Lisa Dailey, PhD

Lisa DaileyAssociate Professor of Microbiology
Ph.D., 1984 New York University

New York University School of Medicine
Department of Microbiology
540 First Ave. MSB252
New York, NY 10016
Office Tel: (212) 263-5836
Lab Tel: (212) 263-5331

Research Theme(s): Stem Cell Biology, Transcriptional Regulation, Transcription Factors, Genomics, Programming, Differentiation, Pluripotency
Keywords: Embryonic Stem Cells, Transcriptional Regulation, Transcription Factors, Chromatin, Functional Elements, Genome, Pluripotency

Research Summary:

Our long-term goal is to understand how the interplay of stage-specific transcription factors, DNA regulatory elements, and epigenetic mechanisms establishes the unique biological features of embryonic stem (ES) cells, and how these mechanisms are dynamically regulated to direct ES cell differentiation along specific lineages. To this end, we have devised a new method for the unbiased, global, functional identification of transcriptional regulatory elements regulating endogenous genes in ES cells, or that become activated as the cells transit along distinct differentiation pathways. These studies aim to expand our knowledge of the transcriptional circuitry of ES cells and their derivatives by

  1. identifying new promoter and enhancer elements,
  2. identifying target genes regulated by these elements,
  3. identifying roles for presently undiscovered, key stage-specific transcription factors (TFs),
  4. defining early events determining lineage-specific ES cell differentiation and,
  5. correlating these activities with stage-specific chromatin modifications.

-Development of a new technology for the FUNCTIONAL identification of novel determinants of the ES cell state and lineage commitment.

The distinguishing properties of ES cells and their differentiated derivatives are largely governed by different sets of core TFs, and a full understanding of these cell states, and the transitions between them, requires the precise identification of the target DNA elements and TFs comprising their distinct transcriptional circuitries.  While the majority of analyses have focused on ChIP-based studies of Oct4, Sox2, and Nanog in ES cells, a multitude of additional factors contributing to pluripotency remain largely uncharacterized, and little is known regarding the TFs and target DNAs mediating the earliest events of lineage specification during the differentiation of ES cells.

To address these challenges, we have developed a new technology allowing the direct, functional isolation of hundreds of stage-specific promoter and enhancer elements from ES cells, and those that become active as ES cells transition towards specific differentiated cell lineages. Further analyses of these functionally-defined elements will allow us to identify the key TFs determining their stage-specific activities.

  Based on the classic observation that active promoter and enhancer elements lie within nucleosome-free regions (NFRs) within cellular chromatin, we devised a simple method for isolating NFR-DNAs in order to enrich for transcriptional regulatory elements that are active within ES cells. Promoter and enhancer elements within this population were identified by cloning the NFRs within a reporter plasmid, and assessing their ability to activate gene transcription in transfected cells. (This work was published in Genome Research and highlighted in Nature Reviews Genetics.)

We have further developed this basic approach for the high-throughput functional identification of new stage-specific regulatory modules, i.e. those active within ES cells or their derivatives. Briefly, we created lentiviral libraries consisting of NFR DNAs isolated from ES cell chromatin and cloned such upstream of a GFP reporter gene within a lentiviral plasmid. GFP expression is dependent on the activity of the inserted NFR DNA fragment. The transcriptional activity of the cloned NFRs is assessed following their transduction into ES cells, differentiating ES cells, Epiblast Stem cells (EpiSCs), or Neural Stem cells (NSCs). Cells displaying differential GFP expression have been isolated using FACS, and the stage-specific regulatory NFR DNAs rescued using PCR. This approach has allowed us to isolate hundreds of promoter- and enhancer elements whose activity is specific to ES cells or becomes activated upon ES cell differentiation. In addition, we have also exploring the application of this approach for the identification of Sox2 target elements that are active in different stem cells, including ES cells, EpiSCs, Trophoblast SCs, and NSCs. Further analyses of this latter group of common elements may provide new insights into regulatory features that are fundamental to the ‘stemness’ of these distinct cell types. Our current and future efforts entail the High-throughput (Illumina) sequencing and subsequent bioinformatic and biochemical characterization of each group of stage-specific regulatory elements to identify the TFs, and accompanying chromatin changes that correlate with their stage-specific activities.

These investigations aim to uncover new regulatory circuits defining the ES cell state, and, more generally, to illuminate novel insights into the mechanisms by which transcription factors determine cell identity and cell fate.

Selected Publications: