Nature Plants最新文献_第5页

Achieving de novo scaffolding of chromosome-level haplotypes using Hi-C data 利用 Hi-C 数据实现染色体级单倍型的从头构建。

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-08-05 DOI: 10.1038/s41477-024-01756-2

引用次数: 0

Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm 水稻胚乳中持久性和阶段特异性印迹基因的多层表观遗传控制

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-30 DOI: 10.1038/s41477-024-01754-4

Kaoru Tonosaki, Daichi Susaki, Hatsune Morinaka, Akemi Ono, Hiroki Nagata, Hiroyasu Furuumi, Ken-Ichi Nonomura, Yutaka Sato, Keiko Sugimoto, Luca Comai, Katsunori Hatakeyama, Taiji Kawakatsu, Tetsu Kinoshita

{"title":"Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm","authors":"Kaoru Tonosaki, Daichi Susaki, Hatsune Morinaka, Akemi Ono, Hiroki Nagata, Hiroyasu Furuumi, Ken-Ichi Nonomura, Yutaka Sato, Keiko Sugimoto, Luca Comai, Katsunori Hatakeyama, Taiji Kawakatsu, Tetsu Kinoshita","doi":"10.1038/s41477-024-01754-4","DOIUrl":"10.1038/s41477-024-01754-4","url":null,"abstract":"In angiosperms, epigenetic profiles for genomic imprinting are established before fertilization. However, the causal relationships between epigenetic modifications and imprinted expression are not fully understood. In this study, we classified ‘persistent’ and ‘stage-specific’ imprinted genes on the basis of time-course transcriptome analysis in rice (Oryza sativa) endosperm and compared them to epigenetic modifications at a single time point. While the levels of epigenetic modifications are relatively low in stage-specific imprinted genes, they are considerably higher in persistent imprinted genes. Overall trends revealed that the maternal alleles of maternally expressed imprinted genes are activated by DNA demethylation, while the maternal alleles of paternally expressed imprinted genes with gene body methylation (gbM) are silenced by DNA demethylation and H3K27me3 deposition, and these regions are associated with an enriched motif related to Tc/Mar-Stowaway. Our findings provide insight into the stability of genomic imprinting and the potential variations associated with endosperm development, different cell types and parental genotypes. Time-course analysis of rice imprinted genes revealed persistent and stage-specific imprinted genes. These two classes showed differences in the degree of epigenetic status and biased expression in a temporal and spatial manner in the endosperm.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141794605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancers associated with unstable RNAs are rare in plants 植物中与不稳定 RNA 相关的增强子很少见

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-30 DOI: 10.1038/s41477-024-01741-9

Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, Sascha H. Duttke

{"title":"Enhancers associated with unstable RNAs are rare in plants","authors":"Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, Sascha H. Duttke","doi":"10.1038/s41477-024-01741-9","DOIUrl":"10.1038/s41477-024-01741-9","url":null,"abstract":"Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans. Unstable transcripts like enhancer RNAs are common in vertebrates. McDonald et al. show that such unstable transcripts are rare in plants and that promoters can function as potent enhancers, suggesting diverse cis-regulatory mechanisms in eukaryotes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01741-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141794606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The dramatic effects of well-intentioned but ill-designed management strategies in plant biological invasions 用心良苦但设计不当的管理策略对植物生物入侵的巨大影响

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-26 DOI: 10.1038/s41477-024-01747-3

Sergi Munné-Bosch, Jessyca Adelle Silva Santos

引用次数: 0

Arabidopsis floral buds are locked through stress-induced sepal tip curving 拟南芥花芽通过胁迫诱导的萼片尖端弯曲来锁定

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-26 DOI: 10.1038/s41477-024-01760-6

Duy-Chi Trinh, Isaty Melogno, Marjolaine Martin, Christophe Trehin, Richard S. Smith, Olivier Hamant

{"title":"Arabidopsis floral buds are locked through stress-induced sepal tip curving","authors":"Duy-Chi Trinh, Isaty Melogno, Marjolaine Martin, Christophe Trehin, Richard S. Smith, Olivier Hamant","doi":"10.1038/s41477-024-01760-6","DOIUrl":"10.1038/s41477-024-01760-6","url":null,"abstract":"In most plant species, sepals—the outermost floral organs—provide a protective shield for reproductive organs. How the floral bud becomes sealed is unknown. In Arabidopsis, we identified a small region at the sepal tip that is markedly curved inward early on and remains curved even after anthesis. Through modelling and quantitative growth analysis, we find that this hook emerges from growth arrest at the tip at a stage when cortical microtubules align with growth-derived tensile stress. Depolymerizing microtubules specifically at young sepal tips hindered hook formation and resulted in open floral buds. Mutants with defective growth pattern at the tip failed to curve inwards, whereas mutants with enhanced alignment of cortical microtubules at the tip exhibited a stronger hook. We propose that floral buds are locked due to a stress-derived growth arrest event curving the sepal tip and forming a rigid hook early on during flower development. Floral buds are closed structures that protect reproductive organs. Here the authors find that differential growth prescribes transverse tensile stress and growth arrest at the sepal tip, which in turn curve it and form a rigid hook to seal the floral bud.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141764313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pollen banking is a critical need for conserving plant diversity. 花粉银行是保护植物多样性的关键需求。

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-25 DOI: 10.1038/s41477-024-01757-1

Dustin Wolkis, Cecily Eltringham, Jeremie Fant, Jeremy Foster, Tiffany Knight, Abby Meyer, Hugo Romero-Saltos, Seana K Walsh, Alina Wood, Kayri Havens

引用次数: 0

Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress 利用植物与链霉菌之间的共同进化互动对抗干旱胁迫

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-24 DOI: 10.1038/s41477-024-01749-1

Hongwei Liu, Jiayu Li, Brajesh K. Singh

引用次数: 0

Spice of life 生活的调味品

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-23 DOI: 10.1038/s41477-024-01762-4

引用次数: 0

Author Correction: Rapid alkalinization factor 22 has a structural and signalling role in root hair cell wall assembly 作者更正：快速碱化因子 22 在根毛细胞壁组装中具有结构和信号作用。

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-23 DOI: 10.1038/s41477-024-01765-1

Sébastjen Schoenaers, Hyun Kyung Lee, Martine Gonneau, Elvina Faucher, Thomas Levasseur, Elodie Akary, Naomi Claeijs, Steven Moussu, Caroline Broyart, Daria Balcerowicz, Hamada AbdElgawad, Andrea Bassi, Daniel Santa Cruz Damineli, Alex Costa, José A. Feijó, Celine Moreau, Estelle Bonnin, Bernard Cathala, Julia Santiago, Herman Höfte, Kris Vissenberg

引用次数: 0

Smart gene, smart canopy 聪明的基因，聪明的天篷。

IF 15.8 1区生物学

Nature Plants Pub Date : 2024-07-19 DOI: 10.1038/s41477-024-01763-3

Jun Lyu

引用次数: 0