Spatial mRNA profiling using Rapid Amplified Multiplexed-FISH (RAM-FISH) DOI Creative Commons
Tirtha Das Banerjee, J. Dale Raine, Ajay S. Mathuru

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 12, 2024

Abstract Localizing multiple RNA molecules simultaneously in intact tissues and organs is valuable for gaining insights into possible gene-regulatory interactions underlying cell differentiation. Existing technologies multiplexed localization are expensive, computationally complex, have elaborate sample preparation steps, size limitations, require weeks of processing time. This limits the widespread use such techniques most labs. Here we describe a cost-effective methodology, Rapid Amplified Multiplexed-FISH (or RAM-FISH), based on Hybridization Chain Reaction 3.0 localizing dozens transcripts same sample. methodology achieves multiplexing by 3 genes per cycle to detect 30 or more within few days. The method can be applied fixed tissue sections, entire organs, whole organisms as larval Danio rerio , without extensive steps. automation used here also adapted perform other amplification-based FISH. Here, demonstrate its utility, flexibility, versatility gene expression analysis two very different types samples, Bicyclus anynana butterfly wings 10-day-old fish larvae.

Language: Английский

Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage DOI Creative Commons
Ling S. Loh, Kyle A. DeMarr, Christa Heryanto

et al.

Development, Journal Year: 2025, Volume and Issue: 152(5)

Published: March 1, 2025

The success of butterflies and moths is tightly linked to the origin scales within group. A long-standing hypothesis postulates that are homologous well-described mechanosensory bristles found in fruit fly Drosophila melanogaster, as both derive from an epithelial precursor. Previous histological candidate gene approaches identified parallels genes involved scale bristle development. Here, we provide developmental transcriptomic evidence differentiation lepidopteran derives sensory organ precursor (SOP). Live imaging pupae shows SOP cells undergo two asymmetric divisions first abrogate neurogenic lineage, then lead a differentiated its associated socket cell. Single-nucleus RNA sequencing using early pupal wings revealed differential expression patterns mirror development, suggesting shared program. Additionally, recovered newly gene, transcription factor pdm3, proper butterfly wing scales. Altogether, these data open up avenues for understanding type specification illustrate how single-cell transcriptomics powerful platform evolution cell types.

Language: Английский

Citations

1
Spatial mRNA Profiling Using Rapid Amplified Multiplexed-FISH (RAM-FISH) DOI
Tirtha Das Banerjee, J. Dale Raine, Ajay S. Mathuru

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Profiling the Regulatory Landscape of Sialylation through miRNA Targeting of CMP- Sialic Acid Synthetase DOI Creative Commons

Faezeh Jame-Chenarboo,

Joseph N. Reyes,

Thusini Uggalla Arachchige

et al.

Journal of Biological Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 108340 - 108340

Published: Feb. 1, 2025

Cell surface sialic acid is an important glycan modification that contributes to both normal and pathological physiology. The enzyme cytidine monophosphate N-acetylneuraminic synthetase (CMAS) biosynthesizes the activated sugar donor (CMP) acid, which required for all sialylation. CMAS levels impact sialylation with corresponding biological effects. mechanisms regulate are relatively uncharacterized. Herein, we use a high throughput genetically encoded fluorescence assay (miRFluR) comprehensively profile posttranscriptional regulation of by miRNA. These small non-coding RNAs have been found glycosylation. Mapping interactions human miRNAome 3'-untranslated region CMAS, identified miRNA whose on expression was either downregulatory or upregulatory. This follows previous work from our laboratory others showing bidirectional. Validation high-throughput results confirmed findings. We also direct binding sites 2 upregulatory miRNAs. Functional enrichment analysis miRNAs upregulating revealed associations pancreatic cancer, where metabolism α-2,6-sialyltransferase ST6GAL1 be important. associated enriched signature enhanced cell-surface α-2,6-sialylation via in absence effects ST6GAL1. find overlap between previously analyzed sialyltransferases. Overall, points importance regulating disease add further evidence bidirectional nature regulation.

Language: Английский

Citations

0
A Comparative Transcriptomic Analysis of miRNAs and Their Target Genes During the Formation of Melanin in Apis mellifera DOI Creative Commons
Xiangjie Zhu,

Yuanmingyue Tian,

Mingjie Cao

et al.

Agriculture, Journal Year: 2025, Volume and Issue: 15(9), P. 992 - 992

Published: May 3, 2025

Melanin is an important component of the body color honeybees, and its formation changes with age a capped brood bees. However, up to now, regulatory mechanism melanin in honeybees remains unclear. To analyze differential expression profile microRNAs (miRNAs) worker bees Apis mellifera reveal roles differentially expressed miRNAs (DEmiRNAs) mRNAs process during stage, we used sRNA-seq technology related software samples from four key developmental stages when develops mellifera, namely, mature larvae (L0), pre-pupae (PP3), early pupae (P6) mid-pupae (P9). A total 1291 were identified by bioinformatics. Three comparison groups analyzed: L0 vs. PP3, PP3 P6, P6 P9. 171, 94, 19 DEmiRNAs these groups, respectively, which regulate 1481, 690, 182 target (target DEmRNAs). The functional analysis DEmRNAs indicated that might activating genes signaling pathways, such as Wnt pathway, melanogenesis, Toll Imd through miR-315-x, miR-8, ple, yellow family genes, wnt1, etc. Our research provides theoretical basis for future role honeybees.

Language: Английский

Citations

0
Spatial mRNA profiling using Rapid Amplified Multiplexed-FISH (RAM-FISH) DOI Creative Commons
Tirtha Das Banerjee, J. Dale Raine, Ajay S. Mathuru

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 12, 2024

Abstract Localizing multiple RNA molecules simultaneously in intact tissues and organs is valuable for gaining insights into possible gene-regulatory interactions underlying cell differentiation. Existing technologies multiplexed localization are expensive, computationally complex, have elaborate sample preparation steps, size limitations, require weeks of processing time. This limits the widespread use such techniques most labs. Here we describe a cost-effective methodology, Rapid Amplified Multiplexed-FISH (or RAM-FISH), based on Hybridization Chain Reaction 3.0 localizing dozens transcripts same sample. methodology achieves multiplexing by 3 genes per cycle to detect 30 or more within few days. The method can be applied fixed tissue sections, entire organs, whole organisms as larval Danio rerio , without extensive steps. automation used here also adapted perform other amplification-based FISH. Here, demonstrate its utility, flexibility, versatility gene expression analysis two very different types samples, Bicyclus anynana butterfly wings 10-day-old fish larvae.

Language: Английский

Citations

1