(8-Sept) Below are a list of references that can help introduce you to the topic of metazoan promoter architecture:
-
Hoskins et al., 2011. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032922/ (Note: we will use the data from this study for part of our analysis.)
-
Carninci et al., 2006. Genome-wide analysis of mammalian promoter architecture and evolution. Link: http://www.nature.com/ng/journal/v38/n6/full/ng1789.html
-
FANTOM Consortium et al., 2014. A promoter-level mammalian expression atlas. Link: http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html
-
Lenhard et al., 2012. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Link: http://www.nature.com/nrg/journal/v13/n4/full/nrg3163.html (Note: this is an important review paper.)
-
Raborn et al., 2016. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. http://www.genetics.org/content/early/2016/08/29/genetics.116.193334. (Hote: this is our recent paper, which looks at peaked and broad promoters in Daphnia.)
- Takahashi et al., 2012. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Link: http://www.ncbi.nlm.nih.gov/pubmed/21938627
- Lack et al., 2015. The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population. Link: http://www.genetics.org/content/early/2015/01/27/genetics.115.174664
- Ward and Kellis, 2012. Evidence of abundant purifying selection in humans for recently-acquired regulatory functions. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104271/.
1 van Heeringen et al., 2011. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Link: http://genome.cshlp.org/content/21/3/410.full.pdf
- From NESCENT: http://popgen.nescent.org/StartSNP.html