Co-transcriptional splicing facilitates transcription of gigantic genes DOI Creative Commons
Jaclyn M. Fingerhut, Romain Lannes,

Troy W. Whitfield

et al.

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(6), P. e1011241 - e1011241

Published: June 13, 2024

Although introns are typically tens to thousands of nucleotides, there notable exceptions. In flies as well humans, a small number genes contain that more than 1000 times larger typical introns, exceeding hundreds kilobases (kb) megabases (Mb). It remains unknown why gigantic exist and how cells overcome the challenges associated with their transcription RNA processing. The Drosophila Y chromosome contains some largest identified date: multiple exceed 4Mb, accounting for over 99% gene span. Here we demonstrate co-transcriptional splicing these Y-linked is important ensure successful transcription: perturbation led attenuation transcription, leading failure produce mature mRNA. Cytologically, defective resulted in disorganization transcripts within nucleus suggestive entanglement transcripts, likely resulting from unspliced long RNAs. We propose maintains length nascent under critical threshold, preventing ensuring proper expression. Our study reveals novel biological significance splicing.

Language: Английский

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes DOI Creative Commons
Amelie A. Raz, Gabriela S. Vida, Sarah R. Stern

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Feb. 16, 2023

Proper differentiation of sperm from germline stem cells, essential for production the next generation, requires dramatic changes in gene expression that drive remodeling almost all cellular components, chromatin to organelles cell shape itself. Here, we provide a single nucleus and RNA-seq resource covering spermatogenesis Drosophila starting in-depth analysis adult testis (snRNA-seq) data Fly Cell Atlas (FCA) study. With over 44,000 nuclei 6000 cells analyzed, identification rare types, mapping intermediate steps differentiation, potential identify new factors impacting fertility or controlling supporting somatic cells. We justify assignment key types using combinations known markers, situ hybridization, extant protein traps. Comparison datasets proved particularly revealing dynamic developmental transitions differentiation. To complement web-based portals hosted by FCA, compatible with commonly used software such as Seurat Monocle. The foundation provided here will enable communities studying interrogate candidate genes test function vivo.

Language: Английский

Citations

47
Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adultAedes aegyptimosquito DOI Creative Commons
Olivia V. Goldman,

Alexandra E. DeFoe,

Yanyan Qi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

The female mosquito's remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Mosquito Cell Atlas (MCA), a comprehensive single-nucleus RNA sequencing dataset of more than 367,000 nuclei from 19 dissected tissues adult male Aedes aegypti , providing cellular-level resolution mosquito We identify novel cell types expand our understanding sensory neuron organization chemoreceptors all tissues. Our analysis uncovers male-specific cells sexually dimorphic gene expression in antenna brain. In mosquitoes, find that glial brain, rather neurons, undergo most extensive transcriptional changes following blood feeding. findings provide insights into cellular basis behavior sexual dimorphism. MCA aims serve as resource for vector biology community, enabling systematic investigation cell-type specific across

Language: Английский

Citations

2
The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster DOI Creative Commons
Nora C. Brown, Benjamin Gordon, Caitlin E. McDonough-Goldstein

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Dec. 21, 2023

In Drosophila melanogaster and other insects, the seminal fluid proteins (SFPs) male sex pheromones that enter female with sperm during mating are essential for fertility induce profound post-mating effects on physiology. The SFPs in D. taxa include several members of large gene family known as odorant binding (Obps). Work has shown some Obp genes highly expressed antennae can mediate behavioral responses to odorants, potentially by carrying these molecules receptors. These observations have led hypothesis Obps might act molecular carriers or compounds important fertility, though functional evidence any species is lacking. Here, we used genetics test role seven response (PMR). We found Obp56g required induction PMR, whereas six dispensable. males lacking fail form a plug mated female's reproductive tract, leading ejaculate loss reduced storage, likely due its expression ejaculatory bulb. also examined evolutionary history genes, studies documented rapid evolution turnover SFP across taxa. extensive lability copy number positive selection acting two Obp22a Obp51a. Comparative RNAseq data from tract multiple revealed shows high subset taxa, conserved head phylogeny. Together, suggest may been co-opted function over time.

Language: Английский

Citations

13
Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution DOI Creative Commons

Zhantao Shao,

Jack Hu,

Allison Jandura

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 7, 2024

Unlike coding genes, the number of lncRNA genes in organism genomes is relatively proportional to complexity. From plants humans, tissues with highest numbers and levels gene expression are male reproductive organs. To learn why, we initiated a genome-wide analysis Drosophila spatial patterns these tissues. The observed greatly exceed those previously reported, due largely preponderance non-polyadenylated transcripts. In stark contrast lncRNAs expressed post-meiotic spermatids. Correlations between levels, localization performed genetic analyses indicate high function requirement. More focused that play major roles evolution by controlling transposable element activities, Y chromosome sperm construction. A new type lncRNA-based particle found seminal fluid may also contribute outcomes.

Language: Английский

Citations

5
scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis DOI Creative Commons
Michael Robben, Balan Ramesh, Shana H. Pau

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(3)

Published: March 1, 2024

Abstract Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded nonmodel systems by a lack of known genes that reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks markers for spermatogenesis found insect species like Drosophila melanogaster. Using sequencing data collected from adult beetle testes, we implement strategy elucidating populations using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify correspond observable points sperm differentiation find specific each stage. Our results indicate molecular pathways underlying Coleoptera are substantially diverged those Diptera. also show most on X chromosome experience meiotic sex inactivation. Temporal MSL complex homologs coupled with spatial analysis potential chromatin entry sites further suggests dosage compensation machinery may mediate escape inactivation postmeiotic reactivation chromosome.

Language: Английский

Citations

3
Running the gauntlet: challenges to genome integrity in spermiogenesis DOI Creative Commons
Maiko Kitaoka, Yukiko Yamashita

Nucleus, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 9, 2024

Species' continuity depends on gametogenesis to produce the only cell types that can transmit genetic information across generations. Spermiogenesis, which encompasses post-meiotic, haploid stages of male gametogenesis, is a process leads formation sperm cells well-known for their motility. Spermiogenesis faces three major challenges. First, after two rounds meiotic divisions, genome lacks repair templates (no sister chromatids, no homologous chromosomes), making it incredibly vulnerable any genomic insults over an extended time (typically days-weeks). Second, becomes transcriptionally silent, difficult respond new perturbations as spermiogenesis progresses. Third, histone-to-protamine transition, essential package genome, counterintuitively involves DNA break formation. How handles these challenges remains poorly understood. In this review, we discuss each challenge and intersection with biology protamines. Finally, implication protamines in evolution.

Language: Английский

Citations

3
Comparative Single Cell Analysis of Transcriptional Bursting Reveals the Role of Genome Organization onde novoTranscript Origination DOI Creative Commons
UnJin Lee, Cong Li, Christopher B. Langer

et al.

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

Published: April 29, 2024

Spermatogenesis is a key developmental process underlying the origination of newly evolved genes. However, rapid cell type-specific transcriptomic divergence

Language: Английский

Citations

3
The Drosophila hematopoietic niche assembles through collective cell migration controlled by neighbor tissues and Slit-Robo signaling DOI Creative Commons
Kara A Nelson, Kari F. Lenhart, Lauren Anllo

et al.

eLife, Journal Year: 2025, Volume and Issue: 13

Published: Jan. 3, 2025

Niches are often found in specific positions tissues relative to the stem cells they support. Consistency of niche position suggests that placement is important for function. However, complexity most niches has precluded a thorough understanding how their proper established. To address this, we investigated formation genetically tractable niche, Drosophila Posterior Signaling Center (PSC), assembly which had not been previously explored. This controls hematopoietic progenitors lymph gland (LG). PSC were shown be specified laterally embryo, but ultimately reside dorsally, at LG posterior. Here, using live-imaging, show migrate as tight collective and associate with multiple during trajectory We find Slit emanating from two extrinsic sources, visceral mesoderm cardioblasts, required remain collective, its attachment cardioblasts migration. Without Slit-Robo signaling, disperse, form aberrant contacts, fail reach stereotypical near progenitors. Our work characterizes novel example identifies an signaling relay precise positioning.

Language: Английский

Citations

0
Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance DOI Creative Commons
Jonathan O. Nelson, Alyssa Slicko, Amelie A. Raz

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 4, 2025

Abstract Preserving a large number of essential yet highly unstable ribosomal DNA (rDNA) repeats is critical for the germline to perpetuate genome through generations. Spontaneous rDNA loss must be countered by copy (CN) expansion. Germline CN expansion best understood in Drosophila melanogaster , which relies on unequal sister chromatid exchange (USCE) initiated breaks at rDNA. The rDNA-specific retrotransposon R2 responsible USCE-inducing typically expressed only when low minimize danger breaks; however, underlying mechanism regulation remains unclear. Here we identify insulin receptor (InR) as major repressor expression, limiting unnecessary activity. Through single-cell RNA sequencing, find that male stem cells (GSCs), cell type undergoes expansion, have reduced InR expression low. Reduced activity turn leads and We further dietary manipulation alters This work reveals pathway integrates surveying with environmental sensing, revealing potential diet exerts heritable changes genomic content.

Language: Английский

Citations

0
Testing the function of widespread transcription of the testis DOI Creative Commons
Tomohiro Kumon, Amelie A. Raz, Jaclyn M. Fingerhut

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 11, 2025

SUMMARY In many organisms including Drosophila and mammals, male germ cells, particularly spermatocytes, have one of the most complex transcriptomes, where a large fraction genome noncoding DNA are transcribed. However, significance this widespread transcription remains enigmatic. Through study satellite in spermatocytes as representational model for transcription, we propose that is required to remodel chromatin preparation sperm packaging. We identified HP2, known heterochromatin protein, being AAGAG DNA. HP2 depletion led retention marks post-meiotic spermatids subsequent failure histone-to-protamine transition. Strikingly, with less can develop normally even when perturbed by depletion. Together, spermatocytes’ serves mechanism facilitate remodeling prepare

Language: Английский

Citations

0