Bryn Mawr College
Park Science Building, room 222
Department of Biology
Bryn Mawr College
101 N. Merion Avenue
Bryn Mawr, PA 19010-2899
Biology 110 is an introductory-level course, designed to encourage students to explore the field of biology at multiple levels of organization: molecular, cellular, organismal and ecological; Biology 110 will explore these areas of biology through a unifying theme. This year, Biology B110-002 will explore the relationship between phenotype and genotype through analyses of inheritance patterns in families and populations, the underlying molecular basis of phenotypes, and an examination of the regulation and decoding of genetic information that ultimately produces the proteins whose structure/function dictate cellular activity. We will also discuss ethical issues associated with genetic testing. Lecture three hours, laboratory three hours a week. There are no prerequisites for this course, but Quantitative Readiness (QR) is required.
Biology 201 - Genetics
This course focuses on the principles of genetics, including classical genetics, population genetics and molecular genetics. Topics to be covered include the genetic and molecular nature of mutations and phenotypes, genetic mapping and gene identification, chromosome abnormalities, developmental genetics, genome editing and epigenetics. Examples of genetics analyses are drawn from a variety of organisms including Drosophila, C. elegans, mice and humans. Lecture, three hours a week. Prerequisite: BIOL B110 and CHEM B104.
Biology 376 - Integrated Biochemistry and Molecular Biology II
This course is the second semester of Integrated Biochemistry and Molecular Biology. Students will continue investigating macromolecules, molecular pathways and gene regulation through lecture, critical reading and discussion of primary literature and laboratory experimentation. Three hours of lecture, three hours of laboratory per week. Prerequisites: Biology 201 - Genetics or Biology 375 - Integrated Biochemistry and Molecular Biology I or permission of instructor.
Biology 393 - Senior Seminar in Molecular Genetics
This seminar course focuses on topics of current interest and significance in genetics, molecular genetics and genomics. Topics vary, and may include the characterization of functional DNA elements, the effects of allelic variation, mechanisms of gene regulation, and/or genetics as a tool for understanding development. Students investigate topics of interest through critical reading of primary literature and hone written and oral communication skills via the presentation and discussion of scientific information and ideas. In addition, students write, defend, and publicly present one long research paper. Three hours of discussion per week, supplemented by regular meetings with individual students. Prerequisites: BIOL 201 or Biology 271 or Biology 376, or permission of instructor.
Biology 399 - Senior Seminar in Laboratory Investigations (taught every spring by various members of the Biology Department)
This seminar provides students with a collaborative forum to facilitate the exchange of ideas and broaden their perspective and understanding of research approaches used in various sub-disciplines of biology. There will be a focus on the presentation, interpretation and discussion of data, and communication of scientific findings to diverse audiences. In addition, students write, defend and publicly present a paper on their supervised research project. Three hours of class discussion each week. Co-requisite: enrollment in BIOL403.
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My lab focuses on understanding the mechanism of genomic imprinting. Genomic imprinting is a mammalian-specific phenomenon whereby the expression of a subset of genes depends on their parental origin. In other words, although we inherit one copy of every gene from our mothers and one copy from our fathers, there are a small number of genes for which only the maternally inherited copy is expressed and a small number for which only the paternally inherited copy is expressesd. There are two major consequences of this unusual form of gene regulation. First, mutations in imprinted genes act in a dominant, parent of origin-specific fashion since there is not a second copy whose wild-type expression can compensate for the mutation. Second, every mammal needs to have a genetic contribution from both a male and a female parent - otherwise, genes critical for normal development will not be expressed. Failure to achieve genomic imprinting can result in developmental disorders such as Beckwith-Wiedemann, Prader-Willi and Angelman syndromes.
One main question in the field of genomic imprinting is: how does the cellular machinery distinguish the maternally inherited allele from the paternally inherited allele so that it knows which copy should be expressed and which copy should remain silent? The simple answer is that the maternal and paternal alleles must be marked so that they appear to be different from each other. To date, the best candidate for the imprinting mark is DNA methylation. In mammals, DNA methylation is a modification of cytosines that are present in CG dinucleotides, such that the cytosines have a methyl group covalently attached at the 5' position. This type of modification is called epigenetic because it is a modification of the DNA structure but does not alter the DNA sequence. The reason DNA methylation stands out as a candidate for the imprinting mark is that most imprinted genes are associated with a region of differential methylation - for example, the silent paternal allele of an imprinted gene may be methylated while the expressed maternal allele is unmethylated.
As mentioned above, all imprinted genes are associated with a primary region of differential DNA methylation which serves as an imprinting control region. However, the precise regulation of imprinted genes requires additional epigenetic modifications, including secondary differentially methylated regions (DMRs) and differential distribution of modified histones on the parental alleles, or copies, of imprinted genes. Secondary DMRs are regions at which differential methylation is not inherited via the gamete; rather, allele-specific methylation at secondary DMRs is acquired post-fertilization. One aspect of my research is focused on understanding when methylation is acquired during embryogenesis, and how these secondary DMRs differ from primary imprinting control regions. To do this, my lab conducts analysis of DNA methylation patterns at imprinted genes during various stages of development in the mouse. Thus far, we have analyzed the acquisition of DNA methylation at secondary DMRs associated with the imprinted genes Cdkn1c, Gtl2 and Dlk1. We have learned that Cdkn1c acquires DNA methylation on its paternal allele at a different developmental stage than Gtl2 and Dlk1, and that the DNA methylation pattern at Dlk1 continues to change during development. These results indicate that there is not a single developmental stage during which allele-specific methylation is established. More recently, we observed that the DNA methylation has an unexpected high level of asymmetry on the complementary strands of the Dlk1 gene. We are currently conducting experiments to determine if this asymmetry is unique to Dlk1 or whether it is a common feature of secondary DMRs, and to determine the biochemical basis for this asymmetry.
While it is clear that DNA methylation plays a role in regulating the expression of imprinted genes, it is also clear that differential DNA methylation cannot be the only factor distinguishing the maternal and paternal alleles from each other. Rasgrf1 is an imprinted gene at which the paternal allele is marked with DNA methylation. However, the DNA methylation pattern at Rasgrf1 does not directly correlate with its expression pattern. Rasgrf1 is an example of a tissue-specific imprinted gene: it is expressed solely from the paternally inherited copy in some tissues, such as brain, but is expressed from both the paternal and the maternal copy in other tissues, such as lung. Therefore, there must be other factors responsible for regulating the tissue-specific imprinting of this gene. Histone modification is one candidate that may be playing a role in the complex regulation of Rasgrf1. Histones are proteins that DNA wraps around in order to achieve the first level of chromosome compaction. The addition of different chemical groups, such as methyl and acetyl groups, to histone proteins affects the structure of the chromatin and the degree of DNA compaction. My lab is currently investigating the distribution of modified histones on the parental alleles of Rasgrf1in both imprinted and non-imprinted tissues in order to determine if they play a role in achieving imprinting at this gene.
There are opportunities for student research in my lab during the course of the academic year as well as in the summer.
Students conducting research with me include:
Nana Raymond, class of 2019
Kristian Sumner, class of 2017
Emma Tunstall, class of 2017
image at right: 2014-2015 research team -
we do science!
Kristian, Megan, Katia, Rachel, Carolyne & Nicole
Former research students include:
Jessica Arbon, class of 2014
Anna Arnaudo, class of 2002
Emily Bergbower, class of 2011
Alison Best, class of 2003
Paige De Rosa, class of 2014
Alyson Dymkowski, class of 2004
Carolyne Face, class of 2015
Sara Fielder, class of 2013
Alyssa Gagne, class of 2011
Jennifer Gerfen, class of 2006
Megan Guntrum, class of 2016
Nicole Hamagami, class of 2016
Christina Harview, class of 2009
Lu Mei He, class of 2006
Aimee Heerd, class of 2014
Abby Hochman, class of 2013
Rebecca Joseph, class of 2013
Kirsten Jusewicz-Haidle, class of 2009
Nelly Khaselev, class of 2011
Francesca Marangell, class of 2009
Sadie Marlow, class of 2011
Sarah McCawley, class of 2002
Kayla McDaniel, class of 2012
Lauren McNelly, class of 2012
Snehal Naik, class of 2003
Anuja Ogirala, class of 2001
Yaena Park, class of 2008
Stephanie Pollack, class of 2008
Charlotte Rahn-Lee, class of 2005
Amelie Raz, class of 2011
Sarah Schnellbacher, class of 2013
Rachel Shields, class of 2015
Geneva Stein, class of 2006
Celia Tong, Haverford College class of 2013
Katia Vlasova, class of 2015
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Gagne, A., Hochman, A., Qureshi, M., Tong, C., Arbon, J., McDaniel, K. and T.L. Davis, 2014, Analysis of DNA methylation acquisition at the imprinted Dlk1 locus reveals asymmetry at CpG dyads, Epigenetics & Chromatin 2014 7:9.
Nowak, K., Stein, G., Powell, E., He, L.M., Naik, S., Morris, J., Marlow, S. and T.L. Davis, 2011, Establishment of paternal allele-specific DNA methylation at the imprinted mouse Gtl2 locus, Epigenetics 6(8): 1012-1020.
Dockery, L., J. Gerfen, C. Harview, C. Rahn-Lee, R. Horton, Y. Park and T.L. Davis, 2009, Differential methylation persists at the mouse Rasgrf1 DMR in tissues displaying monoallelic and biallelic expression, Epigenetics 4(4): 241-247.
Bhogal, B., A. Arnaudo, A. Dymkowski, A. Best and T.L. Davis, 2004,
Methylation at mouse Cdkn1c
is acquired during post-implantation development and functions to
maintain imprinted expression, Genomics
Davis, T.L., G.J. Yang, J. McCarrey and M.S. Bartolomei, 2000, The H19 methylation imprint is erased and reestablished differentially on the parental alleles during male germ cell development, Human Molecular Genetics 9(19): 2885-2894.
Dawes, H.E., D.S. Berlin, D.M. Lapidus, C. Nusbaum, T.L. Davis and B.J. Meyer, 1999, SDC-2 triggers hermaphrodite sexual development and targets nematode dosage compensation machinery to X chromosomes, Science 284(5421): 1800-1804.
Davis, T.L., J.M. Trasler, S.B. Moss, G.J. Yang and M.S. Bartolomei, 1999, Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis, Genomics 58(1): 18-28.
Davis, T.L., K.D. Tremblay and M.S. Bartolomei, 1998, Imprinted expression and methylation of the mouse H19 gene are conserved in extraembryonic lineages, Developmental Genetics 23(2): 111-118.
Davis, T.L. and B.J. Meyer, 1997, SDC-3 coordinates the assembly of a dosage compensation complex on the nematode X chromosome, Development 124(5): 1019-1031.
Davis, T.L., D.R. Helinski, and R.C. Roberts, 1992, Transcription and autoregulation of the stabilizing functions of broad-host-range plasmid RK2 in Escherichia coli, Agrobacterium tumefaciens and Pseudomonas aeruginosa, Molecular Microbiology 6(14): 1981-1994.
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The following is the abstract for a poster presented at the Gordon Research Conference on Epigenetics, August 2-7, 2015.
Analysis of hemimethylation & 5hmC content at primary and secondary DMRs associated with imprinted lociEkaterina Vlasova ('15), Megan Guntrum ('16), Jessica Arbon ('14) and Tamara L. Davis
Differential distribution of DNA methylation on the alleles of imprinted genes functions both to distinguish the alleles based on their parental origin and regulate them to achieve monoallelic expression. DNA methylation at primary differentially methylated regions (DMRs), or imprinting control regions (ICRs) is inherited from the gametes, is consistently maintained on one parental allele throughout development, and functions to modulate expression. In contrast, parent of origin-specific DNA methylation at secondary DMRs is acquired during post-fertilization development; while DNA methylation of these regions is believe to play a role in maintaining imprinted expression, they lack the stability of DNA methylation that is inherited via the gamete. Our analysis of the variable DNA methylation pattern at the mouse Dlk1 gene identified high levels of hemimethylation at individual CpG dyads. We propose that increased levels of hemimethylation at secondary DMRs contribute to the reduced DNA methylation fidelity within these regions. We further propose that increases in 5-hydroxymethylcytosine (5hmC) levels may be responsible for increases in hemimethylation and decreases in DNA methylation fidelity. To test these hypotheses, we are examining CpG dyad methylation patterns and 5hmC content at both primary and secondary DMRs associated with imprinted genes. This poster will describe our recent results and current investigations.
The following is the abstract from
a paper published in 2014 in Epigenetics & Chromatin 2014 7:9.
Analysis of DNA methylation acquisition at the imprinted Dlk1 locus reveals asymmetry at CpG dyads.
Alyssa Gagne ('11), Abigail Hochman ('13), Mahvish Qureshi ('10), Celia Tong ('13), Jessica Arbon ('14), Kayla McDaniel ('12) and Tamara L. Davis
Background: Differential distribution of DNA methylation on the parental alleles of imprinted genes distinguishes the alleles from each other and dictates their parent of origin-specific expression patterns. While differential DNA methylation at primary imprinting control regions is inherited via the gametes, additional allele-specific DNA methylation is acquired at secondary sites during embryonic development and plays a role in the maintenance of genomic imprinting. The precise mechanisms by which this somatic DNA methylation is established at secondary sites are not well defined and may vary as methylation acquisition at these sites occurs at different times for genes in different imprinting clusters. Results: In this study, we show that there is also variability in the timing of somatic DNA methylation acquisition at multiple sites within a single imprinting cluster. Paternal allele-specific DNA methylation is initially acquired at similar stages of post-implantation development at the linked Dlk1 and Gtl2 differentially methylated regions (DMRs). In contrast, unlike the Gtl2-DMR, the maternal Dlk1-DMR acquires DNA methylation in adult tissues. Conclusions: These data suggest that the acquisition of DNA methylation across the Dlk1/Gtl2 imprinting cluster is variable. We further found that the Dlk1 differentially methylated region displays low DNA methylation fidelity, as evidenced by the presence of hemimethylation at approximately one third of the methylated CpG dyads. We hypothesize that the maintenance of DNA methylation may be less efficient at secondary differentially methylated sites than at primary imprinting control regions.
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