Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

@article{Lindgreen2014RobustIO,
  title={Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling},
  author={Stinus Lindgreen and Sinan Uğur Umu and Alicia Sook-Wei Lai and Hisham Eldai and Wenting Liu and Stephanie McGimpsey and Nicole E. Wheeler and Patrick J. Biggs and Nick R. Thomson and Lars Barquist and Anthony M. Poole and Paul P. Gardner},
  journal={PLoS Computational Biology},
  year={2014},
  volume={10}
}
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression… 

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References

SHOWING 1-10 OF 74 REFERENCES

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily

Studying bacterial transcriptomes using RNA-seq

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

It is reported that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain, and the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.

Stem cell transcriptome profiling via massive-scale mRNA sequencing

A massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, is developed, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that the understanding of transcriptional complexity is far from complete.

Approaches to querying bacterial genomes with transposon-insertion sequencing

An overview of studies that have examined the reproducibility and accuracy of these methods, as well as studies showing the advantages offered by the high resolution and dynamic range of high-throughput sequencing over previous methods, are provided.

RNAz 2.0: Improved Noncoding RNA Detection

RNAz 2.0 provides significant improvements in two respects: (1) the accuracy is increased by the systematic use of dinucleotide models, and (2) technical limitations of the previous version are overcome by increased training data and the usage of an entropy measure to represent sequence similarities.

Insights into the phylogeny and coding potential of microbial dark matter

This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.

Regulation by small RNAs in bacteria: expanding frontiers.

...