Honors & Awards

  • Postdoctoral Fellowship, Walter V. and Idun Berry (2016-2019)
  • Graduate Research Fellowship, National Science Foundation (2010-2013)

Professional Education

  • Doctor of Philosophy, University of Washington (2014)

Stanford Advisors


All Publications

  • Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states NATURE GENETICS Kadoch, C., Williams, R. T., Calarco, J. P., Miller, E. L., Weber, C. M., Braun, S. M., Pulice, J. L., Chory, E. J., Crabtree, G. R. 2017; 49 (2): 213-222


    The opposition between Polycomb repressive complexes (PRCs) and BAF (mSWI/SNF) complexes has a critical role in both development and disease. Mutations in the genes encoding BAF subunits contribute to more than 20% of human malignancies, yet the underlying mechanisms remain unclear, owing largely to a lack of assays to assess BAF function in living cells. To address this, we have developed a widely applicable recruitment assay system through which we find that BAF opposes PRC by rapid, ATP-dependent eviction, leading to the formation of accessible chromatin. The reversal of this process results in reassembly of facultative heterochromatin. Surprisingly, BAF-mediated PRC eviction occurs in the absence of RNA polymerase II (Pol II) occupancy, transcription, and replication. Further, we find that tumor-suppressor and oncogenic mutant BAF complexes have different effects on PRC eviction. The results of these studies define a mechanistic sequence underlying the resolution and formation of facultative heterochromatin, and they demonstrate that BAF opposes PRC on a minute-by-minute basis to provide epigenetic plasticity.

    View details for DOI 10.1038/ng.3734

    View details for Web of Science ID 000393148600010

    View details for PubMedID 27941796

  • Histone variants: dynamic punctuation in transcription. Genes & development Weber, C. M., Henikoff, S. 2014; 28 (7): 672-682


    Eukaryotic gene regulation involves a balance between packaging of the genome into nucleosomes and enabling access to regulatory proteins and RNA polymerase. Nucleosomes are integral components of gene regulation that restrict access to both regulatory sequences and the underlying template. Whereas canonical histones package the newly replicated genome, they can be replaced with histone variants that alter nucleosome structure, stability, dynamics, and, ultimately, DNA accessibility. Here we consider how histone variants and their interacting partners are involved in transcriptional regulation through the creation of unique chromatin states.

    View details for DOI 10.1101/gad.238873.114

    View details for PubMedID 24696452

  • Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Molecular cell Weber, C. M., Ramachandran, S., Henikoff, S. 2014; 53 (5): 819-830


    Nucleosomes are barriers to transcription in vitro; however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA polymerase II (RNAPII) at nucleotide resolution. We find that the entry site of the first (+1) nucleosome is a barrier to RNAPII for essentially all genes, including those undergoing regulated pausing farther upstream. In contrast to the +1 nucleosome, gene body nucleosomes are low barriers and cause RNAPII stalling both at the entry site and near the dyad axis. The extent of the +1 nucleosome barrier correlates with nucleosome occupancy but anticorrelates with enrichment of histone variant H2A.Z. Importantly, depletion of H2A.Z from a nucleosome position results in a higher barrier to RNAPII. Our results suggest that nucleosomes present significant, context-specific barriers to RNAPII in vivo that can be tuned by the incorporation of H2A.Z.

    View details for DOI 10.1016/j.molcel.2014.02.014

    View details for PubMedID 24606920

  • Transcribing through the nucleosome. Trends in biochemical sciences 2014; 39 (12): 577–86


    The packaging of DNA into chromatin limits sequence accessibility, which affects all DNA-based processes including transcription. Indeed, the fundamental unit of chromatin, the nucleosome, presents a strong barrier to transcription in vitro. Since the discovery of the nucleosome barrier, the question of how the RNA polymerase II (Pol II) machinery overcomes nucleosomes at high speeds in vivo has remained a central question in chromatin biology. In this review, we discuss the nature of the nucleosomal barrier to transcription and highlight recent findings that provide new insights into the mechanism of transcription through nucleosomes.

    View details for DOI 10.1016/j.tibs.2014.10.004

    View details for PubMedID 25455758

  • Activation of Pax7-Positive Cells in a Non-Contractile Tissue Contributes to Regeneration of Myogenic Tissues in the Electric Fish S. macrurus PLOS ONE Weber, C. M., Martindale, M. Q., Tapscott, S. J., Unguez, G. A. 2012; 7 (5)


    The ability to regenerate tissues is shared across many metazoan taxa, yet the type and extent to which multiple cellular mechanisms come into play can differ across species. For example, urodele amphibians can completely regenerate all lost tissues, including skeletal muscles after limb amputation. This remarkable ability of urodeles to restore entire limbs has been largely linked to a dedifferentiation-dependent mechanism of regeneration. However, whether cell dedifferentiation is the fundamental factor that triggers a robust regeneration capacity, and whether the loss or inhibition of this process explains the limited regeneration potential in other vertebrates is not known. Here, we studied the cellular mechanisms underlying the repetitive regeneration of myogenic tissues in the electric fish S. macrurus. Our in vivo microinjection studies of high molecular weight cell lineage tracers into single identified adult myogenic cells (muscle or noncontractile muscle-derived electrocytes) revealed no fragmentation or cellularization proximal to the amputation plane. In contrast, ultrastructural and immunolabeling studies verified the presence of myogenic stem cells that express the satellite cell marker Pax7 in mature muscle fibers and electrocytes of S. macrurus. These data provide the first example of Pax-7 positive muscle stem cells localized within a non-contractile electrogenic tissue. Moreover, upon amputation, Pax-7 positive cells underwent a robust replication and were detected exclusively in regions that give rise to myogenic cells and dorsal spinal cord components revealing a regeneration process in S. macrurus that is dependent on the activation of myogenic stem cells for the renewal of both skeletal muscle and the muscle-derived electric organ. These data are consistent with the emergent concept in vertebrate regeneration that different tissues provide a distinct progenitor cell population to the regeneration blastema, and these progenitor cells subsequently restore the original tissue.

    View details for DOI 10.1371/journal.pone.0036819

    View details for Web of Science ID 000305338500020

    View details for PubMedID 22685526

  • H2A.Z nucleosomes enriched over active genes are homotypic NATURE STRUCTURAL & MOLECULAR BIOLOGY Weber, C. M., Henikoff, J. G., Henikoff, S. 2010; 17 (12): 1500-U136


    Nucleosomes that contain the histone variant H2A.Z are enriched around transcriptional start sites, but the mechanistic basis for this enrichment is unknown. A single octameric nucleosome can contain two H2A.Z histones (homotypic) or one H2A.Z and one canonical H2A (heterotypic). To elucidate the function of H2A.Z, we generated high-resolution maps of homotypic and heterotypic Drosophila H2A.Z (H2Av) nucleosomes. Although homotypic and heterotypic H2A.Z nucleosomes mapped throughout most of the genome, homotypic nucleosomes were enriched and heterotypic nucleosomes were depleted downstream of active promoters and intron-exon junctions. The distribution of homotypic H2A.Z nucleosomes resembled that of classical active chromatin and showed evidence of disruption during transcriptional elongation. Both homotypic H2A.Z nucleosomes and classical active chromatin were depleted downstream of paused polymerases. Our results suggest that H2A.Z enrichment patterns result from intrinsic structural differences between heterotypic and homotypic H2A.Z nucleosomes that follow disruption during transcriptional elongation.

    View details for DOI 10.1038/nsmb.1926

    View details for Web of Science ID 000284942200016

    View details for PubMedID 21057526

    View details for PubMedCentralID PMC3051840

  • Baculovirus-encoded protein expression for epigenomic profiling in Drosophila cells FLY Bryson, T. D., Weber, C. M., Henikoff, S. 2010; 4 (3): 258-265


    The expression and genome-wide mapping of epitope-tagged DNA- and chromatin-binding proteins in cultured cells has become a powerful strategy for epigenome characterization, especially in Drosophila, where cell lines derived from numerous tissues are now available. However this strategy relies on establishing transfected cell lines, which is time-consuming and introduces variability. Here we show that baculovirus-encoded proteins can be efficiently produced following infection of Drosophila cell lines of different types. Using chromatin affinity purification, we show that epitope-tagged proteins produced in baculovirus-infected cells provide genome-wide profiles of the histone variant H2Av that are comparable to those produced by plasmid-transfected cells. The ability to express multiple epitope-tagged proteins for epigenome analysis from a single culture, and to do this in a variety of Drosophila cell lines, significantly extends the range of epigenome analysis.

    View details for Web of Science ID 000281663500013

    View details for PubMedID 20495356

  • Localization of Synucleins in the Mammalian Cochlea JARO-JOURNAL OF THE ASSOCIATION FOR RESEARCH IN OTOLARYNGOLOGY Akil, O., Weber, C. M., Park, S. N., Ninkina, N., Buchman, V., Lustig, L. R. 2008; 9 (4): 452-463


    Synucleins are widely expressed synaptic proteins within the central nervous system that have been implicated in such neurodegenerative disorders as Parkinson's disease. In this study, an initial characterization of all three synucleins, alpha-, beta-, and gamma-synuclein, within the cochlea was undertaken. Reverse transcriptase-polymerase chain reaction (PCR) demonstrated all three synuclein mRNA species within microdissected cochlear tissue. Quantitative PCR suggests that beta-synuclein is the most abundantly expressed form, followed by gamma- and then alpha-synuclein. Western blot analysis similarly demonstrates all three synuclein proteins within microdissected cochlear tissue. Immunofluorescence localizes the three synucleins predominantly to the efferent neuronal system at the efferent outer hair cell synapse, with some additional localization within the efferent tunnel-crossing fibers (alpha- and gamma-synuclein), spiral ganglion (beta-synuclein), inner spiral bundle (gamma-synuclein), and stria vascularis (alpha- > beta-synuclein). Developmentally, gamma-synuclein can be seen in the region of the outer hair cells by E19, while alpha- and beta-synuclein do not clearly appear there until approximately P10. Additional studies in a null-mutant gamma-synuclein mouse show no histological changes in the organ of Corti with normal hair cell and spiral ganglion cell counts, and normal ABR and DPOAE thresholds in wild-type vs mutant littermates. Together, these results localize synucleins to the efferent cholinergic neuronal auditory system, pointing to a role in normal auditory function, and raising the potential implications for their role in auditory neurodegenerative disorders. However, gamma-synuclein alone is not required for the development and maintenance of normal hearing through P21. Whether overlapping roles of the other synucleins help compensate for the loss of gamma-synuclein remains to be determined.

    View details for DOI 10.1007/s10162-008-0134-y

    View details for Web of Science ID 000260767700005

    View details for PubMedID 18665422

  • Sensorineural deafness and seizures in mice lacking vesicular glutamate transporter 3 NEURON Seal, R. P., Akil, O., Yi, E., Weber, C. M., Grant, L., Yoo, J., Clause, A., Kandler, K., Noebels, J. L., Glowatzki, E., Lustig, L. R., Edwards, R. H. 2008; 57 (2): 263-275


    The expression of unconventional vesicular glutamate transporter VGLUT3 by neurons known to release a different classical transmitter has suggested novel roles for signaling by glutamate, but this distribution has raised questions about whether the protein actually contributes to glutamate release. We now report that mice lacking VGLUT3 are profoundly deaf due to the absence of glutamate release from hair cells at the first synapse in the auditory pathway. The early degeneration of some cochlear ganglion neurons in knockout mice also indicates an important developmental role for the glutamate released by hair cells before the onset of hearing. In addition, the mice exhibit primary, generalized epilepsy that is accompanied by remarkably little change in ongoing motor behavior. The glutamate release conferred by expression of VGLUT3 thus has an essential role in both function and development of the auditory pathway, as well as in the control of cortical excitability.

    View details for DOI 10.1016/j.neuron.2007.11.032

    View details for Web of Science ID 000252758400010

    View details for PubMedID 18215623

  • Distribution of Kv1-like potassium channels in the electromotor and electrosensory systems of the weakly electric fish Apteronotus leptorhynchus JOURNAL OF NEUROBIOLOGY Smith, G. T., Unguez, G. A., Weber, C. M. 2006; 66 (9): 1011-1031


    The electromotor and electrosensory systems of the weakly electric fish Apteronotus leptorhynchus are model systems for studying mechanisms of high-frequency motor pattern generation and sensory processing. Voltage-dependent ionic currents, including low-threshold potassium currents, influence excitability of neurons in these circuits and thereby regulate motor output and sensory filtering. Although Kv1-like potassium channels are likely to carry low-threshold potassium currents in electromotor and electrosensory neurons, the distribution of Kv1 alpha subunits in A. leptorhynchus is unknown. In this study, we used immunohistochemistry with six different antibodies raised against specific mammalian Kv1 alpha subunits (Kv1.1-Kv1.6) to characterize the distribution of Kv1-like channels in electromotor and electrosensory structures. Each Kv1 antibody labeled a distinct subset of neurons, fibers, and/or dendrites in electromotor and electrosensory nuclei. Kv1-like immunoreactivity in the electrosensory lateral line lobe (ELL) and pacemaker nucleus are particularly relevant in light of previous studies suggesting that potassium currents carried by Kv1 channels regulate neuronal excitability in these regions. Immunoreactivity of pyramidal cells in the ELL with several Kv1 antibodies is consistent with Kv1 channels carrying low-threshold outward currents that regulate spike waveform in these cells (Fernandez et al., J Neurosci 2005;25:363-371). Similarly, Kv1-like immunoreactivity in the pacemaker nucleus is consistent with a role of Kv1 channels in spontaneous high-frequency firing in pacemaker neurons. Robust Kv1-like immunoreactivity in several other structures, including the dorsal torus semicircularis, tuberous electroreceptors, and the electric organ, indicates that Kv1 channels are broadly expressed and are likely to contribute significantly to generating the electric organ discharge and processing electrosensory inputs.

    View details for DOI 10.1002/neu.20283

    View details for Web of Science ID 000239544900010

    View details for PubMedID 16779822