Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
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Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain. / Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan; Jensen, Mads Krogh; Hansen, Mathias; Gorodkin, Jan; Kjems, Jørgen.
In: Nucleic Acids Research, Vol. 43, No. 21, 02.12.2015, p. 10168-79.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
AU - Sükösd, Zsuzsanna
AU - Andersen, Ebbe Sloth
AU - Seemann, Ernst Stefan
AU - Jensen, Mads Krogh
AU - Hansen, Mathias
AU - Gorodkin, Jan
AU - Kjems, Jørgen
N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2015/12/2
Y1 - 2015/12/2
N2 - A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
AB - A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
U2 - 10.1093/nar/gkv1039
DO - 10.1093/nar/gkv1039
M3 - Journal article
C2 - 26476446
VL - 43
SP - 10168
EP - 10179
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 21
ER -
ID: 160606030