Biology subjects

Berglund, G.

Publications and source records attributed to Berglund, G..

3 recordsLinked to original sources

bioRxiv2026

Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons

The Drosophila adult central brain contains 240 circadian neurons, of which there are more than 25 different neuron subtypes based on connectomic data. Recent single cell RNA-seq (scRNAseq) characterization of these neurons "around the clock" also indicates a similar number of molecular subtypes of circadian neurons, but other conclusions from these transcriptomic studies warranted verifying and extending with other approaches. To this end: 1) We used a genetic multiplexing strategy to profile the transcriptomes of circadian neurons from multiple time points in a single experiment, reducing confounding technical variation between timepoints; 2) Large numbers of single nuclei were sequenced (snRNA-seq), which was enabled because the new method EL-INTACT purifies nuclei from frozen heads; 3) We assayed 12 time points under both light-dark (LD) and constant darkness (DD) conditions. These approaches showed dramatic transcriptional differences between time points in many circadian neuron types and enhanced time-of-day gene expression analysis. The data indicate that most of this regulation is transcriptional and circadian. There were however a small number of light-dependent transcripts, including a few that correspond to mammalian immediate-early genes. They probably play a role in the light-regulation of gene expression and behavior in specific neurons, perhaps circadian entrainment or phase-shifting. The results taken together provide a more comprehensive picture of gene expression heterogeneity within adult Drosophila circadian neurons including how intrinsic clock mechanisms and light cues are integrated across circadian neuron subtypes.

neuroscience↗

bioRxiv2026

New methods for epigenetic characterization and manipulation of rare fly brain neurons

The molecular circadian clock ticks away similarly in several distinct locations throughout the Drosophila head and body, yet regulation of this clock and specifically that of master transcription factor gene Clock (Clk) and its transcription is largely unknown. ATAC-Seq assays indicate that Clk chromatin appears inaccessible in most head neurons outside the circadian brain network, indicating that circadian clock functionality is gated by access to Clk chromatin. Moreover, distinct Clk enhancers function in circadian neurons versus glia, corresponding to distinct transcripts. To address the chromatin landscape of Clk with more temporal and spatial resolution, we developed a novel, high-purity, nuclear purification method, Elution-based INTACT (El-INTACT). It enabled the first time-resolved, six-timepoint chromatin accessibility landscape of ~120 Drosophila circadian neurons/brain. It moreover allowed chromatin accessibility characterization of the 16 PDF-expressing ventrolateral circadian neurons (LNvs), which identified an additional, previously unidentified Clk enhancer. A CRISPR/Cas9 multiplexed gRNA-based strategy was used to disrupt these enhancers and indicated striking functional specificity. The findings establish a chromatin-level logic for cell type-specific circadian regulation and show that El-INTACT and the multiplexed gRNA-disruption of enhancer function are broadly applicable tools for exploring chromatin regulation in rare cell populations.

genetics↗

bioRxiv2024

Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients.

Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.

microbiology↗