Biology subjects

Hariharan, I. K.

Publications and source records attributed to Hariharan, I. K..

9 recordsLinked to original sources

bioRxiv2026

Coding region changes in the Hippo pathway component YAP1 contribute to body size differences among mammalian species

Animal species differ dramatically in their overall size, yet the mechanisms underlying these differences are poorly understood. The Hippo pathway, first discovered in Drosophila, and widely conserved in mammals, regulates the nuclear levels of YAP1, a transcriptional co-activator that enhances the expression of growth-promoting genes. While experimental manipulations of this pathway elicit dramatic effects on tissue growth and organ size, it is not known whether, and to what extent, evolutionary divergence of this pathway has contributed to size differences across animals. Here we show that although YAP1 protein sequence is highly conserved between diverse mammals such as humans, elephants and blue whales, it diverges considerably among rodent species. While the human YAP1 protein is very similar to that of the largest rodent, the capybara Hydrochoerus hydrochaeris, those of smaller rodents such as the mouse Mus musculus and the vole Microtus oregoni show considerable divergence. An increased ratio of non-synonymous versus synonymous substitutions (dN/dS) in clades of small rodents compared to the background is indicative of relaxed constraint in these lineages, suggesting relative positive selection. When expressed in the developing Drosophila wing, capybara YAP1 was more potent at promoting growth than that of the mouse or vole. Following transfection into mammalian cells, capybara YAP1 is more effective at promoting expression of a reporter gene than either mouse or vole YAP1. Thus, by combining computational and experimental approaches, we show that evolutionarily divergent coding-region changes in YAP1 have likely contributed to the evolution of smaller body size in clades of rodents.

developmental biology↗

bioRxiv2024

Single cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

Even seemingly homogeneous populations of cells can express phenotypic diversity in response to environmental changes. Thus, X-ray irradiation of tissues composed of diverse cell types can have complex outcomes. We have used single-cell RNA-sequencing to study the effects of X-ray radiation on the Drosophila wing imaginal disc, a relatively simple tissue composed mostly of epithelial cells. Transcriptomic clustering of cells collected from the wing disc generates clusters that are mainly grouped based on proximodistal cell location. To quantify heterogeneity of gene expression among clusters, we adapted a metric used to study market concentration, the Herfindahl-Hirschman Index. Genes involved in DNA damage repair, defense against reactive oxygen species, cell cycle progression, and apoptosis are expressed relatively uniformly. In contrast, genes encoding a subset of ligands, notably cytokines that activate the JAK/STAT pathway, some transcription factors including Ets21C, previously implicated in regeneration, and several signaling proteins are expressed more regionally. Though the radiation-responsive transcription factor p53 is expressed relatively uniformly in the wing disc, several regionally-induced genes still require p53 function, indicating that regional and radiation-induced factors combine to regulate their expression. We also examined heterogeneity within regions using a clustering approach based on cell cycle gene expression. A subpopulation of cells, characterized by high levels of tribbles expression, is amplified in irradiated discs. Remarkably, this subpopulation accounts for a considerable fraction of radiation-induced gene expression, indicating that cellular responses are non-uniform even within regions. Thus, both inter-regional and intra-regional heterogeneity are important features of tissue responses to X-ray radiation.

genomics↗

bioRxiv2023

The cell adhesion molecule Echinoid promotes tissue survival and separately restricts tissue overgrowth in Drosophila imaginal discs

The interactions that cells in Drosophila imaginal discs have with their neighbors are known to regulate their ability to survive. In a screen of genes encoding cell surface proteins for gene knockdowns that affect the size or shape of mutant clones, we found that clones of cells with reduced levels of echinoid (ed) are fewer, smaller, and can be eliminated during development. In contrast, discs composed mostly of ed mutant tissue are overgrown. We find that ed mutant tissue has lower levels of the anti-apoptotic protein Diap1 and has increased levels of apoptosis which is consistent with the observed underrepresentation of ed mutant clones and the slow growth of ed mutant tissue. The eventual overgrowth of ed mutant tissue results not from accelerated growth, but from prolonged growth resulting from a failure to arrest growth at the appropriate final size. Ed has previously been shown to physically interact with multiple Hippo-pathway components and it has been proposed to promote Hippo pathway signaling, to exclude Yorkie (Yki) from the nucleus, and restrain the expression of Yki-target genes. We did not observe changes in Yki localization in ed mutant tissue and found decreased levels of expression of several Yorkie-target genes, findings inconsistent with the proposed effect of Ed on Yki. We did, however, observe increased expression of several Yki-target genes in wild-type cells neighboring ed mutant cells, which may contribute to elimination of ed mutant clones. Thus, ed has two distinct functions: an anti-apoptotic function by maintaining Diap1 levels, and a function to arrest growth at the appropriate final size. Both of these are unlikely to be explained by a simple effect on the Hippo pathway.

developmental biology↗

bioRxiv2021

Critical genetic program for Drosophila imaginal disc regeneration revealed by single-cell analysis

Whether regeneration is primarily accomplished by re-activating gene regulatory networks used previously during development or by activating novel regeneration-specific transcriptional programs remains a longstanding question. Currently, most genes implicated in regeneration also function during development. Using single-cell transcriptomics in regenerating Drosophila wing discs, we identified two regeneration-specific cell populations within the blastema. They are each composed of cells that upregulate multiple genes encoding secreted proteins that promote regeneration. In this regenerative secretory zone, the transcription factor Ets21C controls the expression of multiple regenerationpromoting genes. While eliminating Ets21C function has no discernible effect on development, it severely compromises regeneration. This Ets21C-dependent gene regulatory network is also activated in blastema-like cells in tumorous discs, suggesting that pro-regenerative mechanisms can be co-opted by tumors to promote aberrant growth.

developmental biology↗

bioRxiv2020

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

In both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a cell atlas of the Drosophila wing disc at two time points during development. Using these data, we investigate gene expression using a multi-layered model of the wing disc and catalogued ligand-receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the FGF ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, which is critical for proper formation of a subset of the direct flight muscles. More generally, our annotated atlas provides a global view of potential cell-cell interactions between subpopulations of epithelial and myogenic cells.

bioinformatics↗

bioRxiv2020

Membrane potential regulates Hedgehog signaling and compartment boundary maintenance in the Drosophila wing disc

The Drosophila wing imaginal disc is composed of two lineage-restricted populations of cells separated by a smooth boundary. Hedgehog (Hh) from posterior cells activates a signaling pathway in anterior cells near the boundary which is necessary for boundary maintenance. Here, we show that membrane potential is patterned in the wing disc. Anterior cells near the boundary, where Hh signaling is most active, are more depolarized than posterior cells across the boundary. Elevated expression of the ENaC channel Ripped Pocket (Rpk), observed in these anterior cells, requires Hh. Antagonizing Rpk reduces depolarization and disrupts the compartment boundary. Using genetic and optogenetic manipulations, we show that membrane depolarization promotes membrane localization of Smoothened and augments Hh signaling. Thus, membrane depolarization and Hh-dependent signaling mutually reinforce each other in this region. Finally, clones of depolarized cells survive preferentially in the anterior compartment and clones of hyperpolarized cells survive preferentially in the posterior compartment.

developmental biology↗

bioRxiv2019

Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers

Like tissues of many organisms, Drosophila imaginal discs lose the ability to regenerate as they mature. This loss of regenerative capacity coincides with reduced damage-responsive expression of multiple genes needed for regeneration. Our previous work showed that two such genes, wg and Wnt6, are regulated by a single damage-responsive enhancer, which becomes progressively inactivated via Polycomb-mediated silencing as discs mature. Here we explore the generality of this mechanism, and identify numerous damage-responsive, maturity-silenced (DRMS) enhancers, some near genes known to be required for regeneration such as Mmp1, as well as near genes that we now show function in regeneration. Using a novel GAL4-independent tissue ablation system we characterize two DRMS-associated genes, apontic (apt), which curtails regeneration and CG9752/asperous (aspr), which promotes it. This mechanism of suppressing regeneration by silencing damage-responsive enhancers at multiple loci can be partially overcome by reducing activity of the chromatin regulator extra sex combs (esc).

developmental biology↗

bioRxiv2019

The transcriptional co-repressor CtBP is a negative regulator of growth that antagonizes the Yorkie and JNK/AP-1 pathways

Multicellular organisms require strict growth control mechanisms to ensure that an organ reaches, but does not grossly exceed, its appropriate size and shape. In an unbiased mosaic screen for genes involved in growth regulation, we identified a loss-of-function allele of the gene CtBP that conferred a growth advantage to homozygous mutant tissue. CtBP encodes a transcriptional co-repressor found in diverse organisms, yet its role in regulating tissue growth is not known. We found that CtBP functions as a negative regulator of growth by restricting the expression of the growth-promoting microRNA bantam (ban). ban is a known target of the Hippo pathway effector Yorkie (Yki). We show that loss of CtBP function leads to the activation of a minimal enhancer of ban via both Yki-dependent and AP-1 transcription factor-dependent mechanisms. AP-1 is downstream of the Jun N-terminal Kinase (JNK) pathway and thus JNK could regulate growth during development via ban. Furthermore, we show that distinct isoforms of the AP-1 component Fos differ in their ability to activate this enhancer. Since the orthologous pathways in mammalian cells (YAP/TEAD and AP-1) converge on enhancers implicated in tumor progression, a role for mammalian CtBP proteins at those enhancers merits attention.

developmental biology↗

bioRxiv2017

The BMP2/4 ortholog Dpp functions as an inter-organ signal that regulates developmental timing in Drosophila

For many organisms, developmental transitions are triggered by a neuroendocrine axis and are contingent upon multiple organs achieving sufficient growth and maturation. How the status of peripheral organs is communicated to the neuroendocrine axis is not known. In Drosophila larvae, metamorphosis is triggered by the steroid hormone ecdysone, secreted by the prothoracic gland (PG). Here we show that the BMP2/4 ortholog Dpp, which regulates growth and patterning of larval imaginal discs, also functions as a systemic signal to regulate developmental timing. Dpp from peripheral tissues, mostly imaginal discs, can reach the PG and inhibit ecdysone biosynthesis. As the discs grow, Dpp signaling decreases in the PG, thus alleviating the inhibition of ecdysone biosynthesis, and permitting entry into metamorphosis. We suggest that if a tissue can trap more morphogen locally as it grows and matures, then circulating levels of morphogen can provide a systemic readout of organ size and maturation.\n\nOne Sentence SummaryDpp functions as a long-range endocrine signal between peripheral tissues and the prothoracic gland to regulate developmental timing in Drosophila.

developmental biology↗