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

PowerPoint Summary

• Lactase Persistence Summary of Molecular Data

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)
• Morales, E., Azocar, L., Maul, X., Perez, C., Chianale, J., & Miquel, J. F. (2011). The European lactase persistence genotype determines the lactase persistence state and correlates with gastrointestinal symptoms in the Hispanic and Amerindian Chilean population: a case–control and population-based study. BMJ open, 1(1), e000125.
• 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
• Schultheis, P. J., & Bowling, B. V. (2011). Analysis of a SNP linked to lactase persistence: An exercise for teaching molecular biology techniques to undergraduates. Biochemistry and Molecular Biology Education, 39(2), 133-140.
• 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
• Weinlander, K. M., Hall, D. J., & De Stasio, E. A. (2010). RFLP analysis and allelic discrimination with real‐time PCR using the human lactase persistence trait. Biochemistry and Molecular Biology Education, 38(3), 167-171.
• Siggers, T., & Gordân, R. (2013). Protein–DNA binding: complexities and multi-protein codes. Nucleic acids research, gkt1112.
• 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 Structure Exercises

POU2F1 (aka OCT-1)

• OCT-1 structures
• POU2F1 UniProt page

Background

In this exercise, you will explore the structure of a the regulatory transcription factor POU2F1 (OCT-1) from human, bound to its regulatory DNA. The binding of POU2F1 to an enhancer upstream of the LCT gene that encodes lactase activates lactase expression. Variants in the enhancer motif are responsible for lactase persistence, which enables humans to digest the milk sugar, lactose, after weaning.

• Klemm, J. D., Rould, M. A., Aurora, R., Herr, W., & Pabo, C. O. (1994). Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell, 77(1), 21-32.
  • behind paywall

Learning objectives

At the end of this exercise, the student should be able to

• define and show the differences between different levels of protein structure: primary, secondary, tertiary, and quaternary.
• locate a domain and explain its relationship to the levels of structure mentioned above
• identify the types of amino acid side chains that interact with the DNA and name the types of weak, noncovalent bonds responsible for the interaction
• describe the relationship of structure to function for POU2F1 and how this relates to lactase persistence

SNP Data and Human Genome Browser

• NCBI Variation Viewer: rs4988235
• NCBI dbSNP: rs4988235
• UCSC genome browser: rs4988235 (via blat search)

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
• pou2f1 entry for mouse in jaspar w/PWM
• PWM for pou2f1 for human from HOCOMOCO
• MotifMap: genome-wide maps of regulatory elements.

• Image Credit: from MotifMap web site (one of 9 motifs)
• list of TF binding site web sites

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
• http://openstaxcollege.org
• MOOC image
• http://wikiseat.org

Assessment

Links from Development of BioSQuARE, an instrument to assess undergraduate biological quantitative skills Jason Belitsky

• QRLA
• BioSQuaRE v4 online, via Qualtrics

Identifying Primer Locations

Primer Locations

• identify forward and reverse primer sequences
• enter both sequences into Human BLAT Search

• identify sequence locations of forward and reverse primers
• identify which primer (forward or reverse) comes before the other by looking at the start and end locations of each primer

• select the region within Chromosome 2 of the Human Genome containing both the forward and reverse primes
  • click the selected region button
  • enter the start location of the first primer and the end location of the second primer

RFLP Analysis

• link to Lambda phage DNA sequence from NEB
• Webcutter 2.0