Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology
Abstract
:1. Introduction
2. Unlocking the KSHV Genome and Insights into KSHV Infection from Host Genomics: The Contributions of Whole-Genome Sequencing, Whole-Exome-Sequencing and Targeted-Sequencing
3. An Atlas of the KSHV Transcriptome: The Contributions of RNA-Sequencing and Small RNA/Non-Coding RNA-Sequencing
3.1. RNA-Sequencing
3.2. Genome-Wide Analysis of the Latent and Lytic KSHV Transcriptomes
3.3. Small RNA/Non-Coding RNA-Sequencing
3.3.1. Role of miRNAs in KSHV Latency and Lytic Reactivation
3.3.2. Role of ncRNAs in KSHV Lytic Reactivation
4. Whole-KSHV Epigenome-Mapping: The Contributions of DNA Methylation-Sequencing, ChIP-Sequencing and FAIRE-Sequencing
4.1. Sequencing of the KSHV Epigenome during de Novo Infection and Latency
4.2. Sequencing of the KSHV and Host Epigenomes during Lytic Reactivation and Replication
5. Conclusions
Acknowledgments
Conflicts of Interest
References
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Gene | Strand | Start–Stop | Small Open Reading Frame (sORF) | Upstream Open Reading Frame (uORF) | New Features |
---|---|---|---|---|---|
ORF6.1 | + | 3027–3203 | - | uORF | - |
ORF6.2 | + | 3150–3203 | - | uORF | - |
ORF10.1 | + | 14,451–14,531 | - | uORF | - |
ORF10.2 | + | 15,574–15,756 | - | - | Internal ORF |
ORF11.1 | + | 15,633–15,722 | - | uORF | - |
ORF11.2 | + | 15,648–15,722 | - | uORF | - |
ORF11.3 | + | 15,693–15,722 | - | uORF | - |
ORF11.4 | + | 15,745–15,756 | - | uORF | - |
ORF11.5 | + | 15,926–15,991 | - | - | Internal ORF |
vIL6.6 | − | 17,873–17,862 | - | uORF | - |
vIL6.5 | − | 17,915–17,877 | - | uORF | - |
vIL6.4 | − | 18,003–17,902 | - | uORF | - |
vIL6.3 | − | 18,047–17,985 | - | uORF | - |
vIL6.2 | − | 18,086–18,057 | - | uORF | - |
vIL6.1 | − | 18,116–18,057 | - | uORF | - |
ORFK3A | − | 19,128–18,589 | - | - | Internal ORF |
ORF70A | − | 21,099–20,038 | - | - | Alternate start |
ORFK4A | − | 21,820–21,743 | - | uORF | - |
ORFK4.1a | − | 22,517–22,416 | sORF | - | - |
ORFK4.1d | − | 22,610–22,545 | sORF | - | - |
ORFK4.1e | − | 22,653–22,627 | sORF | - | - |
ORFK4.1c | − | 22,806–22,723 | sORF | - | - |
ORFK4.1b | − | 22,850–22,545 | sORF | - | - |
1.4KbB | + | 24,871–24,915 | sORF | - | - |
1.4KbC | + | 24,921–25,058 | sORF | - | - |
ORFK5.1 | − | 26,569–26,555 | - | uORF | - |
ORFK6.1 | − | 27,647–27,615 | - | uORF | - |
ORFK6A | − | 27,443–27,087 | - | - | Alternate start |
ORFK6B | − | 27,422–27,087 | - | - | Alternate start |
PAN1.1 | + | 28,655–28,768 | sORF | - | - |
PAN1.2 | + | 28,831–28,965 | sORF | - | - |
PAN1.3 | + | 28,888–28,965 | sORF | - | - |
ORF20A | − | 35,322–34,429 | - | - | Internal ORF |
ORF20B | − | 35,202–34,429 | - | - | Internal ORF |
ORF21.1 | + | 35,151–35,177 | - | uORF | - |
ORF25.1 | + | 42,345–42,380 | - | uORF | - |
ORF28.1 | + | 48,758–48,811 | - | uORF | - |
ORF30.1 | + | 50,317–50,358 | - | uORF | - |
ORF34.1 | + | 54,399–54,485 | - | uORF | - |
ORF35.1 | + | 55,419–55,445 | - | uORF | - |
ORF35.2 | + | 55,442–55,474 | - | uORF | - |
ORF37.1 | + | 57,040–57,126 | - | uORF | - |
ORF38.1 | + | 58,251–58,259 | - | uORF | - |
ORF38.2 | + | 58,455–58,589 | - | uORF | - |
43.1-AS | + | 63,214–63,228 | sORFs | - | - |
ORF43.2-AS | + | 63,254–63,295 | sORFs | - | - |
ORF45.1 | − | 68,447–68,364 | - | uORF | - |
ORF49.1 | − | 72,425–72,384 | - | uORF | - |
ORF50AS | − | 74,222–74,130 | sORF | - | - |
k8.1 short | + | 75,890–75,971 | - | - | Internal ORF |
ORF54A | + | 77,552–78,439 | - | - | Alternate start |
ORF55.1 | − | 79,501–79,340 | - | uORF | - |
ORF57A | + | 81,464–83,453 | - | - | Splice variant |
ORF61.2 | − | 100,071–100,018 | - | uORF | - |
ORF61.1 | − | 100,095–100,018 | - | uORF | - |
ORF62B | − | 101,019–100,018 | - | - | Alternate start |
ORF62A | − | 101,061–100,018 | - | - | Alternate start |
ORF65.1 | − | 112,321–112,289 | - | uORF | - |
ORF69.1 | + | 116,043–116,138 | - | uORF | - |
Kaposin C2 | − | 119,084–117,738 | - | - | Alternate start |
ORF72.1 | − | 124,182–124,108 | - | uORF | - |
ORF75.1 | − | 134,809–134,729 | - | uORF | - |
ORF75.2 | − | 134,894–134,817 | - | uORF | - |
K15.1 | − | 135,938–135,846 | sORF | - | - |
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Strahan, R.; Uppal, T.; Verma, S.C. Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses 2016, 8, 92. https://doi.org/10.3390/v8040092
Strahan R, Uppal T, Verma SC. Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses. 2016; 8(4):92. https://doi.org/10.3390/v8040092
Chicago/Turabian StyleStrahan, Roxanne, Timsy Uppal, and Subhash C. Verma. 2016. "Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology" Viruses 8, no. 4: 92. https://doi.org/10.3390/v8040092
APA StyleStrahan, R., Uppal, T., & Verma, S. C. (2016). Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses, 8(4), 92. https://doi.org/10.3390/v8040092