Williams LAB @ UC Berkeley
Dept. of Plant & Microbial Biology.
Answering fundamental questions in
plant genetics & epigenetics
1. What is epigenetics & how does it work?
Epigenetics is the study of heritable information that is not contained within the DNA sequence of the genome. One example of this is DNA methylation - a reversible chemical modification to DNA that can be added or removed by specialized enzymes. DNA methylation can profoundly affect how a DNA sequence functions. Two genes with identical sequences can produce very different traits, depending on whether or not methylation is added to the DNA. Below is an example of a gene that changes the leaf surface when its DNA methylation is removed:
In the Williams lab, we are interested in understanding how this epigenetic information is regulated and maintained by cells:
How do the enzymes that add and remove DNA methylation find which sequences to act upon with precision?
How do DNA methylation patterns get accurately inherited over many generations?
How do these mechanisms function during the development of tissues and organs?
2. How do cells recognize different DNA sequences?
Each eukaryotic genome contains an enormously complex array of genetic information. DNA sequences can exhibit a huge diversity of functions and regulations. For example, genes encoding proteins can be highly expressed in all cells, or turned on precisely at particular times or in cell types. Repetitive DNA is often transcriptionally silent, as expressing repetitive sequences can cause problems for the cell. We are interested in understanding how the myriad sequences of the genome are perceived:
How is repetitive DNA recognized?
How are important genes protected from silencing?
How do different DNA sequences regulate their epigenetic state?
3. How does epigenetics influence cell identity and regeneration?
Every cell within an organism contains the same genome sequence, yet cells can differentiate into diverse and specialized cell types. The cells of many plant species show an extraordinary ability to be flexible, reversing or changing their specialized cell identity in response to certain conditions. In the Williams lab, we are fascinated by how this happens at the level of perceiving and processing genetic and epigenetic information.
The information to make different cell types is accessible to every cell - so what determines the conditions under which cells can change their state? How are some plant species able to do this much better than others?
Answering these questions could have a large impact on the world, by changing how we can get different plant species to regenerate. Regenerating whole plants from a few cells is a critical part of the process of plant engineering. The inability to regenerate many types of plants is a significant hurdle to our ability to use gene editing technologies (such as CRISPR/Cas9) to improve these plants to meet future challenges. Mitigating the effects of global climate change on agriculture and environments across the world will likely require the creative and nimble use of gene editing, which will require an understanding of how to regenerate gene edited plants. In the Williams lab, we are motivated to help unlock the secrets of plant regeneration to expand our ability to improve important plants to meet global challenges.
Left: shoots of a passion flower plant regenerating in tissue culture. Right: branches regenerating from the trunk of a felled ash tree
Source: Wikimedia commons
Ben Williams - PI
B.A. Biology, Oxford University
Ph.D. Plant Sciences, Cambridge University
Interests: Genetics, Genomics, Synthetic Biology, Innovation
Hobbies: Music, Hiking
Kevin Tran - Lab Manager
B.A. Biology, Carleton College
Interests: Genetics, Development, Microbiology, Queer/Gender Studies, Equality in Education
Hobbies: Theater, Thrift shopping
Clara Williams - Post-Doc
B.Sc. Plant Biology, UC Davis
Ph.D. Biochemistry & Biotechnology, VIB - University of Ghent, Belgium.
Interests: Molecular Biology, Evolution, Epigenetics, Promoting STEM
Hobbies: Yoga, Rock Climbing
Dawei Dai - Post-Doc
B.S. Bioengineering, Xiangtan University, China
Ph.D. Plant Molecular Genetics, Shanghai University, China
Post-doc. Plant Cell & Molecular Biology, University of Florida
Interests: Molecular Genetics, Developmental Biology, Epigenetics
Hobbies: Basketball, Hiking
Kat Smoot - Grad student
B.S. Genetics and Plant Biology, UC Berkeley
Interests: Microscopy, Regeneration, Development
Hobbies: Ballroom Dance, Houseplants, Photography
Anna Dmitrieva - Grad student
B.S. Integrative Biology, University of Illinois at Urbana-Champaign
Interests: Development, Pluripotency, Adaptation, Diversity
Hobbies: Triathlons, Rock Climbing, Podcasts
Connor Tumelty - Undergrad
Intended B.S. Genetics and Plant Biology & B.A. Classical Civilizations, UC Berkeley
Interests: Consuming Media, Political Advocacy
Hobbies: Reading, Video Games
Isabelle Do - Undergrad
Intended B.S. Molecular Environmental Biology & B.S. Business Administration, UC Berkeley
Interests: Plants, Cosmetics, Gene Editing
Hobbies: Video Games, Drinking Boba
Cindy Li - Undergrad
Intended B.S. Microbial Biology & B.S. Nutritional Sciences: Toxicology
Interests: Biotechnology, Genetic Engineering, Nutrition, Zoology, Philosophy, Folklore
Hobbies: Taekwondo, Comics/Manga, Boxing
Elvis Obiorah - Undergrad
Intended B.S. Genetics and Plant Biology, Chemistry minor
Interests: Plants, Dentistry, Snakes
Hobbies: Propagating, K-dramas, Day Dreaming
Hannah Shadmany - Undergrad
Intended B.S. Genetics and Plant Biology & B.A. Molecular and Cell Biology
Interests: Genetic Engineering, Plant Hormones, Epigenetics
Hobbies: Going on Walks, Trying New Restaurants, & Plant Shopping
Gabriel McAdams - Undergrad
Intended B.S. Genetics and Plant Biology, CalTeach minor
Interests: Regeneration, DNA methylation, Plant Pathology
Hobbies: Windsurfing, Gardening, Fermenting
PhD Positions available!
Post-Doc positions available!
Looking to join the team?
email email@example.com for more info!
Mar 2023 - Kat passes her qualifying exam and becomes a Ph.D. candidate! Congrats, Kat!
Feb 2023 - Undergrad Farrah joins the lab. Welcome, Farrah!
Jan 2023 - Undergrad Jingwen joins the lab. Welcome, Jingwen!
Dec 2022 - A new pre-print from our lab is available! Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity | bioRxiv
Oct 2022 - Undergrad Ken joins the lab. Welcome, Ken!
Sep 2022 - Undergrad Gabriel joins the lab. Welcome, Gabriel!
Aug 2022 - Undergrads Hannah and Elvis join the lab. Welcome, Hannah and Elvis!
Jun 2022 - New Post-Doc Dawei Dai joins the lab after working on maize genetics during his Ph.D. at Shanghai University and during a post-doc at the University of Florida. Welcome, Dawei!
Jun 2022 - Clara receives an NSF Postdoctoral fellowship in biology to study epigenetic regulation in callus regeneration using tomato as a model species. Congrats, Clara!
May 2022 - New Ph.D. students Kat and Anna join the lab. Welcome, Kat and Anna!
May 2022 - Ben Williams is named to the 2022-2023 Society of Hellman Fellows! Congrats, Ben! Learn more about this award here.
Sep 2021 - Undergrads Isabelle and Cindy join the lab. Welcome, Isabelle and Cindy!
Mar 2021 - A new pre-print from the lab on the role of DNA demethylases in plants: https://www.biorxiv.org/content/10.1101/2021.03.29.437569v1
Mar 2021 - Post-Doc Clara Williams joins the lab after finishing her Ph.D. at the University of Ghent, Belgium and helping beat covid-19 at the diagnostics lab in Berkeley. Welcome Clara!
Feb 2020 - Plant biology undergrad Connor Tumelty joins the lab. Welcome, Connor!
Nov 2020 - Kevin Tran joins the team after graduating from Carleton College! Welcome, Kevin!
The Williams lab is open! We opened in the Innovative Genomics Institute building at UC Berkeley in the summer of 2020.
We are excited to be recruiting new team members! Post-Doc candidates with an interest in epigenetics, genomics and biochemistry are especially encouraged to apply. Experience working with plants is welcome but not strictly necessary. Email firstname.lastname@example.org for information about positions.
For the most up-to-date list of publications, check Ben Williams' Google Scholar page
Williams, CJ, Dai, DW, Tran, KA, Monroe, JG, Williams, BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity. bioRxiv, 2022-12
Williams, BP, Bechen, LL, Pohlmann, DA, Gehring, M. (2022). Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time. Plant Cell https://doi.org/10.1093/plcell/koab319
Picard, CL, Povilus, RA, Williams, BP, Gehring, M. (2021). Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution. Nat. Plants 7: 730–738.
Williams, BP, Gehring, M (2020). Principals of epigenetic homeostasis shared between flowering plants and mammals. Trends in Genetics. 36(10):751-763.
Reyna-Llorens, I, Burgess, SJ, Reeves, G, Singh, P, Stevenson, SR, Williams, BP, Stanley, S, Hibberd, JM (2018). Ancient duons may underpin spatial patterning of gene expression in C4 leaves. PNAS 115 (8): 1931-1936.
Williams, BP, Gehring, M. (2017). Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit. Nature Communications 8:2124.
Williams, BP*, Burgess, SJ*, Knerova, JN, Reyna-Llorens, I, Stanley, S, Aubry, S, Hibberd, JM (2016). An untranslated cis-element represses accumulation of multiple C4 enzymes in Gynandropsis gynandra bundle sheath cells. Plant Cell 28: 454-465.
Johnston, IG, Williams, BP (2016). Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention. Cell Systems 2:101-111.
Williams, BP, Pignatta, D, Henikoff, S, Gehring, M (2015). Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PloS Genetics 11(3):e1005142.
Eastmond, PJ, Astley, H, Parsley, K, Aubry, S, Williams, BP, Craddock, C, Nunes-Nesi, A, Fernie, AR, Hibberd, JM (2015). Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment. Nature Communications 6:6659.
Williams, BP*, Johnson, IG*, Covshoff, S, Hibberd, JM (2013). Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis. eLife 2:e00961.
Williams, BP, Aubry, S, Hibberd, JM (2012). Molecular evolution of genes recruited into C4 photosynthesis. Trends in Plant Sciences 17:213-220.
Kajala, K, Brown. NJ, Williams, BP, Borrill, P, Taylor, LE, Hibberd, JM (2012). Multiple Arabidopsis genes primed for recruitment into C4 photosynthesis. Plant Journal 69:47-56.