Relationships between genome methylation, levels of non‐coding RNAs, mRNAs and metabolites in ripening tomato fruit

Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control

(2019) Jinhua Zuo et al.   Scientific Reports

Genome-wide identification of circRNAs involved in tomato fruit coloration

(2018) Rong Zhou et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling

(2018) Jinhua Zuo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MicroRNA1917 targets CTR4 splice variants to regulate ethylene responses in tomato

(2018) Yanling Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

The genetics of fruit flavour preferences

(2018) Harry J. Klee et al.   NATURE REVIEWS GENETICS

The mode of action of remorin1 in regulating fruit ripening at transcriptional and post-transcriptional levels

(2018) Jianghua Cai et al.   NEW PHYTOLOGIST

Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants

(2018) Pingchuan Deng et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative epigenomics reveals evolution of duplicated genes in potato and tomato

(2018) Lin Wang et al.   PLANT JOURNAL

CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening

(2018) Ran Li et al.   PLANT JOURNAL

Identification of circular RNAs and their targets during tomato fruit ripening

(2018) Junliang Yin et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

(2018) Yoshihito Shinozaki et al.   Nature Communications

A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening

(2018) Shan Li et al.   NEW PHYTOLOGIST

The RIN-regulated Small Auxin-Up RNA SAUR69 is involved in the unripe-to-ripe phase transition of tomato fruit via enhancement of the sensitivity to ethylene

(2018) Jun-Hye Shin et al.   NEW PHYTOLOGIST

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

(2017) Yunxiang Wang et al.   PHYSIOLOGIA PLANTARUM

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

(2017) Jidi Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

The regulation of carotenoid formation in tomato fruit

(2017) Eugenia M.A. Enfissi et al.   PLANT JOURNAL

TheRIN-MCFusion of MADS-Box Transcription Factors Has Transcriptional Activity and Modulates Expression of Many Ripening Genes

(2017) Shan Li et al.   PLANT PHYSIOLOGY

Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus

(2017) Mingming Cui et al.   PLoS One

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

(2017) Zhaobo Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen

(2017) Yuan Xia et al.   Scientific Reports

Identification and Functional Characterization of Tomato CircRNAs Derived from Genes Involved in Fruit Pigment Accumulation

(2017) Jinjuan Tan et al.   Scientific Reports

Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation

(2017) Phil Chi Khang Au et al.   Genes

Salt stress responsiveness of a wild cotton species (Gossypium klotzschianum) based on transcriptomic analysis

(2017) Yangyang Wei et al.   PLoS One

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

Evidence for ARGONAUTE4–DNA interactions in RNA-directed DNA methylation in plants

(2016) Sylvie Lahmy et al.   GENES & DEVELOPMENT

Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development

(2016) Zhengkun Qiu et al.   Molecular Plant

Comprehensive profiling of Ethylene Response Factors expression identifies ripening-associated ERF genes and their link to key regulators of fruit ripening in tomato (Solanum lycopersicum).

(2016) Mingchun Liu et al.   PLANT PHYSIOLOGY

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

(2016) Philippe Gallusci et al.   Frontiers in Plant Science

Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato

(2016) Da-Qi Fu et al.   Scientific Reports

Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance

(2015) Liyan Su et al.   BMC PLANT BIOLOGY

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

(2015) Benzhong Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Methylation of microRNA genes regulates gene expression in bisexual flower development in andromonoecious poplar

(2015) Yuepeng Song et al.   JOURNAL OF EXPERIMENTAL BOTANY

Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato

(2015) Xin Wang et al.   NEW PHYTOLOGIST

Tomato fruit carotenoid biosynthesis is adjusted to actual ripening progression by a light-dependent mechanism

(2015) Briardo Llorente et al.   PLANT JOURNAL

Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase

(2015) Qin Liu et al.   PLANT PHYSIOLOGY

A DEMETER-like DNA demethylase governs tomato fruit ripening

(2015) Ruie Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Battles and hijacks: noncoding transcription in plants

(2015) Federico Ariel et al.   TRENDS IN PLANT SCIENCE

Role of plant hormones and their interplay in development and ripening of fleshy fruits

(2014) Rahul Kumar et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptional control of fleshy fruit development and ripening

(2014) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Fruit Development and Ripening

(2013) Graham B. Seymour et al.   Annual Review of Plant Biology

Epigenetic regulation by long noncoding RNAs in plants

(2013) Jae Bok Heo et al.   CHROMOSOME RESEARCH

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

Molecular and genetic regulation of fruit ripening

(2013) Nigel E. Gapper et al.   PLANT MOLECULAR BIOLOGY

Network Inference Analysis Identifies an APRR2-Like Gene Linked to Pigment Accumulation in Tomato and Pepper Fruits

(2013) Y. Pan et al.   PLANT PHYSIOLOGY

Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

(2012) Jinhua Zuo et al.   BMC GENOMICS

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Genetics and Control of Tomato Fruit Ripening and Quality Attributes

(2011) Harry J. Klee et al.   Annual Review of Genetics

Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs

(2011) Padubidri V Shivaprasad et al.   EMBO JOURNAL

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation

(2011) Je Min Lee et al.   PLANT JOURNAL

Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor ( nor, rin ) and Ethylene Receptor ( Nr ) Mutants Reveals Novel Regulatory Interactions

(2011) Sonia Osorio et al.   PLANT PHYSIOLOGY

Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of thesftmutant

(2010) Xiaohui Zhang et al.   FEBS LETTERS

Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening

(2008) E. Teyssier et al.   PLANTA