Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition

Nature Structural & Molecular Biology, Journal Year: 2023, Volume and Issue: 30(2), P. 200 - 215

Published: Jan. 16, 2023

Abstract Poly(A)-tail-mediated post-transcriptional regulation of maternal mRNAs is vital in the oocyte-to-embryo transition (OET). Nothing known about poly(A) tail dynamics during human OET. Here, we show that length and internal non-A residues are highly dynamic OET, using poly(A)-inclusive RNA isoform sequencing (PAIso-seq). Unexpectedly, undergo global remodeling: after deadenylation or partial degradation into 3ʹ-UTRs, they re-polyadenylated to produce polyadenylated intermediates, coinciding with massive incorporation residues, particularly long consecutive U newly synthesized tails. Moreover, TUT4 TUT7 contribute these BTG4-mediated produces substrates for mRNA re-polyadenylation, TENT4A TENT4B incorporate G residues. The remodeling further confirmed PAIso-seq2. Importantly, essential first cleavage embryos. Together, findings broaden our understanding

Language: Английский

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Epigenetics in the modern era of crop improvements

Science China Life Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract Epigenetic mechanisms are integral to plant growth, development, and adaptation environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body knowledge on both locus-specific genome-wide patterns. Studies initially grounded in model Arabidopsis have been broadened encompass diverse array crop species, revealing multifaceted roles epigenetics physiological agronomic traits. With recent technological advancements, epigenetic regulations at single-cell level large-scale population emerging as new focuses. This review offers an in-depth synthesis regulations, detailing catalytic machinery functions. It delves into intricate interplay among various elements their collective influence modulation Furthermore, it examines breakthroughs technologies for modifications integration strategies improvement. The underscores transformative potential bolstering performance, advocating development efficient tools fully exploit agricultural benefits insights.

Language: Английский

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Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 22, 2023

Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there little focus on reference-free assembly. We introduce "RNA-Bloom2 [ https://github.com/bcgsc/RNA-Bloom ]", a method data. Using simulated datasets spike-in control data, we show that the quality of RNA-Bloom2 competitive those methods. Furthermore, find requires 27.0 80.6% peak memory 3.6 10.8% total wall-clock runtime competing method. Finally, showcase in assembling sample Picea sitchensis (Sitka spruce). Since our does not rely reference, it further sets groundwork large-scale comparative transcriptomics where high-quality draft genome assemblies readily available.

Language: Английский

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Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(6)

Published: Jan. 29, 2024

Light plays a central role in plant growth and development, providing an energy source governing various aspects of morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play rapidly responding to changes environmental signals. However, mechanism underlying post-transcriptional regulation during initial light exposure young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, Nanopore-based sequencing technique, analyze nuclear RNAs Arabidopsis ( thaliana ) under different conditions found numerous light-responsive introns. We also single-nucleus (snRNA-seq) profile transcripts single investigate distribution across distinct cell types. established light-induced are predominant mesophyll cells seedling de-etiolation following light. further demonstrated involvement splicing-related factor A. PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working concert with E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), critical repressor signaling pathways. these two proteins orchestrate events facilitate chloroplast photosynthesis, morphogenesis response ever-changing conditions. These findings provide crucial insights into intricate mechanisms acclimation at cell-type level.

Language: Английский

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Birth of a poly(A) tail: mechanisms and control of mRNA polyadenylation

FEBS Open Bio, Journal Year: 2022, Volume and Issue: 13(7), P. 1140 - 1153

Published: Nov. 23, 2022

During their synthesis in the cell nucleus, most eukaryotic mRNAs undergo a two‐step 3′‐end processing reaction which pre‐mRNA is cleaved and released from transcribing RNA polymerase II polyadenosine (poly(A)) tail added to newly formed 3′‐end. These biochemical reactions might appear simple at first sight (endonucleolytic cleavage of homopolymeric tail), but catalysis requires multi‐faceted enzymatic machinery, polyadenylation complex (CPAC), composed more than 20 individual protein subunits. The activity CPAC further orchestrated by Poly(A) Binding Proteins (PABPs), decorate poly(A) during its guide mRNA through subsequent gene expression steps. Here, we review structure, molecular mechanism, regulation machineries with focus on step. We concentrate PABPs mammals budding yeast, Saccharomyces cerevisiae , because these systems are best‐characterized present. Comparison functions provides valuable insights into principles processing.

Language: Английский

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Structured 3′ UTRs destabilize mRNAs in plants

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 22, 2024

Abstract Background RNA secondary structure (RSS) can influence the regulation of transcription, processing, and protein synthesis, among other processes. 3′ untranslated regions (3′ UTRs) mRNA also hold key for many aspects gene regulation. However, there are often contradictory results regarding roles RSS in UTRs expression different organisms and/or contexts. Results Here, we incidentally observe that primary substrate miR159a (pri-miR159a), when embedded a UTR, could promote accumulation. The enhanced is attributed to earlier polyadenylation transcript within hybrid pri-miR159a-3′ UTR and, resultantly, poorly structured UTR. decay assays indicate stability, whereas highly destabilize vivo. Genome-wide DMS-MaPseq reveals prevailing inverse relationship between UTRs’ accumulation transcriptomes Arabidopsis , rice, even human. Mechanistically, transcripts with preferentially degraded by 3′–5′ exoribonuclease SOV 5′–3′ XRN4, leading decreased . Finally, engineer an endogenous FT alter -regulated flowering time Conclusions We conclude typically cause reduced harbored This pattern extends rice mammals. Furthermore, our study provides new strategy engineering modify plant traits agricultural production stability biotechnology.

Language: Английский

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Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

Plant Communications, Journal Year: 2022, Volume and Issue: 4(2), P. 100457 - 100457

Published: Oct. 4, 2022

Translational regulation is a critical step in the process of gene expression and governs synthesis proteins from mRNAs. Many studies have revealed translational plants response to various environmental stimuli. However, there been no documenting comprehensive landscape allele-specific efficiency multiple plant tissues, especially those rice, main staple crop that feeds nearly half world's population. Here we used RNA sequencing ribosome profiling data analyze transcriptome translatome an elite hybrid Shanyou 63 (SY63), its parental varieties Zhenshan 97 Minghui 63. The results patterns varied more among tissues than at transcriptional levels. We identified 3392 upstream open reading frames (uORFs), uORF-containing genes were enriched transcription factors. Only 668 13 492 long non-coding RNAs could be translated into peptides. Finally, discovered numerous with SY63 demonstrated some cis-regulatory elements may contribute allelic divergence efficiency. Overall, these findings improve our understanding rice provide information for molecular breeding research.

Language: Английский

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Transcriptome-wide m6A modification and poly(A) tail length changes in moso bamboo induced by gibberellin revealed by nanopore direct RNA sequencing

Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 225, P. 120549 - 120549

Published: Jan. 22, 2025

Language: Английский

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Developmentally-controlled generation of tRNA halves facilitates translational repression during sexual reproduction

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

Published: April 20, 2025

Abstract The role of transfer RNAs (tRNAs) as mediators between the genetic code and protein synthesis is well established. In parallel, tRNAs can generate different types functional small (sRNAs) that accumulate during stress certain developmental processes across diverse organisms. Interestingly, this class sRNAs (termed tRNA-derived sRNAs, tsRNAs) in male gamete mammals, insects, plants but their these reproductive cells unclear. Here, we determine molecular pathway tsRNA biogenesis plant gamete-containing structure (the pollen grain) identify mediating characteristic translational repression taking place tissue. Our data demonstrates male-accumulating tsRNAs are generated by a cell-controlled to aid accumulation key ensuring proper function grain.

Language: Английский

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Comprehensive genome annotation of the model ciliateTetrahymena thermophilaby in-depth epigenetic and transcriptomic profiling

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

Published: Feb. 1, 2024

Abstract The ciliate Tetrahymena thermophila is a well-established unicellular model eukaryote, contributing significantly to foundational biological discoveries. Despite its acknowledged importance, current biology studies face challenges due gene annotation inaccuracy, particularly the notable absence of untranslated regions (UTRs). To comprehensively annotate macronuclear genome, we collected extensive transcriptomic data spanning various cell stages. ascertain transcript orientation and transcription start/end sites, incorporated epigenetic marks displaying enrichment towards 5’ end bodies, including H3 lysine 4 tri-methylation (H3K4me3), H2A.Z, nucleosomes, N 6 -methyldeoxyadenine (6mA). Additionally, integrated Nanopore direct sequencing (DRS), strand-specific RNA-seq, ATAC-seq data. Using newly-developed bioinformatic pipeline, coupled with manual curation experimental validation, our work yielded substantial improvements models, addition 2,481 new genes, updates 6,257 existing incorporation 5,917 alternatively spliced isoforms. Furthermore, novel UTR information was annotated for 26,223 high-confidence genes. Intriguingly, 16% protein-coding genes were identified have natural antisense transcripts (NATs) characterized by high diversity in alternative splicing, thus offering insights into understanding transcriptional regulation. Our will enhance utility as robust genetic toolkit advancing research.

Language: Английский

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