Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Spring 5-15-2017 The ffecE ts of the Gut Microbiota on the Host Chromatin Landscape Nicholas Semenkovich Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Biology Commons, Genetics Commons, and the Medicine and Health Sciences Commons Recommended Citation Semenkovich, Nicholas, "The Effects of the Gut Microbiota on the Host Chromatin Landscape" (2017). Arts & Sciences Electronic Theses and Dissertations. 1145. https://openscholarship.wustl.edu/art_sci_etds/1145 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Molecular Genetics and Genomics Dissertation Examination Committee: Jeffrey I. Gordon, Chair Barak Cohen Gautam Dantas Todd Druley Daniel Goldberg Ting Wang The Effects of the Gut Microbiota on the Host Chromatin Landscape by Nicholas Paul Semenkovich A dissertation presented to The Graduate School of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2017 St. Louis, Missouri © 2017, Nicholas Paul Semenkovich Table of Contents List of Figures ................................................................................................................................ iv List of Tables ....................................................................................................................................v Acknowledgments .......................................................................................................................... vi Abstract ......................................................................................................................................... vii Chapter 1 Introduction Introduction ......................................................................................................................................2 Epigenetic interactions between the gut microbiota and its host .........................................2 Potential mechanisms by which the gut influences the host epigenome .............................4 Overview of the thesis .....................................................................................................................6 References ........................................................................................................................................8 Figure legend .................................................................................................................................10 Figure .............................................................................................................................................11 Chapter 2 The impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes Abstract ..........................................................................................................................................14 Significance ....................................................................................................................................14 Results ............................................................................................................................................16 Experimental Design and Approach to Analysis. ..............................................................16 The Super-Enhancer Landscapes of IELs and Circulating T Cells, Independent of Colonization Status. ...........................................................................................................17 Contrasting the Chromatin Landscapes of TCR αβ+ vs. TCR γδ+ IELs, Independent of Colonization Status. ...........................................................................................................19 Chromatin Landscape in TCR αβ+ IELs from CONV-R vs. GF Mice. .............................20 Chromatin Landscape in TCR γδ+ IELs from CONV-R vs. GF Mice. .............................22 Analysis of Enhancers in IELs Purified from CONV-D Mice. ..........................................23 Transcription Factor Regulatory Circuitry. ........................................................................24 ii Discussion ..........................................................................................................................26 References ......................................................................................................................................29 Materials and methods ...................................................................................................................35 Acknowledgments ��������������������������������������������������������������������������������������������������������������������������35 Figure legends ................................................................................................................................36 Figures............................................................................................................................................38 List of tables ...................................................................................................................................40 Supplemental materials ..................................................................................................................44 SI Materials and methods ...............................................................................................................45 Supplemental figure legends ..........................................................................................................54 Supplemental figures ......................................................................................................................58 Chapter 3 Future Directions Future Directions ...........................................................................................................................66 References ......................................................................................................................................69 Appendices Appendix A ....................................................................................................................................72 Appendix B ....................................................................................................................................88 iii List of Figures Figure 1.1: An ATAC-seq analysis overview. ..........................................................................11 Figure 2.1: The effects of colonization on enhancer populations in IELs. ..............................38 Figure 2.2: Analysis of colonization-associated TF circuitry. .................................................39 Figure 2.1.1: FACS sorting strategies and reproducibility of ATAC-seq datasets ..........................................................................................58 Figure 2.1.2: Overview of the RIESLING pipeline. ..........................................59 Figure 2.1.3: The enhancer landscape of TCR αβ+ and TCR γδ+ IELs and peripheral CD4+ and CD8+ T cells, independent of colonization status. ............................................................................................60 Figure 2.1.4: Predicted GeNets communities from both IEL lineages. ..............61 Figure 2.1.5: Enhancer populations distinguish IEL lineages. ...........................62 Figure 2.1.6: Comparison of gut microbial community structure in CONV-R and CONV-D mice. ..............................................................................63 Figure 2.1.7: Track graphs comparing normalized median ATAC-seq signals obtained from analysis of TCR αβ+IELs purified from CONV-R and GF mice. ................................................................................64 iv List of Tables Table 2.1: Dataset S1. Overview of samples and ATAC-seq datasets. Table 2.2: Dataset S2. Super-enhancers identified in all populations, independent of colonization status, rank ordered by signal intensity. Table 2.3: Dataset S3. Pathway analysis within the GeNets-predicted communities from the top IEL super-enhancers. Table 2.4: Dataset S4. Lineage-specific enhancers independent of colonization status. Table 2.5: Dataset S5. Pathway analysis of lineage-specific differentially accessible enhancers independent of colonization status. Table 2.6: Dataset S6. Pathway analysis of genes near predicted enhancers in IEL populations, independent of colonization status. Table 2.7: Dataset S7. Pathway analysis of genes near predicted enhancers in CD4+ and CD8+ T-cell populations, independent of colonization status. Table 2.8: Dataset S8.Differentially accessible regions of chromatin identified comparing GF to CONV-R mice. Table 2.9: Dataset S9. Pathway analysis within the GeNets-predicted communities from the genes adjacent to differentially accessible enhancers identified in IELs purified from CONV-R vs. GF mice. Table 2.10: Dataset S10. GREAT analysis applied to differentially accessible enhancers and their adjacent genes identified in IELs from CONV-R vs. GF mice. Table 2.11: Dataset S11.