Institute of Molecular Biology

Home | About | Faculty | Calendar | Facilities | Graduate program | Contact | Apply

This page is optimized for viewing with javascript.

Chris Doe

Chris Doe

Professor, Biology
Member, IMB

Ph.D., Stanford University
B.S., New College

Lab website
Office: LISB 303C
Office Phone: 541-346-4877
Lab: LISB Room 302
Lab Phone: 541-346-3041

Loading profile for Chris Doe

Research Interests

We investigate Drosophila CNS development. Current interests are (1) how stem cell-like neural precursors (neuroblasts) establish cell polarity and divide asymmetrically; (2) how neuroblasts maintain stem cell-like features as they divide to produce differentiating progeny; (3) how transcription factors regulate temporal identity within neuroblast lineages; and (4) the genetic program governing the production of motoneurons, serotonergic interneurons, or glia.

Asymmetric cell division of neural precursors

Doe research

Drosophila neural precursors (called neuroblasts) repeatedly divide along their apical/basal axis to regenerate an apical neuroblast and bud off a smaller basal daughter cell (called a GMC) that differentiates into a neurons or glia. Normal asymmetric division requires alignment of the mitotic spindle along the apical/basal axis as well as polarized localization of cell fate determinants to the apical or basal poles of the cell -- which allows two molecularly distinct daughter cells to be produced.

We are interested how neuroblasts establish cell polarity, and how cell polarity is used to generate two different cell types at each cell division. Work from our lab and others has identified basally-localized mRNA and proteins (e.g. prospero RNA and Miranda, Prospero, and Numb proteins) as well as apically-localized proteins (e.g. Baz, Par-6, and aPKC). We have done genetic screens to identify new genes involved in apical protein localization, spindle orientation, and basal protein localization, and have identified 12 loci that are required for one or more of these events. A graduate student in the lab, Sarah Siegrist, has developed methods for timelapse imaging of asymmetric neuroblast division both in vivo and in vitro, which is providing new insights into wild type and mutant cell division phenotypes.

Two former graduate students, Chian-Yu Peng and Roger Albertson, have characterized three basal localization mutants, the previously identified "tumor suppressor genes" lethal giant larvae (lgl), discs large (dlg), and scribble. All three mutants show normal apical protein localization and spindle orientation, but a loss of basal protein targeting. Interestingly, these phenotypes can be suppressed by reducing the level of non-muscle myosin II protein, and mimicked by a pan-myosin inhibitor, leading to a model in which both positive and negative myosins regulate basal transport of Miranda and Numb proteins. A third graduate student, Karsten Siller, is working on the role of the dynactin complex and Lis1 in regulating basal protein targeting and spindle orientation in neuroblasts. Karsten has shown that Lis1 is essential for normal asymmetric division (both basal targeting and spindle orientation). His results are likely to aid in our understanding of the human Lissencephaly phenotype, which has yet to be characterized at the cellular level. Our work on cell polarity and asymmetric cell division has been supported by HHMI and the NIH.

Temporal regulation of cell fate within neuroblast cell lineages

Doe research

Producing the right cells at the right time is essential for normal development, yet it is not well understood how an embryonic precursor cell or a stem cell reproducibly generates a characteristic sequence of different cell types. To begin to study this question, we have done comprehensive cell lineage studies to identify the clone of neurons and glia produced by all 30 different embryonic neuroblasts , as well as the precise birth-order of all progeny for selected neuroblasts. (

We recently showed that nearly all of the 30 different Drosophila neuroblasts in each segment sequentially express the transcription factors Hunchback -> Krüppel -> Pdm -> Castor, raising the possibility of a molecular "clock" for distinguishing GMC birth-order (Isshiki et al., 2001, Cell 106:511). Interestingly, while neuroblast only transiently expressed each gene, the daughter GMCs born during each window of expression maintained expression of that gene as they differentiated. Thus, first-born GMCs maintain Hunchback as they differentiate, whereas second-born GMCs maintain Kruppel as they differentiate. Mutant and misexpression studies show that Hunchback is necessary and sufficient for first-born cell fates, whereas Krüppel is necessary and sufficient for second-born cell fates; we observe this in multiple neuroblast lineages and is independent of the cell type involved. We postulate that Hunchback -> Krüppel -> Pdm -> Castor are "temporal coordinate genes" that act together with "spatial coordinate genes" known to specify each neuroblast identity to uniquely specify the identity of each neuron or glia in the CNS.

Doe research

More recently, Bret Pearson in the lab has shown that Hunchback has the potential to "restart" the lineage of older neuroblasts, revealing a surprising degree of plasticity in neuroblast developmental potential. Bret has also shown that transient expression of Hunchback can produce long-term heritable specification of first-born cell fate, suggesting that Hunchback-mediated chromatin remodeling may be involved in the specification of neuronal temporal identity, similar to the role of Hunchback in establishing heritable HOX gene expression.

Other questions that we are interested in are: Do Pdm and Castor have similar functions in specifying later-born fates? What regulates the timing of the gene expression "clock" that controls Hunchback -> Krüppel -> Pdm -> Castor? And, do hunchback and Krüppel orthologs have similar functions during vertebrate neurogenesis or hematopoiesis?

Generation of motoneuron, interneuron, and glial cell fates

Doe Research

A long-term interest of the lab has been to understand how neural diversity is generated. A graduate student in the lab, Joanne Odden, is investigating how specific types of motoneurons are produced. Her initial work has been on the Drosophila homologue of homeodomain transcription factor HB9/MNR2. Drosophila HB9 is expressed in a subset of motoneurons that project to the lateral body wall muscles; these are distinct from the pool of Eve+ motoneurons that project to dorsal body wall muscles and from a small pool of motoneurons that project to the ventral-most muscles. RNAi and misexpression experiments are consistent with a model that HB9 is necessary and sufficient for motoneuron targeting to lateral muscles. Additional studies on other transcription factors expressed in some or all motoneurons are ongoing.

A postdoctoral fellow in the lab, Marc Freeman, has begun a comprehensive analysis of glial development. Marc is using a novel computational method, microarray technology, and saturation mutagenesis to identify new genes involved in glial development. The computational method identifies putative target genes for the glial cells missing transcription factor, a "master regulator" of glial development. The microarray method looks for genes upregulated following Gcm overexpression in the CNS. These two approaches have already given us over 40 new genes that are involved in glial specification, migration, differentiation, or function. Most of these genes have murine or human orthologs, so it will be interesting to see if they play similar roles in Drosophila and vertebrate gliogenesis.

Recent publications

(pulled from pubmed)

Recent publications

(pulled from pubmed)

The RanGEF Bj1 promotes prospero nuclear export and neuroblast self-renewal.
Joy T, Hirono K, Doe CQ
Dev Neurobiol 2015 May;75(5):485-93
Applying thiouracil tagging to mouse transcriptome analysis.
Gay L, Karfilis KV, Miller MR, Doe CQ, Stankunas K
Nat Protoc 2014 Feb;9(2):410-20
Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.
Heckscher ES, Long F, Layden MJ, Chuang CH, Manning L, Richart J, Pearson JC, Crews ST, Peng H, Myers E, Doe CQ
Development 2014 Jun;141(12):2524-32
Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA.
Gay L, Miller MR, Ventura PB, Devasthali V, Vue Z, Thompson HL, Temple S, Zong H, Cleary MD, Stankunas K, Doe CQ
Genes Dev 2013 Jan 1;27(1):98-115
Developmentally regulated subnuclear genome reorganization restricts neural progenitor competence in Drosophila.
Kohwi M, Lupton JR, Lai SL, Miller MR, Doe CQ
Cell 2013 Jan 17;152(1-2):97-108
Combinatorial temporal patterning in progenitors expands neural diversity.
Bayraktar OA, Doe CQ
Nature 2013 Jun 27;498(7455):449-55
Formin-mediated actin polymerization cooperates with Mushroom body defect (Mud)-Dynein during Frizzled-Dishevelled spindle orientation.
Johnston CA, Manning L, Lu MS, Golub O, Doe CQ, Prehoda KE
J Cell Sci 2013 Oct 1;126(Pt 19):4436-44
A conserved haplotype controls parallel adaptation in geographically distant salmonid populations.
Miller MR, Brunelli JP, Wheeler PA, Liu S, Rexroad CE 3rd, Palti Y, Doe CQ, Thorgaard GH
Mol Ecol 2012 Jan;21(2):237-49
Identification of hunchback cis-regulatory DNA conferring temporal expression in neuroblasts and neurons.
Hirono K, Margolis JS, Posakony JW, Doe CQ
Gene Expr Patterns 2012 Jan-Feb;12(1-2):11-7
Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis.
Carney TD, Miller MR, Robinson KJ, Bayraktar OA, Osterhout JA, Doe CQ
Dev Biol 2012 Jan 1;361(1):137-46
Sgt1 acts via an LKB1/AMPK pathway to establish cortical polarity in larval neuroblasts.
Andersen RO, Turnbull DW, Johnson EA, Doe CQ
Dev Biol 2012 Mar 1;363(1):258-65
Structure of an enzyme-derived phosphoprotein recognition domain.
Johnston CA, Doe CQ, Prehoda KE
PLoS One 2012;7(4):e36014
A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.
Manning L, Heckscher ES, Purice MD, Roberts J, Bennett AL, Kroll JR, Pollard JL, Strader ME, Lupton JR, Dyukareva AV, Doan PN, Bauer DM, Wilbur AN, Tanner S, Kelly JJ, Lai SL, Tran KD, Kohwi M, Laverty TR, Pearson JC, Crews ST, Rubin GM, Doe CQ
Cell Rep 2012 Oct 25;2(4):1002-13
Asymmetric cortical extension shifts cleavage furrow position in Drosophila neuroblasts.
Connell M, Cabernard C, Ricketson D, Doe CQ, Prehoda KE
Mol Biol Cell 2011 Nov;22(22):4220-6
An image-free opto-mechanical system for creating virtual environments and imaging neuronal activity in freely moving Caenorhabditis elegans.
Faumont S, Rondeau G, Thiele TR, Lawton KJ, McCormick KE, Sottile M, Griesbeck O, Heckscher ES, Roberts WM, Doe CQ, Lockery SR
PLoS One 2011;6(9):e24666
Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing.
Johnston CA, Whitney DS, Volkman BF, Doe CQ, Prehoda KE
Proc Natl Acad Sci U S A 2011 Nov 1;108(44):E973-8
Canoe binds RanGTP to promote Pins(TPR)/Mud-mediated spindle orientation.
Wee B, Johnston CA, Prehoda KE, Doe CQ
J Cell Biol 2011 Oct 31;195(3):369-76
A spindle-independent cleavage furrow positioning pathway.
Cabernard C, Prehoda KE, Doe CQ
Nature 2010 Sep 2;467(7311):91-4
TU-tagging: cell type-specific RNA isolation from intact complex tissues.
Miller MR, Robinson KJ, Cleary MD, Doe CQ
Nat Methods 2009 Jun;6(6):439-41
Allosteric control of regulated scaffolding in membrane-associated guanylate kinases.
Marcette J, Hood IV, Johnston CA, Doe CQ, Prehoda KE
Biochemistry 2009 Oct 27;48(42):10014-9
Preview. Stem cell transcriptional loops generate precise temporal identity.
Kohwi M, Doe CQ
Cell Stem Cell 2009 Dec 4;5(6):577-8