Presentation Title

HHV8 PAN RNA Structure Analysis via SHAPE-MaP

Presenter Information

Tim ReznicekFollow

Advisor Information

William Tapprich

Location

112

Presentation Type

Oral Presentation

Start Date

1-3-2019 10:30 AM

End Date

1-3-2019 11:45 AM

Abstract

Kaposi’s sarcoma-associated herpesvirus (KSHV/human herpesvirus 8/HHV8) is a herpesvirus linked to Kaposi’s sarcoma and two forms of lymph node cancer. HHV8 infects cells and replicates its viral genetic material, creating an RNA transcript with no known protein coding function. The lncRNA encoded by HHV8 is known as polyadenylated nuclear RNA (PAN RNA). PAN RNA has been shown to promote important functions of HHV8, such as gene expression, replication, and immune modulation, despite PAN RNA’s lack of direct protein translation. PAN has been shown to associate with multiple transcription related complexes that promote lytic replication including k-Rta, the driving transcription factor of the HHV8 lytic cycle. Analysis of the structure of the PAN RNA molecule gives perspective on how the molecule performs its role in the lytic cycle. SHAPE-MaP is the most accurate secondary structure analysis method available. The process chemically modifies the 2’ hydroxyl group of nucleotides that are structurally flexible. The modified molecule is then converted into cDNA, where modified nucleotides are mutated in the resulting cDNA. By analyzing the sequence of nucleotides, the shape of the molecule can be inferred through algorithmic analysis. Using the exceptionally accurate SHAPE-MaP method to analyze PAN structure will refine the current understanding of the secondary structure of the molecule.

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Mar 1st, 10:30 AM Mar 1st, 11:45 AM

HHV8 PAN RNA Structure Analysis via SHAPE-MaP

112

Kaposi’s sarcoma-associated herpesvirus (KSHV/human herpesvirus 8/HHV8) is a herpesvirus linked to Kaposi’s sarcoma and two forms of lymph node cancer. HHV8 infects cells and replicates its viral genetic material, creating an RNA transcript with no known protein coding function. The lncRNA encoded by HHV8 is known as polyadenylated nuclear RNA (PAN RNA). PAN RNA has been shown to promote important functions of HHV8, such as gene expression, replication, and immune modulation, despite PAN RNA’s lack of direct protein translation. PAN has been shown to associate with multiple transcription related complexes that promote lytic replication including k-Rta, the driving transcription factor of the HHV8 lytic cycle. Analysis of the structure of the PAN RNA molecule gives perspective on how the molecule performs its role in the lytic cycle. SHAPE-MaP is the most accurate secondary structure analysis method available. The process chemically modifies the 2’ hydroxyl group of nucleotides that are structurally flexible. The modified molecule is then converted into cDNA, where modified nucleotides are mutated in the resulting cDNA. By analyzing the sequence of nucleotides, the shape of the molecule can be inferred through algorithmic analysis. Using the exceptionally accurate SHAPE-MaP method to analyze PAN structure will refine the current understanding of the secondary structure of the molecule.