Extensive genome evolution distinguishes maize within a stable tribe of grasses

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

Published: Jan. 24, 2025

Abstract Over the last 20 million years, Andropogoneae tribe of grasses has evolved to dominate 17% global land area. Domestication these in 10,000 years yielded our most productive crops, including maize, sugarcane, and sorghum. The majority species, show a history polyploidy – condition that, while offering evolutionary advantage multiple gene copies, poses challenges basic cellular processes, expression, epigenetic regulation. Genomic studies have been limited by sparse sampling taxa groups with events. Here, we present 33 genome assemblies from 27 chromosome-scale maize relatives Zea Tripsacum . In after-effects widely studied, showing reduced chromosome number, biased fractionation duplicate genes, transposable element (TE) expansions. While observe patterns within genus , 12 other events deviate significantly. Those tetraploids hexaploids retain elevated maintain nearly complete complements only stochastic TE amplifications. These genomes reveal variable outcomes polyploidy, challenging simple predictions providing foundation for understanding its implications an ecologically economically important clade.

Language: Английский

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FMRP Regulates Neuronal RNA Granules Containing Stalled Ribosomes, Not Where Ribosomes Stall

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

Published: Feb. 21, 2025

Local protein synthesis is a crucial process that maintains synaptic proteostasis. A large percentage of mRNAs translated in developing neurons are associated with stalled ribosomes. FMRP, the lost Fragile X syndrome, highly enriched RNA granules contain Previous examination ribosome protected fragments (RPFs) from neuronal ribosomes has identified motifs match those found as recognized by FMRP cross-linking immunoprecipitation (CLIP) (Anadolu et al, 2023, Journal Neuroscience doi: 10.1523/JNEUROSCI.1002-22.2023). To investigate whether recognition these sequences important for determining where on mRNAs, we examined RPFs isolated P5 mice both sexes lacking protein. We loss had no effect proteins ribosomes, structure or stalling sites (locations accumulated). However, observed significant decrease amount previously shown to be CLIP Additionally, number containing assayed ribopuromycylation distal neurites, decreased. Unlike WT neurons, remaining were resistant reactivation stimuli induce mGLuR-LTD. These results highlight roles regulating though it does not influence and directly involved formation.

Language: Английский

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Transcriptomic profiling in canine B-cell lymphoma supports a synergistic effect of BTK and PI3K inhibitors

Frontiers in Veterinary Science, Journal Year: 2025, Volume and Issue: 12

Published: April 25, 2025

Introduction B-cell receptor (BCR) signaling has revealed itself as a critical pathway in the pathogenesis of lymphoma. Within this pathway, inhibition Bruton's tyrosine kinase (BTK) or Phosphoinositide 3-kinases (PI3Ks) alone presents encouraging efficacy treatment certain both canine and human hematological malignancies. Methods Here we characterized effects BTK inhibitor Ibrutinib PI3K AS-605240 single combined agents pre-clinical diffuse large B cell lymphoma (DLBCL) model CLBL-1 by assaying proliferation metabolic activity, performing RNA-seq to measure gene expression changes. Results We found 2,336 differentially expressed genes (DEGs) across all types time points relative control. The largest number DEGs were induced combination AS-605240. These involved adaptive immune response, leukotriene D4 terms related regulation GTP GTPase mediated signal transduction. Weighted co-expression network analysis (WGCNA) detected nine modules, five which associated with response. Eighteen-percent within these modules also expressed. Notably, observed one module that was exclusively whose members cellular metabolism, homeostasis signaling, protein synthesis regulation. Conclusion Narrowing on highly connected response fold changes treatments play roles main targeted pathways identified PAG1, PRKAR2A, ACACA, FOS , PRKCA potential primary candidates synergistic effect.

Language: Английский

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A genome wide code to define cell-type specific CTCF binding and chromatin organization

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

Published: Nov. 3, 2024

CTCF-mediated chromatin folding plays a key role in gene regulation, however the mechanisms underlying cell type-specific control are not fully elucidated. Comprehensive analyses reveal that CTCF binding stability and cohesin overlap mice humans is regulated by species specific differences accessibility, presence of extended Up Downstream site sequences motifs corresponding to expressed TFs enriched at most bound sites. repositions nucleosomes asymmetrically, with linker spacing altered while cohesin-mediated nucleosome phasing affected surrounding similarly impact insulation. Importantly, transcriptional programs determine motif enrichment sites, reflecting stabilizing/destabilizing effect individual TFs. These studies identify profiles, linked local long-range organization.

Language: Английский

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Diversification and conservation of DNA binding specificities of SPL family of transcription factors

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

Published: Sept. 16, 2024

Abstract SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL Arabidopsis thaliana , providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) target genes to reveal convergent diverse biological functions among family proteins. Comparative between paralogs AtSPL9 AtSPL15 revealed differences binding motifs, suggesting divergent regulatory functions. Additionally, expanded our investigation homologs AtSPL9/15 Zea mays (ZmSBP8/30) Triticum aestivum (TaSPL7/13), identifying conserved unique patterns across species. These findings provide key resources understanding molecular mechanisms regulating evolution different

Language: Английский

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ALBA proteins facilitate cytoplasmic YTHDF-mediated reading of m6A in Arabidopsis

The EMBO Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 29, 2024

Language: Английский

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