Analysis of the regulation of viral transcription.
Despite the small genomes and number of genes of papillomaviruses, regulation of their transcription is very complex and governed by numerous transcription factors, cis-responsive elements, and epigenetic phenomena. This chapter describes the strategies of how one can approach a systematic analysis of these factors, elements, and mechanisms. From the numerous different techniques useful for studying transcription, we describe in detail three selected protocols of approaches that have been relevant in shaping our knowledge of human papillomavirus transcription. These are DNAse I protection ("footprinting") for location of transcription-factor binding sites, electrophoretic mobility shifts ("gelshifts") for analysis of bound transcription factors, and bisulfite sequencing for analysis of DNA methylation as a prerequisite for epigenetic transcriptional regulation.
Gloss
Bernd
B
Neurotransgenic Laboratory, Duke University Medical Center, Durham, NC, USA.
Kalantari
Mina
M
Bernard
Hans-Ulrich
HU
D045744:Cell Line, Tumor; D018983:DNA Footprinting / Q000379:methods; D004279:DNA, Viral / Q000235:genetics; D003850:Deoxyribonuclease I; D005260:Female; D015967:Gene Expression Regulation, Viral; D017930:Genes, Reporter; D016679:Genome, Viral; D006367:HeLa Cells; D006801:Humans; D027383:Papillomaviridae / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014162:Transfection
D004279:DNA, Viral; D014157:Transcription Factors; D003850:Deoxyribonuclease I