Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?

@article{Lee2019LongNR,
  title={Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?},
  author={Hyunmin Lee and Zhaolei Zhang and Henry M. Krause},
  journal={Trends in genetics : TIG},
  year={2019}
}

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

This review reports and integrates numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.

Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

Newly reported information on estrogen-regulated eRNAs and lnc RNAs and their associated biological functions are explored to help outline their markedly prominent roles in estrogen-dependent signaling.

Comparative genomics in the search for conserved long noncoding RNAs

Current advancements and challenges associated with four levels of lncRNA conservation: genomic sequences, splicing signals, secondary structures and syntenic transcription are reviewed.

Mosquito long non-coding RNAs are enriched with Transposable Elements

It is demonstrated that transposable elements substantially contribute to lncRNAs biogenesis in A. albopictus and C. quinquefasciatus and may have an impact on regulatory modulation in these species.

Genomic and functional conservation of lncRNAs: lessons from flies

The features and roles of lncRNAs in the fruit fly Drosophila melanogaster are described, focusing on genomic and functional comparisons with human and mouse lnc RNAs, and the current state of advances and limitations in the study of lNCRNA conservation are discussed.

Pleiotropic fitness effects of the lncRNA Uhg4 in Drosophila melanogaster

Drosophila Uhg4 deletion mutants showed delayed development and decreased viability, and changes in sleep and responses to stress, and Gene ontology analyses highlighted a broad spectrum of biological processes, including regulation of transcription and translation, morphogenesis, and stress response.

Measuring and interpreting transposable element expression

The main challenges associated with the detection of transposable element expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape are highlighted, as well as the different experimental and computational strategies to solve them.

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

The increased accumulation of TEs in the introns of stress-responsive genes of pines is demonstrated and the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs is suggested.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

Evidence is assembled to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences, and hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes.

Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus

The data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level and show that the expression of RE is independent of its copy number in the genome.
...

References

SHOWING 1-10 OF 100 REFERENCES

The Case for Junk DNA

The excitement and subsequent backlash of the ENCODE claims served to illustrate the widespread interest among scientists and nonspecialists in determining how much of the human genome is functionally significant at the organism level.

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs.

An analysis of 3122 long and full-length, noncoding RNAs from the mouse is described, and it is found that these macroRNAs possess the imprint of purifying selection, thereby indicating their functionality.

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

Transposable elements (TEs) are nearly ubiquitous in lncRNAs and have played an important role in the lineage-specific diversification of vertebrate lncRNA repertoires.

Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

Newly reported information on estrogen-regulated eRNAs and lnc RNAs and their associated biological functions are explored to help outline their markedly prominent roles in estrogen-dependent signaling.

Long Noncoding RNAs in Imprinting and X Chromosome Inactivation

This review will discuss what is known about the lncRNAs of major imprinted loci, and the roles they play in the regulation of imprinting.

Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster.

It is proposed that noncoding transcription is of fundamental importance for the opening and maintenance of the active state of HOX clusters.
...