Dahlquist:Evo-Ed Evolution of Lactase Persistence

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This page contains notes from the BioQUEST Curriculumm Consortium Summer Workshop 2015 project on the Evo-Ed Case: The Evolution of Lactase Persistence.

Other Case Studies

• previous case
• previous case

Annotated Bibliography

• Boyd, M., Bressendorff, S., Møller, J., Olsen, J., & Troelsen, J. T. (2009). Mapping of HNF4α target genes in intestinal epithelial cells. BMC gastroenterology, 9(1), 68.
• Fang, L., Ahn, J. K., Wodziak, D., & Sibley, E. (2012). The human lactase persistence-associated SNP− 13910* T enables in vivo functional persistence of lactase promoter–reporter transgene expression. Human genetics, 131(7), 1153-1159. (PubMedCentral)
• Fang, R., Santiago, N. A., Olds, L. C., & Sibley, E. (2000). The homeodomain protein Cdx2 regulates lactase gene promoter activity during enterocyte differentiation. Gastroenterology, 118(1), 115-127.
  • behind paywall
• Gerstein, M. B., Kundaje, A., Hariharan, M., Landt, S. G., Yan, K. K., Cheng, C., ... & Zilberman-Schapira, G. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91-100.
• Grand, R. J., Montgomery, R. K., Chitkara, D. K., & Hirschhorn, J. N. (2003). Changing genes; losing lactase. Gut, 52(5), 617-619.
  • nice review
• Jensen, T. G., Liebert, A., Lewinsky, R., Swallow, D. M., Olsen, J., & Troelsen, J. T. (2011). The− 14010* C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity. Human genetics, 130(4), 483-493.
  • behind paywall
• Kuokkanen, M., Enattah, N. S., Oksanen, A., Savilahti, E., Orpana, A., & Järvelä, I. (2003). Transcriptional regulation of the lactase-phlorizin hydrolase gene by polymorphisms associated with adult-type hypolactasia. Gut, 52(5), 647-652.
• Lewinsky, R. H., Jensen, T. G., Møller, J., Stensballe, A., Olsen, J., & Troelsen, J. T. (2005). T− 13910 DNA variant associated with lactase persistence interacts with Oct-1 and stimulates lactase promoter activity in vitro. Human molecular genetics, 14(24), 3945-3953.
• Linnell, J., Mott, R., Field, S., Kwiatkowski, D. P., Ragoussis, J., & Udalova, I. A. (2004). Quantitative high‐throughput analysis of transcription factor binding specificities. Nucleic acids research, 32(4), e44-e44.
• Mattar, R., de Campos Mazo, D. F., & Carrilho, F. J. (2012). Lactose intolerance: diagnosis, genetic, and clinical factors. Clinical and experimental gastroenterology, 5, 113. (PubMedCentral)
• Olds, L. C., Ahn, J. K., & Sibley, E. (2011). − 13915* G DNA polymorphism associated with lactase persistence in Africa interacts with Oct-1. Human genetics, 129(1), 111-113. (PubMedCentral)
• Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A., & Bejerano, G. (2013). Enhancers: five essential questions. Nature Reviews Genetics, 14(4), 288-295.
• Pruimboom, L., Fox, T., & Muskiet, F. A. (2014). Lactase persistence and augmented salivary alpha-amylase gene copy numbers might have been selected by the combined toxic effects of gluten and (food born) pathogens. Medical hypotheses, 82(3), 326-334.
  • behind paywall
• Sibley, E., & Ahn, J. K. (2011). Theodore E. Woodward Award: lactase persistence SNPs in African populations regulate promoter activity in intestinal cell culture. Transactions of the American Clinical and Climatological Association, 122, 155. (PubMedCentral)
• Stegmann, A., Hansen, M., Wang, Y., Larsen, J. B., Lund, L. R., Ritié, L., ... & Olsen, J. (2006). Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation. Physiological genomics, 27(2), 141-155.
  • Link to database of mouse enterocyte expression data
  • BUT the gene encoding Lactase-phlorizin hydrolase was not on the Affy chip in this dataset.
• Troelsen, J., Mitchelmore, C., Spodsberg, N., Jensen, A., Noren, O., & Sjostrom, H. (1997). Regulation of lactase–phlorizin hydrolase gene expression by the caudal-related homoeodomain protein Cdx-2. Biochem. J, 322, 833-838.
• Troelsen, J. T. (2005). Adult-type hypolactasia and regulation of lactase expression. Biochimica et Biophysica Acta (BBA)-General Subjects, 1723(1), 19-32.
  • behind paywall
• Wang, Z., Fang, R., Olds, L. C., & Sibley, E. (2004). Transcriptional regulation of the lactase-phlorizin hydrolase promoter by PDX-1. American Journal of Physiology-Gastrointestinal and Liver Physiology, 287(3), G555-G561.
• Wang, Z., Maravelias, C., & Sibley, E. (2006). Lactase gene promoter fragments mediate differential spatial and temporal expression patterns in transgenic mice. DNA and cell biology, 25(4), 215-222.
  • behind paywall
• Wilt, T. J., Shaukat, A., Shamliyan, T., Taylor, B. C., MacDonald, R., Tacklind, J., ... & Levitt, M. (2010). Lactose intolerance and health. Evidence Reports/Technology Assessments, No. 192 (NCBI Bookshelf)

Protein Structures

• OCT-1 structures

Gene Regulatory Network

• OCT-1 Gene Regulatory Network in Human
• LCT gene page in NCBI gene database
• http://www.regulatorynetworks.org/ human
• pazar
• oreganno
• Genome-wide map of regulatory interactions in the human genome

Open Education Resources

Links from "Open Education Resources (OER) for science teaching - an evolving landscape" talk by Ahrash Bissell, Monterey Institute for Technology and Education

• http://www.hippocampus.org
• http://www.thenrocproject.org/#/
• http://www.goorulearning.org
• https://www.oercommons.org/
• https://nsdl.oercommons.org/
• http://openrefine.org
• http://learningregistry.org
• http://www.lrmi.net
• http://www.corestandards.org
• http://www.dataone.org
• http://opencontext.org: for archaeology