References
- Lorch Y, Kornberg RD. Chromatin-remodeling for transcription. Q Rev Biophys. 2017;50:e5.
- Kumar MA, Kasti K, Balakrishnan L, et al. Directed nucleosome sliding in SV40 minichromosomes during the formation of the virus particle exposes DNA sequences required for early transcription. J Virol. 2018;93. DOI:10.1128/JVI.01678-18.
- Voong LN, Xi L, Wang JP, et al. Genome-wide mapping of the nucleosome landscape by micrococcal nuclease and chemical mapping. Trends Genet. 2017;33:495–507.
- Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas. 2019;156:29.
- Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10:669–680.
- Balakrishnan L, Milavetz B. Epigenetic analysis of SV40 minichromosomes. Curr Protoc Microbiol. 2017;46:14F 13 11–14F 13 26.
- Kumar MA, Christensen K, Woods B, et al. Nucleosome positioning in the regulatory region of SV40 chromatin correlates with the activation and repression of early and late transcription during infection. Virology. 2017;503:62–69.
- Joshi NA, Fass JN. Sickle - A windowed adaptive trimming tool for FASTQ files using quality. 2011. Available at https://github.com/najoshi/sickle
- Andrews S. FastQC: a quality control for high throughput sequence data. 2010. Available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Buffalo V. Scythe: a bayesian adapter trimmer. 2011. Available at https://github.com/vsbuffalo/scythe
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359.
- HB LH, Wysoker A, Fennell T, et al.; 1000 Genome Project Data Processing Subgroup. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078–2079.
- Ramirez F, Ryan DP, Gruning B, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–165.
- Robinson JT, Thorvaldsdottir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–26.
- Dynan WS, Tjian R. Isolation of transcription factors that discriminate between different promoters recognized by RNA polymerase II. Cell. 1983;32:669–680.
- Dynan WS, Tjian R. The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter. Cell. 1983;35:79–87.
- Barrera-Saldana H, Takahashi K, Vigneron M, et al. All six GC-motifs of the SV40 early upstream element contribute to promoter activity in vivo and in vitro. Embo J. 1985;4:3839–3849.
- Kondoleon SK, Kurkinen NA, Hallick LM. The SV40 nucleosome-free region is detected throughout the virus life cycle. Virology. 1989;173:129–135.
- Scott WA, Wigmore DJ. Sites in simian virus 40 chromatin which are preferentially cleaved by endonucleases. Cell. 1978;15:1511–1518.
- Varshavsky AJ, Sundin OH, Bohn MJ. SV40 viral minichromosome: preferential exposure of the origin of replication as probed by restriction endonucleases. Nucleic Acids Res. 1978;5:3469–3477.
- Kube D, Milavetz B. Generation of a nucleosome-free promoter region in SV40 does not require T-antigen binding to site I. Virology. 1989;172:100–105.