Our Research

laboratory equipment


The goal of the Emerson Lab is to understand the molecular and cellular mechanisms that underlie the development of the vertebrate retina. In particular we focus on cone photoreceptors, which are the cells that mediate the first steps in high acuity and color vision.

Despite their functional importance, our knowledge of the developmental mechanisms involved in cone photoreceptor generation and subsequent differentiation are poorly understood. Some of the questions we seek to answer are as follows:

  • What are the gene-regulatory networks that promote cone photoreceptor genesis from retinal progenitor cells?
  • How is the generation of other cell types coordinated with that of cones?
  • How are cones and the other major photoreceptor type (rods) related developmentally?
By addressing these questions, we will lay the foundation for the development of new therapies for the treatment of retinal diseases with cone photoreceptor loss. This will include new strategies for the de novo generation of cones from stem cells or in vivo retinal cell populations.

cis=regulatory analysis experiment

Cis-Regulatory Analysis

To study the early events in cone photoreceptor genesis, we primarily use a cis-regulatory approach. Cis-regulatory modules, also known as enhancers, are pieces of DNA that recruit sequence-specific transcription factors and affect the regulation of transcription. Candidate enhancers for genes involved in cone photoreceptor genesis or other retinal cell types are identified bioinformatically and tested for the ability to drive cell type specific reporter expression.

Electroporation of reporter constructs into retinal cells in vivo or ex vivo is our preferred method of analysis because of the relative ease, cost, expediency, and reliability of this method. These cis-regulatory modules serve as tools to probe the architecture of genetic regulatory networks, allow for the identification of transient states of cell fate and the targeted isolation of these populations for transcriptome analysis.

dissection photo

Retinal Progenitor Cells with Restricted Cell Fate Potential

Using a cis-regulatory approach, we have recently identified a cis-regulatory element active in a subset of retinal progenitors that preferentially generate cone photoreceptors and horizontal cells. This led us to identify the Otx2 and Onecut1 transcription factors as key co-regulators of this retinal progenitor type. We are currently using whole transcriptome analysis and further cis-regulatory studies to identify the genetic programs that establish this cell state, promote the fates of its daughter cells, and repress alternative retinal fates such as rod photoreceptors.

the City College of New York campus


Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain
Lin CH, Sun Y, Chan CSY, Wu MR, Gu L, Davis AE, Gu B, Zhang W, Tanasa B, Zhong LR, Emerson MM, Chen L, Ding JB, Wang S
Early cis-regulatory events in the formation of retinal horizontal cells
Schick E, Gonzalez KC, Dutta P, Hossain K, Ghinia Tegla MG, Emerson MM
Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states
Chen X, Emerson MM
OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification
Ghinia Tegla MG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori S, Jean-Charles N, Gopal A, Sulaiman S, Gopal S, Wang B, Souferi B, Emerson MM
Identification of genes with enriched expression in early developing mouse cone photoreceptors
Buenaventura DF, Corseri A, Emerson MM
Lineage tracing analysis of cone photoreceptor associated cis-regulatory elements in the developing chicken retina
Schick E, McCaffery SD, Keblish EE, Thakurdin C, Emerson MM
Quantitative analysis of the ThrbCRM1-centered gene regulatory network
Souferi B, Emerson MM
Identification and characterization of early photoreceptor cis-regulatory elements and their relation to Onecut1
Jean-Charles N, Buenaventura DF, Emerson MM
Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells
Buenaventura DF, Ghinia-Tegla MG, Emerson MM
A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina
Wang S, Sengel C, Emerson MM, Cepko CL
Drosophila semaphorin2b is required for the axon guidance of a subset of embryonic neurons
Emerson MM, Long JB, Van Vactor D
Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptor
Emerson MM, Cepko CL
Analysis of thyroid response element activity during retinal development
Billings NA, Emerson MM, Cepko CL
Enabled plays key roles in embryonic epithelial morphogenesis in Drosophila
Gates J, Mahaffey JP, Rogers SL, Emerson M, Rogers EM, Sottile SL, Van Vactor D, Gertler FB, Peifer M
Novel insights into the regulation of the timeless protein
Ashmore LJ, Sathyanarayanan S, Silvestre DW, Emerson MM, Schotland P, Sehgal A
A Drosophila homolog of cyclase-associated proteins collaborates with the Abl tyrosine kinase to control midline axon pathfinding
Wills Z, Emerson M, Rusch J, Bikoff J, Baum B, Perrimon N, Van Vactor D
Robo is Abl to block N-Cadherin function
Emerson MM, Van Vactor D
Structure and evolution of the alternatively spliced fast troponin T isoform gene
Bucher EA, Dhoot GK, Emerson MM, Ober M, Emerson CP
Response of the timeless protein to light correlates with behavioral entrainment and suggests a nonvisual pathway for circadian photoreception
Yang Z, Emerson M, Su HS, Sehgal A
Conserved regions of the timeless (tim) clock gene in Drosophila analyzed through phylogenetic and functional studies
Ousley A, Zafarullah K, Chen Y, Emerson M, Hickman L, Sehgal A