Biology subjects

Mannervik, M.

Publications and source records attributed to Mannervik, M..

8 recordsLinked to original sources

bioRxiv2026

The Little Transib That Could -- and Could Not: Contrasting Invasion Outcomes within a Novel DDE DNA Transposon Lineage

Transposable-element (TE) abundance can vary substantially among populations, yet population-specific differences in TE content remain incompletely characterized. Here, we compared known TE families across long-read genome assemblies representing geographically and historically distinct Drosophila melanogaster populations. Several genomes showed pronounced strain-specific expansions, including an exceptional increase in copies of the element historically annotated as Hopper in A6-Wild5B. Investigation of this expansion revealed a previously uncharacterized full-length autonomous element encoding a 648-amino-acid transposase. We named this element Nozomi and its non-autonomous derivative Kodama, corresponding to the published Hopper consensus. Protein-sequence, phylogenetic and structural analyses placed Nozomi within the Transib superfamily and showed close correspondence between the predicted Nozomi transposome and the experimentally determined Helicoverpa zea Transib strand-transfer complex. Autonomous Nozomi copies were restricted to a small number of D. melanogaster genomes, where they were associated with extensive but separate expansions of Kodama. All Kodama elements carried the same precise 1,380-bp internal deletion, with breakpoint microhomology suggesting an alternative end-joining-related origin. Comparative searches identified a broader group of related Transib elements with contrasting invasion histories. Unlike the restricted Nozomi distribution, Hayabusa showed minimal sequence divergence, limited structural decay and broad distribution across the Drosophila suzukii and montium groups, consistent with a recent, highly successful horizontal invasion. Thus, closely related Transib elements can follow markedly different trajectories after horizontal acquisition: Nozomi remained restricted while driving local amplification of a shorter non-autonomous derivative, whereas Hayabusa spread broadly across species.

molecular biology↗

bioRxiv2026

Single-cell chromatin landscapes visualize epigenetic barriers and reveal lineage-specific Polycomb-mediated repression

Understanding how chromatin state contributes to developmental trajectories remains central to deciphering cell specification and differentiation. Using dual-modality nano-CUT&Tag, we profiled two antagonistic histone modifications--active H3K27ac and repressive H3K27me3--in thousands of single cells from Drosophila embryos across early lineage diversification and terminal differentiation. Joint embedding of both marks enabled robust cell-type classification and revealed increasing epigenetic specificity over developmental time. We ordered cells by developmental age and epigenomic similarity, and defined an epigenetic potential metric that visualizes repressive chromatin barriers as landscapes that predict transcriptional activity. While many genes conform to a classical model in which expression resides in low-potential epigenetic valleys, a substantial subset shows co-occurrence of H3K27ac, H3K27me3, and transcription within the same cell lineage. This indicates that Polycomb-mediated H3K27me3 repression frequently acts within, rather than solely between, lineages. Consistently, tissue-specific E(z) knockdown demonstrates that partial loss of H3K27me3 predominantly de-represses lineage-matched genes rather than inducing fate conversion. Systematic analysis showed that H3K27me3 occurs in multiple distributional modes, ranging from ubiquitous to highly cell-type-specific deposition, co-occuring with accessible but silent gene promoters. These findings demonstrate that cell-type-specific deployment of H3K27ac and H3K27me3 sculpts epigenetic potential landscapes that shape developmental gene expression patterns.

developmental biology↗

bioRxiv2026

Oncogenic ERK signaling represses chaperone-mediated autophagy through transcriptional control of LAMP-2A

Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation pathway governed by the rate-limiting receptor LAMP-2A and increasingly implicated in cancer. However, the oncogenic circuits that enforce CMA repression and whether this state is therapeutically reversible remain unclear. Here, we developed a quantitative bioluminescence-based reporter to measure CMA activity in human cancer cells and combined parallel chemical and genome-scale CRISPR-Cas9 screens to define regulatory pathways. The chemical screen identified GSK1059615 as a CMA-restoring compound that increased LAMP-2A transcription and protein abundance in vitro and in vivo. In parallel, the CRISPR screen revealed ERK signaling as a pathway-level suppressor of CMA. Genetic or pharmacologic ERK inhibition de-repressed LAMP-2A expression, while integrated modulation of ERK, PI3K-AKT, and p38 signaling coordinated transcriptional induction and stabilization of LAMP-2A. Transcriptomic analyses further implicated FOXO1/FOXP1-driven programs in LAMP-2A regulation. Together, these findings position CMA as an integrated output of oncogenic signaling networks and establish a mechanistic framework for restoring CMA activity in defined cancer contexts.

cell biology↗

bioRxiv2024

Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation

Immediately after fertilization the genome is transcriptionally quiescent. Maternally encoded pioneer transcription factors reprogram the chromatin state and facilitate the transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation in zygotic genome activation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CBP is essential for zygotic transcription. CBP catalytic activity is necessary for release of RNA Polymerase II (Pol II) into transcription elongation and for embryonic development. However, CBP also activates zygotic transcription independent of acetylation through Pol II recruitment. Neither acetylation nor CBP are required for the pioneering function of Zelda. Our data suggest that pioneer factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but that this role is separable from the function of pioneer factors in restructuring chromatin accessibility.

developmental biology↗

bioRxiv2022

Comprehensive interrogation of a Drosophila embryonic patterning network reveals the impact of chromatin state on tissue-specific burst kinetics and RNA Polymerase II promoter-proximal pause release

Formation of tissue-specific transcriptional programs underlies multicellular development, but how the chromatin landscape influences transcription is not fully understood. Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila dorsoventral (DV) patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues. The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.

molecular biology↗

bioRxiv2022

Separation of transcriptional repressor and activator functions in HDAC3

The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex and its canonical function is in transcriptional repression, but it can also activate transcription. Here we show that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N-terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhance repressor activity beyond wild-type in the early embryo. We conclude that the critical functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery.

molecular biology↗

bioRxiv2021

The control of transcriptional memory by stable mitotic bookmarking

To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is thought to be mediated, in part, by mitotic bookmarking by transcription factors (TF). However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that the pioneer-like transcription factor GAF acts as stable mitotic bookmarker during zygotic genome activation. We report that GAF remains associated to a large fraction of its interphase targets including at cis-regulatory sequences of key developmental genes, with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and are bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we provide evidence that GAF binding establishes competence for rapid activation upon mitotic exit.

developmental biology↗

bioRxiv2020

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

The relationship between the 3D organisation of chromatin inside the nucleus and the regulation of gene expression remains unclear. While disruption of domains and domain boundaries can lead to mis-expression of developmental genes, acute depletion of key regulators of genome organisation, such as CTCF and cohesin, and major reorganisation of genomic regions have relatively small effects on gene expression. Therefore, it is unclear whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell type-specific activation of genes and their regulatory elements. Here, using the Drosophila melanogaster dorsoventral patterning system as a model, we demonstrate the independence of 3D chromatin organisation and developmental gene regulation. We define tissue-specific enhancers and link them to expression patterns at the single-cell level using single cell RNA-seq. Surprisingly, despite tissue-specific differences in chromatin state and gene expression, 3D chromatin organisation is maintained across tissues. Our results provide strong evidence that tissue-specific chromatin conformation is not required for tissue-specific gene expression, but rather acts as an architectural framework to facilitate proper gene regulation during development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗