Biology subjects

Andrew, D. J.

Publications and source records attributed to Andrew, D. J..

5 recordsLinked to original sources

bioRxiv2025

VIDEO - Visual Integration of Drosophila Enhancer Organization: A tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes

AO_SCPLOWBSTRACTC_SCPLOWDissecting gene regulation today relies on many genomic assays - including transcriptional output from RNA-seq, chromatin accessibility from ATAC-seq, and transcription factor (TF) binding from ChIP-seq. Whereas numerous tools exist for each modality and some integrate data across modalities, few allow researchers to interactively explore and visualize how TF binding motifs intersect with transcriptional activity and chromatin accessibility in a tissue-specific context. Here we introduce VIDEO (Visual Integration of Drosophila Enhancer Organization), a web-based analysis tool that enables visualization of conserved TF binding motifs within proximal promoters of genes differentially expressed in specific tissues. Starting with gene lists derived from in situ hybridization, microarray, and/or scRNA-seq studies of WT or mutant samples, one can identify the TFs expressed in each tissue and learn if and where the consensus binding motifs for those TFs are found within the proximal enhancers of a custom gene set. This pipeline also allows for coincident visualization of active chromatin, as determined from ATAC-seq data, and for the visualization of DNA binding data from ChIP-seq datasets for specific TFs. To demonstrate its utility, we apply VIDEO to the well-characterized regulatory system of CrebA and the secretory pathway in the Drosophila salivary gland. We also explore a lesser-known system in the embryonic hindgut to show how utilization of this tool can serve to generate hypotheses regarding regulatory interactions.

genomics↗

bioRxiv2025

CrebA regulation of secretory capacity: Genome-wide transcription profiling coupled with in vivo DNA binding studies

DNA binding assays, expression analyses, and binding site mutagenesis revealed that the Drosophila CrebA transcription factor (TF) boosts secretory capacity in the embryonic salivary gland (SG) through direct regulation of secretory pathway component genes (SPCGs). The mammalian orthologues of CrebA, the Creb3L-family of leucine zipper TFs, not only activate SPCG expression in a variety of mammalian tissues but can also activate SPCG expression in Drosophila embryos, suggesting a highly conserved role for this family of proteins in boosting secretory capacity. However, in vivo assays reveal that CrebA binds far more genes than it regulates, and it remains unclear what distinguishes functional binding. It is also unclear if CrebA is the major factor driving SPCG gene expression in all Drosophila embryonic tissues and/or if CrebA also regulates other tissue-specific functions. Thus, we did single cell RNA sequencing (scRNA-seq) of wild-type (WT) and CrebA null embryos to explore the relationship between CrebA binding and gene regulation. We find that CrebA binds the proximal promoters of its targets, that SPCGs are the major class of genes regulated by CrebA across tissues, and that CrebA is sufficient to activate SPCG expression even in cells that do not normally express the protein. A comparison of scRNA-Seq to other methods for capturing regulated transcripts reveals that the different methodologies identify overlapping but distinct sets of CrebA targets.

genomics↗

bioRxiv2024

Arc controls organ architecture through modulation of Crb and MyoII

Precise orchestration of morphogenetic processes is required to generate organs that are optimally situated within the organism, and that are of the right size and shape to fit and maximize functionality. Here, we describe the role of Arc, a large apical membrane-associated PDZ domain-containing protein, that works through the apical determinant Crumb (Crb) to limit MyoII activity during tissue invagination in the forming Drosophila salivary gland (SG). We show that loss of Arc, attenuation of Crb function, as well as increased activation of non-muscle Myosin II (MyoII) leads to the simultaneous internalization of more precursor cells than normal. Consequently, mature SGs are significantly shorter with more cells surrounding the lumen at all positions along the tube. Correspondingly, overexpression of Arc or SG-specific knockdown of MyoII leads to the formation of longer SGs with fewer cells surrounding the lumen. We show that both Arc PDZ domains are required for Arc function and that they have distinct activities. Finally, we show that Arc facilitates Crb plasma membrane (PM) localization and suggests a model wherein PM-associated Crb stabilizes cellular junctions countering the destabilizing effects of apical medial and junctional pools of activated MyoII, thus limiting the number of primordial cells internalizing at any given time.

developmental biology↗

bioRxiv2021

The Ribb-osome: Ribbon boosts ribosomal protein gene expression to coordinate organ form and function

Cell growth is well defined for the late (post-embryonic) stages of development, but evidence for early (embryonic) cell growth during post-mitotic morphogenesis is quite limited. Here, we identify early cell growth as a key characteristic of tubulogenesis in the Drosophila embryonic salivary gland (SG). A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates this early cell growth. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG) and is required for full expression of all RPGs tested. Rib binding to RPG promoters in vitro is weak and not sequence-specific, suggesting that specificity is achieved through co-factor interactions. Consistent with this hypothesis, we demonstrate Ribs ability to physically interact with each of the three known contributors to RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ--the embryonic trachea--is not mediated by direct RPG transcription. These findings support a model of early cell growth sustained by transcriptional regulatory networks customized for organ form and function.

developmental biology↗

bioRxiv2020

Isoform-specific roles of the Drosophila filamin-type protein Jitterbug (Jbug) during development

Filamins are highly conserved actin-crosslinking proteins that regulate organization of the actin cytoskeleton. As key components of versatile signaling scaffolds, filamins are implicated in developmental anomalies and cancer. Multiple isoforms of filamins exist, raising the possibility of distinct functions for each isoform during development and in disease. Here, we provide an initial characterization of jitterbug (jbug), which encodes one of the two filamin-type proteins in Drosophila. We generate Jbug antiserum that recognizes all of the spliced forms and reveals differential expression of different Jbug isoforms during development, and a significant maternal contribution of Jbug protein. To reveal the function of Jbug isoforms, we create new genetic tools, including a null allele that deletes all isoforms, hypomorphic alleles that affect only a subset, and UAS lines for Gal4-driven expression of the major isoforms. Using these tools, we demonstrate that Jbug is required for viability and that specific isoforms are required in the formation of actin-rich protrusions including thoracic bristles in adults and ventral denticles in the embryo. We also show that specific isoforms of Jbug show differential localization within epithelia and that maternal and zygotic loss of jbug disrupts Crumbs (Crb) localization in several epithelial cell types.

developmental biology↗