Kata, L. | Search bioRxiv

bioRxiv2025

Apoptosis reveals human evolutionary heritage sequestered in non-coding DNA

Cell-free chromatin particles (cfChPs), primarily derived from non-coding DNA (ncDNA) and released from apoptotic cells into the bloodstream, can be horizontally transferred into living cells. However, their potential role in generating ncDNA within recipient cells remains unknown. We previously reported that cfChP- sized fragments generated upon sonicating high-molecular-weight DNA can indiscriminately transmit themselves into foreign cells across species and kingdom boundaries. We hypothesized that cfChP-like DNA-protein complexes generated following organismal death have been exchanged among species and have progressively accumulated to form a dense patchwork that now constitutes the ncDNA, and that apoptosis may dissociate these complexes, rendering them amenable to detection. To test this hypothesis, we used species-specific DNA fluorescent in situ hybridisation probes and antibodies against archaea, eubacteria, plants, algae, fungi, protozoa, Drosophila, fish, chicken, mouse, rat, pig, dog, and monkey on intact and apoptotic human cells. We detected no reactivity with intact cells but strong reactivity with the ncDNA component of apoptotic cells. These findings indicate that ncDNA represents a dense conglomeration of DNA-protein complexes derived from different species that become detectable following apoptosis. This suggests that human evolutionary heritage is conserved within ncDNA formed through progressive accumulation of genetic fragments transferred horizontally following organismal death.

evolutionary biology↗

bioRxiv2023

Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells

BackgroundHorizontal gene transfer (HGT) plays an important evolutionary role in prokaryotes, but it is thought to be less frequent in mammals. We previously reported that cell-free chromatin particles (cfChPs) - chromosomal fragments released from the billions of dying cells that circulate in human blood - are horizontally transferred to healthy cells with biological effects. However, the underlying mechanism and function of these effects remained unclear. MethodsWe treated NIH3T3 mouse fibroblasts cells with cfChPs isolated from human serum and serially passaged the cells. The intracellular activities of cfChPs were analysed using chromatin fibre fluorography, cytogenetic analysis, immuno-fluorescence and fluorescent in situ hybridisation. ResultsWe discovered that the internalised cfChPs were almost exclusively comprised of non-coding DNA, and the disparate DNA sequences contained within them had randomly combined to form complex concatemers some of which were ostensibly multi-mega base pairs in size. The concatemers exhibited variable and bizarre spatial relationships with the host cell interphase DNA with many remaining in the cytoplasm and others aligning themselves with the mouse chromosomal DNA. The concatemers autonomously performed many functions attributable to the nuclear genome. Being associated with DNA polymerase, the concatemers could synthesize DNA and autonomously replicate themselves without heed to the mitotic cycle of the host cell. They could synthesise RNA, RNA polymerase, ribosomal RNA, ribosomal proteins, and generate numerous human proteins, including oncogenes, within the mouse cells which manifested as complex and highly amplified multi-peptide fusion proteins. The concatemers harboured human LINE-1 and Alu elements, which being associated with DNA polymerase, reverse transcriptase and transposes could markedly amplify themselves and increase their copy number with time in culture with the potential to rearrange themselves within the mouse genome. The above findings were reproducible in four other cell lines derived from different species suggesting that horizontal transfer of cfChPs may be a universal phenomenon. ConclusionsOur results lead us to propose that: 1) a cell simultaneously harbours two autonomous genome forms: one that is inherited (hereditary genome) and numerous others that are acquired (satellite genomes); 2) satellite genomes may potentially have evolutionary functions given their ability to serve as vehicles for transposable elements and to generate a plethora of novel proteins; 3) transposable elements are "foreign" genetic elements that are acquired from dying cells via HGT; 4) non-coding DNA has many hidden biological functions that remain dormant but are activated following cellular apoptosis to become detectable in association with the cfChP concatemers; 5) "within-self" HGT occurs in mammals on a massive scale via the medium of cfChP concatemers that have undergone extensive and complex modifications resulting in their behaviour as "foreign" genetic elements. Video Abstracthttps://drive.google.com/file/d/1I6NbrYmT9BRM63ywYj47AU0O9WJ_NrcR/view?usp=drive_link

evolutionary biology↗

bioRxiv2023

Gcn5 - mTORC1 - TFEB signalling axis mediated control of autophagy regulates Drosophila blood cell homeostasis

Blood progenitors are regulated by a variety of systemic and nutritional cues from their environment. In the Drosophila lymph gland (LG), the Posterior Signalling Center (PSC) acts as a stem cell niche striking a balance between progenitors and differentiated blood cells. Autophagy is a vital cellular process that maintains homeostasis by removing unnecessary or dysfunctional cell components through autophagic degradation and recycling. Here, using genetic perturbation analysis, we show that autophagy plays a critical role in regulating LG blood cell homeostasis. General control non-derepressible 5 (Gcn5), a histone acetyltransferase is expressed in the primary LG lobe and modulation of Gcn5 levels perturbs LG homeostasis. Our results show that hemocyte specific Gcn5 modulation controls autophagic flux in the hemocytes. Furthermore, we show that modulation of mTORC1 activity can perturb hematopoiesis. Our results indicate that organismal Gcn5 levels respond to dietary shifts and are modulated by mTORC1 signaling. Chemical intervention shows that mTORC1 over-rides the effect exerted by Gcn5 in regulating LG hematopoiesis. Taken together, our findings demonstrate that Gcn5 and mTORC1 regulates autophagy to maintain blood cell homeostasis in Drosophila.

developmental biology↗