Research Interests

Our studies are centered on the impact of gene regulatory circuits in normal development and disease.  

Our laboratory is interested in how transcriptional and post-transcriptional pathways impact normal development and how they are disrupted in disease. Our research interests overlap with the following fields:

  • RNA
  • Stem cell biology
  • Epigenetics
  • Reproductive biology
  • Developmental biology
  • Neurobiology 
  • Cancer


Nonsense-Mediated RNA Decay.  Biological systems are often controlled by the levels of specific mRNAs, as they encode the repertoire of proteins essential for cellular identify and function.  Not surprisingly, there is tremendous interest in determining how RNA levels are controlled in specific biological contexts, including during development and in disease.  While most focus has been on pathways that control the synthesis of mRNAs cell-graphical-abstract(transcription), the steady-state level of mRNAs are equally dictated by their rate of decay.  Thus, a long-term interest of our laboratory is a conserved and highly selective RNA degradation pathway called nonsense-mediated RNA decay (NMD) (Chang et al. Annu Rev Biochem 2007).   Analogous to how transcription factors control the synthesis of subsets of mRNAs, NMD controls the decay rate of specific subsets of mRNAs.  By collaborating with transcriptional mechanisms, NMD can dramatically up- and down-regulate mRNAs during developmental transitions.  NMD also drives the rapid decline in mRNA levels required for many biological events.  Our recent work has shown that NMD impacts a wide range of processes, including neural development, stress responses, and cancer.  We have identified regulatory factors (e.g., microRNAs and specific proteins) that modulate the magnitude of NMD in order to control developmental processes, as well as feedback mechanisms that buffer NMD from insults.

One of our current interests is to understand the functional role of two NMD gene paralogs—Upf3a and Upf3b—which we discovered have opposing roles in NMD (Shum et al. Cell 2016).  Upf3a encodes a NMD repressor that appears to act as a molecular rheostat to upf3ablastcontrol NMD magnitude during development, while Upf3b encodes an activator of the NMD pathway that when mutated causes intellectual disability (ID) in humans (see upper Fig).  We have shown that Upf3a expression in germ cells is essential for normal male fertility.  Our working hypothesis is that Upf3a represses NMD so that mRNAs encoding proteins essential for male meiosis are stabilized and thus give rise to high levels of protein.  Upf3a is also highly expressed in early embryos (the lower Fig shows UPF3A protein expression in inner cell mass cells in mouse blastocysts).  Consistent with this expression pattern, global loss of Upf3a causes early embryonic lethality.  We are currently investigating why repressed RNA decay is essential for normal embryonic development.  To understand the role of Upf3a’s counterpart—Upf3b—in neural development and function, we have developed a mouse model lacking functional Upf3b.   These NMD-deficient mice exhibit both behavioral and olfactory defects, which we are investigating in depth.   To complement these studies, we are examining the effect of loss of human UPF3B in induced pluripotent stem cells from ID patient with schizophrenia and/or autism, as well as in human embryonic stem cells and neural progenitor cells.



The Rhox homeobox gene cluster.  The first homeobox genes were cloned in the early 1980s—from flies—and shown to be critical developmental regulators.  Soon afterwards, homeobox genes were found to encode transcription factors that regulate critical developmental decisions (as well as a variety of other biological events) in organisms rhox10-bus-low-resolution-002spanning the phylogenetic scale – from yeast to man.  In the midst of this burst of activity, our laboratory identified a novel X-linked homeobox gene—Rhox5—which we found was selectively expressed in a stage- and cell type-specific manner during embryonic development and in the adult reproductive tract in mammals.  Later we found that Rhox5 is part of a giant homeobox gene cluster on the X chromosome that we named the reproductive homeobox (Rhox) gene cluster (MacLean et al. Cell 2005).  All family members of the Rhox gene cluster are selectively expressed in the male and female reproductive tracts in mammals, suggesting that this gene cluster encodes a suite of transcription factors devoted to regulating events in the reproductive system.  The focus of our studies for many years was on mouse Rhox5 (which we originally named “Pem”), which we discovered is an androgen-regulated homeobox gene important for spermatogenesis that encodes a transcription factor that regulates a plethora of genes in Sertoli cells.  Several lines of evidence suggest that Rhox5 is a major mediator of androgen signaling in Sertoli cells, the key somatic cell type that androgens act through to drive spermatogenesis.

Our more recent studies have switched focus to germ cell-expressed Rhox genes, based, in part, on our discovery that most mouse Rhox genes and all human RHOX genes are rhox-image-cropped-002primarily expressed in male and female germ cells.  We recently conditionally knocked out the entire Rhox cluster (33 genes) in male germ cells of mice and found that the most striking phenotype was highly suggestive of a spermatogonial stem cell (SSC) defect (Song et al. Cell Reports 2016).  We subsequently identified the particular Rhox gene responsible—Rhox10—and demonstrated that this homeobox gene drives SSC-precursor cells to differentiate into SSCs (Song et al. Cell Reports 2016).  RHOX10 is the first transcription factor definitively shown to function in SSC establishment.  Given that SSCs are the only self-renewing germ cells in the testis, understanding how they are established and maintained is critical for future clinical applications, including human male infertility therapy.  Our current studies are devoted to (i) elucidating precisely how RHOX10 drives SSC establishment, (ii) identifying the functions of human RHOX transcription factors, and (iii) elucidating conditions to study and manipulate human SSCs towards the future goal of stem cell therapy.