Examining Expression Profiles in IncRNA and eRNA
Previously a senior associate member of the Broad Institute, John Rinn, PhD, is now the Leslie Orgel Professor of RNA Science at the University of Colorado Boulder’s BioFrontiers Institute. A leader in RNA biology (John Rinn Biofrontiers), Dr. John Rinn has authored and co-authored several notable papers, including a cover story in Genome Research examining how DNA promoters choose between activity and selectivity.
Both coding and noncoding genomic components are capable of initiating transcription, including IncRNA, such as mRNA or long noncoding RNA core promoters, and enhancer RNAs (eRNA). That said, each class, particularly IncRNA and eRNAs, manifests specific expression profiles for reasons biologists do not fully understand. IncRNA and mRNA core promoters, for example, both demonstrate enhanced capabilities for driving transcription compared to their nondivergent counterparts. Meanwhile, intergenic IncRNAs and eRNAs are less adept at driving transcription and are instead defined by greater tissue specificity than divergent genes.
The paper published in Genome Research Volume 29, Number 3, addressed the complex differences in tissue specificity and expression profiles via an array of computational approaches and massively parallel reporter assays (MPRA), which consisted of hundreds of promoter and enhancer surveys. The paper also validated the assertion that a greater level of tissue specificity is linked with simpler transcription factor profiles in the core promoter. The latter included tests for engineered single-nucleotide deletions, as well as human single-nucleotide polymorphisms.
To read the paper in full, please visit www.genome.cshlp.org.
The Rinn laboratory has also developed a new variant of the MPRA assay, termed massively parallel RNA Assay (MPRNA). In this study the Rinn lab tested thousands of lncRNA sequences for regions that are sufficient to retain genes in the nucleus. To read this paper in full please visit: embo.embopress.org.
John Rinn BioFrontiers: https://www.colorado.edu/biofrontiers/john-rinn
John Rinn University of Colorado Biochemistry: https://www.colorado.edu/biochemistry/john-rinn
John Rinn University of Colorado Profiles: https://profiles.ucdenver.edu/display/15074425
John Rinn University of Colorado Biochemistry: https://www.colorado.edu/biochemistry/john-rinn
John Rinn University of Colorado Profiles: https://profiles.ucdenver.edu/display/15074425
