Kathrin Plath

Professor, Biological Chemistry, University of California Los Angeles

‪(424) 426-0291‬

Laboratory Address:
615 Charles E. Young Drive South
BSRB 35410-14
Los Angeles, CA 90095

Lab Number:
(310) 267-0087

Mailing Address:
615 Charles E. Young Drive South
Department of Biological Chemistry
BSRB 390D
Los Angeles, CA 90095

UC Profile
https://plathlab.dgsom.ucla.edu/pages/

The Plath lab focuses on the epigenetic mechanisms that maintain pluripotency and control differentiation and reprogramming processes. Within this context, we are studying six fundamental problems: (i) How do long-noncoding (lnc) RNAs build nuclear compartments and regulate chromatin changes during differentiation and reprogramming? This aspect of our work particularly centers on understanding how the X chromosome dosage compensation is regulated by the lncRNA Xist in mouse and human. (ii) We are dissecting the cellular decision-making governing reprogramming to induced pluripotency as a means to understand how transcription factors drive cell fate changes and induce new chromatin and gene expression states. (iii) We are examining how the three-dimensional organization of the genome changes during differentiation and reprogramming processes, how transcriptional networks and lncRNAs regulate 3D genome organization, and how 3D genome organization in turn influences gene expression, chromatin states, and lncRNA function. (iv) We are aiming to understand how nutrients that vary with diet can regulate stem cell states and cell fate decisions, particularly those during development, with the ultimate goal to define dietary alterations that enable more accurate models of differentiation in the culture dish or lead to new treatments of pregnancy complications and diseases. (v) We are using embryonic stem cells, induced pluripotent stem cells and new embryo models to understand the gene regulatory networks underlying cellular specification during development and pathophysiologies. (vi) We aim to develop new single cell genomics technologies and to apply them to diverse biological model systems to, for instance, understand the difference between the healthy and disease lung.

Affiliations

Member, Biochemistry, Biophysics & Structural Biology GPB Home Area, Bioinformatics GPB Home Area, CTSI, Cell & Developmental Biology GPB Home Area, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, Gene Regulation GPB Home Area, Molecular Biology Institute
 

Research Interests

The Plath lab aims to understand molecular mechanisms that control genome organization, chromatin states, and gene expression during cell fate changes, with a particular focus on the pluripotent state and pluripotent stem cells, the differentiation of pluripotent stem cells, and reprogramming of somatic cells to pluripotent stem cells. Our team of experimental and computational biologists uses embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC) model systems, state-of-the-art microscopy, biochemistry and mass spectrometry, high throughput screening approaches, gene editing and transgenic/knockout mouse models, genomic approaches (to map patterns of RNA expression at the single cell and population level, open chromatin, DNA methylation, histone modifications, transcription factor binding, three dimensional genome organization, RNA-protein and RNA-chromatin interactions), and computational modelling.

To understand basic principles of gene regulation during cell fate changes and in diseases, we focus on four fundamental problems of mammalian biology that are intimately connected and inform each other:

1. Our lab is studying how one of the two X chromosomes in female mammalian cells is transcriptionally silenced. This chromosome-wide silencing process, called X-inactivation, is initiated when female pluripotent cells differentiate, and represents the most dramatic example of developmentally regulated heterochromatin formation in mammalian cells. X-inactivation is essential for development and equalizes the dose of X-linked genes to that in male cells with their single X chromosome, and leads to cancer if deregulated in the adult. The silencing of the entire X chromosome is orchestrated by Xist, a long non-coding (lnc) RNA. Mammalian genomes encode thousands of lncRNAs, many of which regulate gene expression. While lncRNAs are clearly functionally important, the mechanisms by which they act are still largely elusive. We systematically identify the proteins that interact with Xist, define how Xist RNA spreads along the X chromosome, modifies chromatin states, the three-dimensional architecture of the chromosome and gene expression, and recruits regulatory complexes. Most of our studies are done in the mouse system. Another exciting finding is that the epigenetic regulation of X chromosome dosage differs between mouse and human development. To this end, we have recently established a cell system that allows us to model the human-specific aspects of X chromosome dosage compensation, which also offers insights into early human development. Our findings on Xist RNA and X chromosome dosage compensation are influential for the general understanding of lncRNA function, and guide us in the study of other lncRNAs.

2. We have been among the first to reprogram human differentiated cells to an embryonic stem cell-like state, known as induced pluripotent stem cells (iPSCs), by simply overexpressing four pluripotency-related transcription factors following a strategy first proposed by Shinya Yamanaka in 2006. While it is now clear that differentiated cells can be reprogrammed to iPSCs, the mechanisms by which this occurs are currently largely unknown. An important goal of our lab is to systematically define how the reprogramming factors reset cell identity and determine their interplay with somatic chromatin states and signaling pathways, to understand how cell fate decisions can be modulated. We are particuarly interested in uncovering how enhancers are selected and activated by the reprogramming factors and how somatic cell identity is destabilized by the reprogramming factors. Our work has revealed unexpected mechanisms underlying these processes, which we are now studying further.

3. Another main interest in our lab is to understand the role of the three-dimensional organization of the genome in the regulation of gene expression and developmental identity. DNA is stored in a non-random and highly organized fashion in the nucleus and the 3D-architecture of the genome is beginning to be incorportated in studies of gene regulation. The spatial organization of chromosomes is a fascinating problem of metazoan biology, but many questions have remained unanswered. A particular challenge has been to decipher the mechanisms driving the co-localization of genetic loci and the importance of co-localization. Our goals are to understand how higher-order genome organization is established and dynamically regulated, and how it influences transcriptional networks, chromatin states, and the function of lncRNAs.

4. Finally, we are also interested in understanding how disease states develop. To this end, we are using patient and disease-specific iPSCs to model human diseases and define where deregulation occurs. We are also studying cancer models by defining the cellular heterogeneity and how it develops.

updated 2017

Biography:

Kathrin Plath earned her doctorate degree in cell biology from Humboldt University (Berlin, Germany) for her work with Dr. Tom Rapoport at Harvard Medical School on how the signal sequence of a secretory protein is recognized by the translocation channel in the endoplasmic reticulum membrane. She did her post-doctoral training at the University of California San Francisco and the Whitehead Institute at MIT with Drs. Barbara Panning and Rudolf Jaenisch and support from fellowships of the Life Sciences Research Foundation and the Leukemia and Lymphoma Foundation. In her postdoctoral research, she uncovered that Polycomb proteins can be recruited to their site of action by long non-coding RNAs, and that this group of transcriptional repressors is important for the maintenance of pluripotency and developmental plasticity through the repression of developmental pathways. She joined the faculty of the Department of Biological Chemistry at the University of California Los Angeles in 2006, where her laboratory studies the gene expression controls that operate during cell fate changes. To decode the genetic instructions that orchestrate the conversion of the single cell zygote into a complex organism and uncover broad principles underlying gene regulation, the Plath lab is focusing on cis-regulatory DNA sequences (such as enhancers), long-noncoding RNAs (lncRNAs), and the three-dimensional organization of the genome. Research in her lab in the past few years has focused on four fundamental problems: (a) Differentiation and reprogramming processes as mean to understand how transcription factors interpret cis-regulatory elements in the context of cellular state and signaling milieu. (b) The function of long-noncoding (lnc) RNAs in the regulation of chromatin and gene expression by understanding how lncRNA-protein complexes form, localize to regulatory targets, and give rise to phenotypic states. To achieve this goal, we currently focus on the X-inactivation process and its regulation by the lncRNA Xist, how the X-inactivation process differs between mouse and human pluripotent stem cells, and how the epigenetic state of the X chromosome influences developmental potency. (c) 3D-organization of the genome changes as a means to understand how transcriptional networks regulate genome organization, and how genome organization influences gene expression and chromatin states. (d) The deregulation of gene regulation processes in disease using iPSC disease models. To accomplish these goals, the Plath lab uses a wide range of approaches including proteomics, genomics, genetics, cell biology, and bioinformatics. Dr. Plath serves on the editorial boards of various journals including Science, Cell, Cell Stem Cell, Cell Reports, and is the chair of the publications committee of the International Society for Stem Cell Research. Recently, she was named a Faculty Scholar of the Howard Hughes Medical Institute.

Awards and Honors

  • CIRM Young Investigator Award, 2008.
  • V Foundation Scholar, 2007.
  • Kimmel Foundation Scholar, 2007.
  • HHMI Faculty Scholar Award, 2016.
  • Byk-Gulden Graduate Thesis Award, German Society of Biochemistry, 2000.
  • Postdoctoral Fellowship, Life Sciences Research Foundation, 2001-2004.
  • Undergraduate Fellowship, Humboldt University, Germany, 1989-1990.
  • Special Fellowship, Leukemia and Lymphoma Society, 2004-2007.
  • NIH Director’s New Innovator Award, 2007.
  • Graduate Fellowship, Max-Delbrück-Center, Berlin, Germany, 1995-1998.
  • Junior Scientist Award of the States Berlin and Brandenburg, Germany, 2001.
  • John H. Walsh Young Investigator Research Price, David Geffen School of Medicine, UCLA, 2009.

Publications