Matthew James McCoy

All Publications

• The genetic basis of novel trait gain in walking fish. bioRxiv : the preprint server for biology Herbert, A. L., Allard, C. A., McCoy, M. J., Wucherpfennig, J. I., Krueger, S. P., Chen, H. I., Gourlay, A. N., Jackson, K. D., Abbo, L. A., Bennett, S. H., Sears, J. D., Rhyne, A. L., Bellono, N. W., Kingsley, D. M. 2023

  Abstract

  A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.

  View details for DOI 10.1101/2023.10.14.562356

  View details for PubMedID 37873105

  View details for PubMedCentralID PMC10592820

• Ancient origins of complex neuronal genes. bioRxiv : the preprint server for biology McCoy, M. J., Fire, A. Z. 2023

  Abstract

  How nervous systems evolved is a central question in biology. An increasing diversity of synaptic proteins is thought to play a central role in the formation of specific synapses leading to nervous system complexity. The largest animal genes, often spanning millions of base pairs, are known to be enriched for expression in neurons at synapses and are frequently mutated or misregulated in neurological disorders and diseases. While many of these genes have been studied independently in the context of nervous system evolution and disease, general principles underlying their parallel evolution remain unknown. To investigate this, we directly compared orthologous gene sizes across eukaryotes. By comparing relative gene sizes within organisms, we identified a distinct class of large genes with origins predating the diversification of animals and in many cases the emergence of dedicated neuronal cell types. We traced this class of ancient large genes through evolution and found orthologs of the large synaptic genes driving the immense complexity of metazoan nervous systems, including in humans and cephalopods. Moreover, we found that while these genes are evolving under strong purifying selection as demonstrated by low dN/dS scores, they have simultaneously grown larger and gained the most isoforms in animals. This work provides a new lens through which to view this distinctive class of large and multi-isoform genes and demonstrates how intrinsic genomic properties, such as gene length, can provide flexibility in molecular evolution and allow groups of genes and their host organisms to evolve toward complexity.

  View details for DOI 10.1101/2023.03.28.534655

  View details for PubMedID 37034725

  View details for PubMedCentralID PMC10081198

• Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integrative and comparative biology Baden, T., Briseño, J., Coffing, G., Cohen-Bodénès, S., Courtney, A., Dickerson, D., Dölen, G., Fiorito, G., Gestal, C., Gustafson, T., Heath-Heckman, E., Hua, Q., Imperadore, P., Kimbara, R., Król, M., Lajbner, Z., Lichilín, N., Macchi, F., McCoy, M. J., Nishiguchi, M. K., Nyholm, S. V., Otjacques, E., Pérez-Ferrer, P. A., Ponte, G., Pungor, J. R., Rogers, T. F., Rosenthal, J. J., Rouressol, L., Rubas, N., Sanchez, G., Santos, C. P., Schultz, D. T., Seuntjens, E., Songco-Casey, J. O., Stewart, I. E., Styfhals, R., Tuanapaya, S., Vijayan, N., Weissenbacher, A., Zifcakova, L., Schulz, G., Weertman, W., Simakov, O., Albertin, C. 2023

  Abstract

  Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single cell transcriptomics, metagenomics and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks and potential solutions. The article highlights the interdisciplinary nature of the cephalopod -omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.

  View details for DOI 10.1093/icb/icad087

  View details for PubMedID 37370232

• MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity. Proceedings of the National Academy of Sciences of the United States of America Lu, Y. L., Liu, Y., McCoy, M. J., Yoo, A. S. 2021; 118 (22)

  Abstract

  Neuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing antineurogenic genes. How these miRNAs function after the repression of fibroblast genes for neuronal fate remains unclear. Here, we identified targets of miR-9/9*-124 as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function. The mode of miR-124 as a positive regulator is determined by the binding of both AGO and a neuron-enriched RNA-binding protein, ELAVL3, to target transcripts. Although existing literature indicates that miRNA-ELAVL family protein interaction can result in either target gene up-regulation or down-regulation in a context-dependent manner, we specifically identified neuronal ELAVL3 as the driver for miR-124 target gene up-regulation in neurons. In primary human neurons, repressing miR-124 and ELAVL3 led to the down-regulation of genes involved in neuronal function and process outgrowth and cellular phenotypes of reduced inward currents and neurite outgrowth. Our results highlight the synergistic role between miR-124 and RNA-binding proteins to promote target gene regulation and neuronal function.

  View details for DOI 10.1073/pnas.2015454118

  View details for PubMedID 34031238

• An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes. mSphere Wahba, L., Jain, N., Fire, A. Z., Shoura, M. J., Artiles, K. L., McCoy, M. J., Jeong, D. 2020; 5 (3)

  Abstract

  In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265-269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270-273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.

  View details for DOI 10.1128/mSphere.00160-20

  View details for PubMedID 32376697

• Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. Cell stem cell Cates, K. n., McCoy, M. J., Kwon, J. S., Liu, Y. n., Abernathy, D. G., Zhang, B. n., Liu, S. n., Gontarz, P. n., Kim, W. K., Chen, S. n., Kong, W. n., Ho, J. N., Burbach, K. F., Gabel, H. W., Morris, S. A., Yoo, A. S. 2020

  Abstract

  Cell-fate conversion generally requires reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal insights into the activity of microRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts into motor neurons by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. We identify KLF-family transcription factors as direct target genes for miR-9/9∗-124 and show their repression is critical for erasing fibroblast fate. Subsequent gain of neuronal identity requires upregulation of a small nuclear RNA, RN7SK, which induces accessibilities of chromatin regions and neuronal gene activation to push cells to a neuronal state. Our study defines deterministic components in the microRNA-mediated reprogramming cascade.

  View details for DOI 10.1016/j.stem.2020.08.015

  View details for PubMedID 32961143

• Intron and gene size expansion during nervous system evolution. BMC genomics McCoy, M. J., Fire, A. Z. 2020; 21 (1): 360

  Abstract

  The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation.Here we show that the longest genes are enriched for expression in neuronal tissues of diverse vertebrates and of invertebrates. Additionally, we show that neuronal gene size expansion occurred predominantly through net gains in intron size, with a positional bias toward the 5' end of each gene.We find that intron and gene size expansion is a feature of many genes whose expression is enriched in nervous systems. We speculate that unique attributes of neurons may subject neuronal genes to evolutionary forces favoring net size expansion. This process could be associated with tissue-specific constraints on gene function and/or the evolution of increasingly complex gene regulation in nervous systems.

  View details for DOI 10.1186/s12864-020-6760-4

  View details for PubMedID 32410625

• LONGO: an R package for interactive gene length dependent analysis for neuronal identity McCoy, M. J., Paul, A. J., Victor, M. B., Richner, M., Gabel, H. W., Gong, H., Yoo, A. S., Ahn, T. OXFORD UNIV PRESS. 2018: 422–28

  Abstract

  Reprogramming somatic cells into neurons holds great promise to model neuronal development and disease. The efficiency and success rate of neuronal reprogramming, however, may vary between different conversion platforms and cell types, thereby necessitating an unbiased, systematic approach to estimate neuronal identity of converted cells. Recent studies have demonstrated that long genes (>100 kb from transcription start to end) are highly enriched in neurons, which provides an opportunity to identify neurons based on the expression of these long genes.We have developed a versatile R package, LONGO, to analyze gene expression based on gene length. We propose a systematic analysis of long gene expression (LGE) with a metric termed the long gene quotient (LQ) that quantifies LGE in RNA-seq or microarray data to validate neuronal identity at the single-cell and population levels. This unique feature of neurons provides an opportunity to utilize measurements of LGE in transcriptome data to quickly and easily distinguish neurons from non-neuronal cells. By combining this conceptual advancement and statistical tool in a user-friendly and interactive software package, we intend to encourage and simplify further investigation into LGE, particularly as it applies to validating and improving neuronal differentiation and reprogramming methodologies.LONGO is freely available for download at https://github.com/biohpc/longo.Supplementary data are available at Bioinformatics online.

  View details for DOI 10.1093/bioinformatics/bty243

  View details for Web of Science ID 000438247800048

  View details for PubMedID 29950021

  View details for PubMedCentralID PMC6022641

• MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts CELL STEM CELL Abernathy, D. G., Kim, W., McCoy, M. J., Lake, A. M., Ouwenga, R., Lee, S., Xing, X., Li, D., Lee, H., Heuckeroth, R. O., Dougherty, J. D., Wang, T., Yoo, A. S. 2017; 21 (3): 332-+

  Abstract

  Directed reprogramming of human fibroblasts into fully differentiated neurons requires massive changes in epigenetic and transcriptional states. Induction of a chromatin environment permissive for acquiring neuronal subtype identity is therefore a major barrier to fate conversion. Here we show that the brain-enriched miRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) trigger reconfiguration of chromatin accessibility, DNA methylation, and mRNA expression to induce a default neuronal state. miR-9/9∗-124-induced neurons (miNs) are functionally excitable and uncommitted toward specific subtypes but possess open chromatin at neuronal subtype-specific loci, suggesting that such identity can be imparted by additional lineage-specific transcription factors. Consistently, we show that ISL1 and LHX3 selectively drive conversion to a highly homogeneous population of human spinal cord motor neurons. This study shows that modular synergism between miRNAs and neuronal subtype-specific transcription factors can drive lineage-specific neuronal reprogramming, providing a general platform for high-efficiency generation of distinct subtypes of human neurons.

  View details for DOI 10.1016/j.stem.2017.08.002

  View details for Web of Science ID 000409527700011

  View details for PubMedID 28886366

  View details for PubMedCentralID PMC5679239