Biology subjects

Marcotte, E.

Publications and source records attributed to Marcotte, E..

10 recordsLinked to original sources

bioRxiv2025

Molecular organization of the distal tip of vertebrate motile cilia

The beating of cilia on multi-ciliated cells (MCCs) is essential for normal development and homeostasis in animals. But while the structure and function of basal bodies and axonemes have received significant attention recently, the distal tips of MCC cilia remain relatively poorly defined. Here, we characterize the molecular organization of the distal tip of vertebrate MCC cilia, characterizing two distinct domains occupied by distinct protein constituents. Using frog, mouse, and human MCCs, we find that two largely uncharacterized proteins, Ccdc78 and Ccdc33 occupy a previously undefined region at the extreme distal tip, and these are required for the normal organization of all other known tip proteins. Ccdc78 and Ccdc33 each display robust microtubule-bundling activity both in vivo and in vitro, yet each is independently required for normal length regulation of MCC cilia. Moreover, loss of each protein elicits a distinct pattern of defective cilia beating and resultant fluid flow. Thus, two previously undefined proteins form a key module essential for organizing and stabilizing the distal tip of motile cilia in vertebrate MCCs. We propose that these ill-defined proteins represent potential disease loci for motile ciliopathies.

cell biology↗

bioRxiv2024

The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture

Cilia are essential organelles and variants in genes governing ciliary function result in ciliopathic diseases. The Ciliogenesis and PLANar polarity Effectors (CPLANE) protein complex is essential for ciliogenesis in animals models but remains poorly defined. Notably, all but one subunit of the CPLANE complex have been implicated in human ciliopathy. Here, we identify three families in which variants in the remaining CPLANE subunit CPLANE2/RSG1 also cause ciliopathy. These patients display cleft palate, tongue lobulations and polydactyly, phenotypes characteristic of Oral-Facial-Digital Syndrome. We further show that these alleles disrupt two vital steps of ciliogenesis, basal body docking and recruitment of intraflagellar transport proteins. Moreover, APMS reveals that Rsg1 binds the CPLANE and also the transition zone protein Fam92 in a GTP-dependent manner. Finally, we show that CPLANE is generally required for normal transition zone architecture. Our work demonstrates that CPLANE2/RSG1 is a causative gene for human ciliopathy and also sheds new light on the mechanisms of ciliary transition zone assembly.

cell biology↗

bioRxiv2021

Cell adhesions link subcellular actomyosin dynamics to tissue scale force production during vertebrate convergent extension.

Axis extension is a fundamental biological process that shapes multicellular organisms. The design of an animals body plan is encoded in the genome and execution of this program is a multiscale mechanical progression involving the coordinated movement of proteins, cells, and whole tissues. Thus, a key challenge to understanding axis extension is connecting events that occur across these various length scales. Here, we use approaches from proteomics, cell biology, and tissue biomechanics to describe how a poorly characterized cell adhesion effector, the Armadillo Repeat protein deleted in Velo-Cardio-Facial syndrome (Arvcf) catenin, controls vertebrate head-to-tail axis extension. We find that Arvcf catenin is required for axis extension within the intact organism but is not required for extension of isolated tissues. We then show that the organism scale phenotype is caused by a modest defect in force production at the tissue scale that becomes apparent when the tissue is challenged by external resistance. Finally, we show that the tissue scale force defect results from dampening of the pulsatile recruitment of cell adhesion and cytoskeletal proteins to cell membranes. These results not only provide a comprehensive understanding of Arvcf function during an essential biological process, but also provide insight into how a modest cellular scale defect in cell adhesion results in an organism scale failure of development.

developmental biology↗

bioRxiv2021

Spatiotemporal transcriptional dynamics of the cycling mouse oviduct

Female fertility in mammals requires iterative remodeling of the entire adult female reproductive tract across the menstrual/estrous cycle. However, while transcriptome dynamics across the estrous cycle have been reported in human and bovine models, no global analysis of gene expression across the estrous cycle has yet been reported for the mouse. Here, we examined the cellular composition and global transcriptional dynamics of the mouse oviduct along the anteroposterior axis and across the estrous cycle. We observed robust patterns of differential gene expression along the anteroposterior axis, but we found surprisingly few changes in gene expression across the estrous cycle. Notable gene expression differences along the anteroposterior axis included a surprising enrichment for genes related to embryonic development, such as Hox and Wnt genes. The relatively stable transcriptional dynamics across the estrous cycle differ markedly from other mammals, leading us to speculate that this is an evolutionarily derived state that may reflect the extremely rapid five-day mouse estrous cycle. This dataset fills a critical gap by providing an important genomic resource for a highly tractable genetic model of mammalian female reproduction.

developmental biology↗

bioRxiv2020

Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation

The dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells and in vitro systems have provided an exceptionally deep understanding of actin dynamics. However, we still know relatively little of how these systems are tuned in cell-type specific ways, for example in the context of collective cell movements that sculpt the early embryo. Here, we provide an analysis of the actin severing and depolymerization machinery during vertebrate gastrulation, with a focus on Twinfilin1. We confirm previous results on the role of Twf1 in lamellipodia and extend those findings by linking Twf1, actin turnover, and cell polarization required for convergent extension during vertebrate gastrulation.

cell biology↗

bioRxiv2020

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins

Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.

cell biology↗

bioRxiv2017

A phase separated organelle at the root of motile ciliopathy

Hundreds of different cell types emerge in the developing embryo, each of which must compartmentalize cell type specific biochemical processes in a crowded intracellular environment. To study cell type specific compartmentalization, we examined motile ciliated cells, which must assemble vast numbers of dynein motors to drive ciliary beating, as mutation of dyneins or their assembly factors causes motile ciliopathy. We show that dyneins, their assembly factors, and chaperones all concentrate together in Dynein Assembly Particles (DynAPs). These phase-separated organelles are specific to ciliated cells but share machinery with stress granules. Our data suggest that a common framework underlies ubiquitous and cell-type specific phase separated organelles and that one such organelle is defective in a human genetic disease.

cell biology↗

bioRxiv2017

High-content protein localization screening in vivo reveals novel regulators of multiciliated cell development and function

Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for development and homeostasis of the vertebrate central nervous system, airway, and reproductive tracts. These cells are characterized by dozens or hundreds of long, motile cilia that beat in a coordinated and polarized manner (Brooks and Wallingford, 2014). In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification, but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating, or cilia polarization (e.g. (Choksi et al., 2014b; Chung et al., 2014; Hoh et al., 2012; Ma et al., 2014; Treutlein et al., 2014)). Interestingly, this burst of genomic data has also highlighted the obvious importance of the \"ignorome,\" that large fraction of vertebrate genes that remain only poorly characterized (Pandey et al., 2014). Understanding the function of novel proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we explored the MCC ignorome by defining the subcellular localization of 260 poorly defined proteins in vertebrate MCCs in vivo. Moreover, functional analyses that arose from results of the screen provide novel insights into the mechanisms by which the actin cytoskeleton simultaneously influences diverse aspects of MCC biology, including basal body docking, and ciliogenesis.

cell biology↗

bioRxiv2017

WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum

Gene networks provide a system-level overview of genetic organizations and enable the dissection of functional modules underlying complex traits. Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. A unique feature of WheatNet is that each network node represents either a single gene or a group of genes. We computationally partitioned gene groups mimicking homeologous genes by clustering 99,386 wheat genes, resulting in 20,248 gene groups comprising 63,401 genes and 35,985 individual genes. Thus, WheatNet was constructed using 56,233 nodes, and the final integrated network has 20,230 nodes and 567,000 edges. The edge information of the integrated WheatNet and all 20 component networks are available for download.

genetics↗

bioRxiv2016

A highly parallel strategy for storage of digital information in living cells

Encoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and reading the data (biases and systematic error arising from synthesis and sequencing), and overall scalability. To this end, we have developed and implemented an encoding scheme that is suitable for detecting and correcting errors that may arise during storage, writing, and reading, such as those arising from nucleotide substitutions, insertions, and deletions. We propose a scheme for parallelized long term storage of encoded sequences that relies on overlaps rather than the address blocks found in previously published work. Using computer simulations, we illustrate the encoding, sequencing, decoding, and recovery of encoded information, ultimately demonstrating the possibility of a successful round-trip read/write. These demonstrations show that in theory a precise control over error tolerance is possible. Even after simulated degradation of DNA, recovery of original data is possible owing to the error correction capabilities built into the encoding strategy. A secondary advantage of our method is that the statistical characteristics (such as repetitiveness and GC-composition) of encoded sequences can also be tailored without sacrificing the overall ability to store large amounts of data. Finally, the combination of the overlap-based partitioning of data with the LZMA compression that is integral to encoding means that the entire sequence must be present for successful decoding. This feature enables inordinately strong encryptions. As a potential application, an encrypted pathogen genome could be could be distributed and carried by cells without danger of being expressed, and could not even be read out in the absence of the entire DNA consortium.

synthetic biology↗