Dataset Information


Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.

ABSTRACT: Lentiviral RNA genomes contain structural elements that play critical roles in viral replication. Although structural features of 5'-untranslated regions have been well characterized, attempts to identify important structures in other genomic regions by Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) have led to conflicting structural and mechanistic conclusions. Previous approaches accounted neither for sequence heterogeneity that is ubiquitous in viral populations, nor for selective constraints operating at the protein level. We developed an approach that augments SHAPE with phylogenetic analyses and applied it to investigate structure in coding regions (cRNA) within the HIV and SIV envelope genes. Analysis of single-genome SHAPE data with phylogenetic information from diverse lentiviral sequences argues against the conservation of a putative global gp120 RNA structure but points to the existence of core RNA sub-structures. Our findings establish a framework for considering sequence heterogeneity and protein function in de novo RNA structure inference approaches.

SUBMITTER: Rife Magalis B 

PROVIDER: S-EPMC6014367 | BioStudies | 2018-01-01

REPOSITORIES: biostudies

Similar Datasets

2003-01-01 | S-EPMC156722 | BioStudies
2019-01-01 | S-EPMC6687061 | BioStudies
2013-01-01 | S-EPMC3884649 | BioStudies
2006-01-01 | S-EPMC1557575 | BioStudies
2015-01-01 | S-EPMC4439019 | BioStudies
2019-01-01 | S-EPMC6441010 | BioStudies
2017-01-01 | S-EPMC5399792 | BioStudies
1000-01-01 | S-EPMC4598872 | BioStudies
2012-01-01 | S-EPMC3367176 | BioStudies
2003-01-01 | S-EPMC309052 | BioStudies