Biology subjects

Apostolou, Z.

Publications and source records attributed to Apostolou, Z..

5 recordsLinked to original sources

bioRxiv2025

Reciprocal targeting of the unfolded protein response regulator Xbp1 and the Dom-A nucleosome remodeler in Drosophila

The DOM-A complex regulates cell growth and proliferation in Drosophila. Like the orthologous human P400 complex, DOM-A combines two epigenetic effectors: a SWR1-type histone exchange enzyme, Dom-A, and the Tip60 acetyltransferase. We found Xbp1, a conserved transcription regulator of the unfolded protein response (UPR), as tightly associated with immunopurified DOM-A and explored the functional implications of this interaction. We biochemically determined the Xbp1 DNA recognition motif in chromatin-reconstituted Drosophila genomes. Intersection of the chromatin binding profiles for Xbp1 and Dom-A in proliferating cells and reciprocal protein depletion studies revealed two distinct modes through which Xbp1 binds chromatin. Xbp1 recruits Dom-A to motif-bearing promoters of genes involved in the UPR, such as Xbp1, Hsc70-3 and Gp93, and activates their transcription. Xbp1 also localizes to hundreds of high-confidence Dom-A binding sites that lack Xbp1 recognition motifs. These interactions depend on Dom-A, pointing to a reverse targeting scenario. Upon depletion of Dom-A, Xbp1 protein levels, but not mRNA levels, are reduced. The Xbp1 may thus be stabilized upon binding to DOM-A. The complex interactions of Xbp1 and DOM-A in the genome bear potential to integrate signals from the UPR with the general, DOM-mediated regulation of cell growth and proliferation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/682518v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@4b60eborg.highwire.dtl.DTLVardef@c7f2d0org.highwire.dtl.DTLVardef@1164265org.highwire.dtl.DTLVardef@612ddd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Intrinsic specificity of a 'core' Tip60 acetyltransferase complex in Drosophila

The lysine acetyltransferase Tip60 (KAT5) regulates gene expression through acetylation of histone N-terminal tail domains. We determined the intrinsic substrate selectivity of a recombinant, 4-subunit TIP60 core module from Drosophila melanogaster with synthetic nucleosome arrays. We compared matched arrays of nucleosomes containing either the replication-dependent histone H2A, or the variant H2A.V (H2A.Z in mammals), a prominent substrate of Tip60. Targeted mass spectrometry allowed to quantify acetylation of individual lysines in histones H2A, H2A.V and H4. Overall, H4 and H2A/H2A.V were equally well acetylated. The analysis comprehensively identified selected sites of acetylation, their relative acetylation levels, diacetylation patterns and revealed surprisingly different acetylation rates of individual lysines. We also applied this defined acetylation system to evaluate the effectiveness and selectivity of a TIP60 inhibitor, NU9056. Remarkably, the inhibitor shows variable effectiveness at different acetylation sites. Knowledge about the intrinsic substrate selectivity of Tip60 is a prerequisite for a mechanistic understanding of the enzymes mode of action.

biochemistry↗

bioRxiv2025

The Tip60 acetylome is a hallmark of the proliferative state in Drosophila

The acetyltransferase KAT5/Tip60 is an epigenetic regulator of transcription and the DNA damage response. In Drosophila, Tip60 acetylates histones as part of the DOM-A complex, but it is unclear whether it has other substrates. In this work, we comprehensively studied the functions of Tip60 in a Drosophila proliferative cell model. Depletion of Tip60 arrests the cell cycle, but remaining viable cells resist mutagenic irradiation. The impaired proliferation is explained by reduced expression of critical cell cycle genes. Tip60 binds their transcription start sites and Tip60-dependent acetylation of the histone variant H2A.V correlates with transcription activity. A potentially synergistic pathway for cell cycle regulation involves the acetylation of proteins other than histones. The Tip60-dependent nuclear acetylome contains hundreds of proteins, many of which are involved in diverse aspects of cell growth and division, including replication, mitosis, gene expression, chromatin organization and ribosome biogenesis. We hypothesize that Tip60 coordinates the proliferative state through histone and non-histone effectors. Reversible acetylation of diverse effector proteins bears potential for fine-tuning energy-intensive processes in response to stresses or nutritional shortcomings. Our study portrays the DOM-A/TIP60 complex as a general promoter of cell proliferation.

molecular biology↗

bioRxiv2024

Optimizing biomedical information retrieval with a keyword frequency-driven Prompt Enhancement Strategy

BackgroundMining the enormous pool of biomedical literature to extract accurate responses and relevant references is a daunting challenge, made more difficult by the domains interdisciplinary nature, specialized jargon, and continuous evolution. Early natural language processing (NLP) approaches faced considerable hurdles in comprehending the nuances of natural language which frequently led to false answers. However, the discovery of transformer models has immensely boosted the cause by enabling researchers to create larger and more potent language models known as large language models (LLMs). These LLMs have opened up new possibilities for enhancing question-answering (QA) tasks. Even with these technological advances, the current LLM-based solutions for querying specialized domains like biology and biomedicine still have issues in generating up to date responses while preventing "hallucination" or the generation of plausible but factually incorrect responses. ResultsThis paper focuses on prompt enhancement using retrieval-augmented architecture as a strategy to guide LLMs towards generating more meaningful responses for biomedical question-answering tasks. We evaluated two prompt enhancement approaches using GPT-3 and GPT-4, examining their effectiveness in retrieving relevant information from complex landscape of biomedical literature. Our proposed approach leverages explicit signals in user queries to extract meaningful contexts from a vast pool of information, addressing the shortcomings of traditional text embedding-based prompt enhancement methods. We developed a QA bot WeiseEule (https://github.com/wasimaftab/WeiseEule-LocalHost) utilizing these prompt enhancement methods and allowing for comparative analysis of their performances. ConclusionsOur findings highlight the importance of prompt enhancement methods that utilize explicit signals in users query over traditional text embedding based counterparts to improve LLM-generated responses in specialized domains such as biology and biomedicine. By providing users complete control over the information that goes into the LLM, our approach tackles some of the major drawbacks of existing web-based chatbots and LLM-based QA systems including hallucinations and the generation of irrelevant or outdated responses.

bioinformatics↗

bioRxiv2020

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms

Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene. HighlightsO_LIIsoforms of DOMINO dictate the formation of distinct complexes C_LIO_LIDOM-B complex is the Drosophila SWR1 and incorporates H2A.V genome-wide C_LIO_LIDOM-A complex acetylates H4K12 and is the Drosophila NuA4 C_LI

molecular biology↗