs) rather than encoding proteins. These stable RNAs act by multiple mechanisms such as RNA-RNA base pairing, RNA-protein interactions and intrinsic RNA activity, as well as regulate diverse cellular functions, including RNA processing, mRNA stability, translation, protein stability and secretion. Non-protein-coding RNAs are known to play significant roles. Along with transfer RNAs, ribosomal RNAs and mRNAs, ncRNAs contribute to gene splicing, nucleotide modification, protein transport and regulation of gene expression.

/pdf/noncoding-rna-transcripts-4v1xbhejzb.pdf

Miroslawa Z. Barciszewska

Papers

5S Ribosomal RNA Database

The non-coding RNAs as riboregulators

A new frontier for molecular medicine: noncoding RNAs.

Global DNA methylation changes in blood of patients with essential hypertension.

Noncoding RNA transcripts.