4.5 Article

Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

Related references

Note: Only part of the references are listed.
Article Biology

Molecular studies of cellulose synthase supercomplex from cotton fiber reveal its unique biochemical properties

Xingpeng Wen et al.

Summary: The study revealed the existence of a unique cellulose synthase supercomplex in cotton fibers, involved in the synthesis of secondary cell walls. Knocking out key genes led to the disappearance of this supercomplex, resulting in failure to thicken the SCW in cotton fibers. Additionally, cotton fiber CSS exhibited higher enzyme activity and a distinct microfibril structure.

SCIENCE CHINA-LIFE SCIENCES (2022)

Article Multidisciplinary Sciences

RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis

Lanxin Li et al.

Summary: This study investigates the mechanism of rapid alkalinization factors (RALFs) in regulating plant growth. It is found that RALF1 inhibits the growth of Arabidopsis thaliana roots by inducing apoplast alkalinization, which is mediated by the receptor FERONIA (FER) through net H+ influx. Additionally, the study reveals cross-talk between RALF1 and auxin signaling pathways, where RALF1 up-regulates auxin biosynthesis to regulate root growth. The biphasic action of RALF1 on growth allows plants to respond rapidly to environmental stimuli and reprogram growth and development in the long term.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

Andrew Farmer et al.

Summary: Plants consist of diverse and specialized cell types, with unique biological functions regulated by cell-type-specific transcriptional programs. Single-nucleus RNA sequencing and single-nucleus assay for transposase accessible chromatin sequencing technologies can establish plant cell-type-specific transcriptomes and uncover additional cell subtypes. The differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

MOLECULAR PLANT (2021)

Article Multidisciplinary Sciences

Ground tissue circuitry regulates organ complexity in maize and Setaria

Carlos Ortiz-Ramirez et al.

Summary: A cell-resolution map of maize root was generated using single-cell RNA sequencing, revealing an alternative configuration of the tissue formative transcription factor SHR. The study shows that the SHR pathway controls the expansion of cortical tissue, impacting the anatomical complexity of plants.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

A cis-regulatory atlas in maize at single-cell resolution

Alexandre P. Marand et al.

Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Article Cell Biology

Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf

Camila B. Lopez-Anido et al.

Summary: The study investigates the development and regulation of stomatal lineage in Arabidopsis leaf epidermis, revealing detailed cell differentiation processes using single-cell transcriptomics and genetics. It identifies the extended role of transcriptional regulator in reinforcing cell fate commitment through integration of genome-scale datasets and precise functional manipulations.

DEVELOPMENTAL CELL (2021)

Article Genetics & Heredity

The genomic basis of geographic differentiation and fiber improvement in cultivated cotton

Shoupu He et al.

Summary: The study revealed that extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated cotton, and haplotypic diversity from landraces is essential for adaptive evolution. Introgression and association analyses identified new fiber quality-related loci, showing that introgressed alleles from diploid cottons have a large effect on fiber quality improvement.

NATURE GENETICS (2021)

Article Multidisciplinary Sciences

Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

Tian-Qi Zhang et al.

Summary: Through single-cell RNA sequencing and chromatin accessibility survey, researchers profiled gene expression of different cell types during rice root development, elucidating regulatory networks and characteristic processes underlying root development.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Stochastic gene expression drives mesophyll protoplast regeneration

Mengxue Xu et al.

Summary: This study identified two transcription factors whose ectopic activation promotes protoplast regeneration, and found that isolating protoplasts induces enhanced expression variation at the genome level. Isolating protoplasts also leads to genome-wide increases in chromatin accessibility, which enhances protoplast regeneration by promoting stochastic activation of gene expression.

SCIENCE ADVANCES (2021)

Article Biotechnology & Applied Microbiology

Transcriptional landscape of highly lignified poplar stems at single-cell resolution

Yang Chen et al.

Summary: This study utilized optimized single-cell RNA sequencing technology to reveal the transcriptional landscape of cell types in highly lignified poplar stems. Different cell clusters with distinct phytohormone response patterns were identified, allowing reconstruction of cell differentiation trajectories involved in phloem and xylem development.

GENOME BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Yanping Long et al.

Summary: The study introduces a protoplasting-free approach for large-scale full-length RNA profiling at a single-nucleus level in plants, demonstrating its robustness in Arabidopsis root cells and developing endosperm. The method allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, facilitating the characterization of cell identities.

GENOME BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing

Zhixin Liu et al.

MOLECULAR PLANT (2020)

Article Biochemistry & Molecular Biology

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana

Ken Jean-Baptiste et al.

PLANT CELL (2019)

Article Biochemistry & Molecular Biology

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

Tian-Qi Zhang et al.

MOLECULAR PLANT (2019)

Article Biochemistry & Molecular Biology

Comprehensive Integration of Single-Cell Data

Tim Stuart et al.

Article Multidisciplinary Sciences

SCALE method for single-cell ATAC-seq analysis via latent feature extraction

Lei Xiong et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton

Kun Wang et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Double-slit photoelectron interference in strong-field ionization of the neon dimer

Maksim Kunitski et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Aaron T. L. Lun et al.

GENOME BIOLOGY (2019)

Article Biotechnology & Applied Microbiology

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

Laleh Haghverdi et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Nicholas Schaum et al.

NATURE (2018)

Article Biochemical Research Methods

TACO produces robust multisample transcriptome assemblies from RNA-seq

Yashar S. Niknafs et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

Jinpu Jin et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

Michiru Nishita et al.

SCIENTIFIC REPORTS (2017)

Article Genetics & Heredity

Domestication selected for deceleration of the circadian clock in cultivated tomato

Niels A. Mueller et al.

NATURE GENETICS (2016)

Article Multidisciplinary Sciences

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Polly Yingshan Hsu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Cell Biology

The Plant Circadian Clock: From a Simple Timekeeper to a Complex Developmental Manager

Sabrina E. Sanchez et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2016)

Review Biochemistry & Molecular Biology

Circadian Clock Genes Universally Control Key Agricultural Traits

Claire Bendix et al.

MOLECULAR PLANT (2015)

Review Biochemistry & Molecular Biology

SAUR Proteins as Effectors of Hormonal and Environmental Signals in Plant Growth

Hong Ren et al.

MOLECULAR PLANT (2015)

Article Biotechnology & Applied Microbiology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Plant Sciences

PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation

Zuoren Yang et al.

NEW PHYTOLOGIST (2014)

Editorial Material Multidisciplinary Sciences

PLANT SCIENCE Leaf veins share the time of day

Maria C. Marti et al.

NATURE (2014)

Article Biotechnology & Applied Microbiology

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion

Miyoshi Haruta et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3

Chun-Min Shan et al.

NATURE COMMUNICATIONS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Plant Sciences

Multiplex micro-respiratory measurements of Arabidopsis tissues

Yun Shin Sew et al.

NEW PHYTOLOGIST (2013)

Article Genetics & Heredity

The draft genome of a diploid cotton Gossypium raimondii

Kunbo Wang et al.

NATURE GENETICS (2012)

Article Biochemistry & Molecular Biology

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Plant Sciences

How cotton fibers elongate: a tale of linear cell-growth mode

Yong-Mei Qin et al.

CURRENT OPINION IN PLANT BIOLOGY (2011)

Article Plant Sciences

GhMYB25-like: a key factor in early cotton fibre development

Sally-Ann Walford et al.

PLANT JOURNAL (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Plant Sciences

The MYB transcription factor GhMYB25 regulates early fibre and trichome development

Adriane Machado et al.

PLANT JOURNAL (2009)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Control of plant trichome development by a cotton fiber MYB gene

S Wang et al.

PLANT CELL (2004)

Article Plant Sciences

Circadian ethylene production in cotton

RL Jasoni et al.

PLANT GROWTH REGULATION (2002)