4.8 Article

Distinct chromatin signatures in the Arabidopsis male gametophyte

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

Cell biology of primary cell wall synthesis in plants

Ying Gu et al.

Summary: Building a complex structure like the cell wall is a well-orchestrated process that requires assembling many individual parts from different sources within the cell. Cell wall components are actively transported to and from the plasma membrane during diffuse growth. Motor proteins and interactions with the cytoskeleton help transport polysaccharides and enzymes to the correct location for cell wall construction, while newly formed cell walls during cytokinesis have special features.

PLANT CELL (2022)

Article Biochemistry & Molecular Biology

Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes

Mohamed Belhocine et al.

Summary: Broad H3K4 methylation domains are associated with T cell differentiation and T cell acute lymphoblastic leukemia. The varying breadth of these domains can distinguish between normal and neoplastic cells, and the genes associated with broad domains are deregulated in T-ALL. The ectopic expression of T-ALL oncogenic transcription factor affects the expression of broad domain-associated genes in preleukemic cells. Additionally, an H3K4me3 demethylase inhibitor selectively targets T-ALL cell lines depending on the extent and number of broad domains.

GENOME RESEARCH (2022)

Article Biochemistry & Molecular Biology

Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation

Guokai Xu et al.

Summary: This study reveals the molecular mechanisms underlying the reactivation of the FLC gene during plant embryonic development, ensuring that each generation must experience winter cold before flowering.

PLANT CELL (2022)

Article Biochemical Research Methods

pyGenomeTracks: reproducible plots for multivariate genomic datasets

Lucille Lopez-Delisle et al.

Summary: pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks, enabling the generation of highly customizable and publication ready images in a reproducible and standardized manner.

BIOINFORMATICS (2021)

Review Plant Sciences

From birth to function: Male gametophyte development in flowering plants

Jiaying Huang et al.

Summary: This article discusses the development of male germ cells in flowering plants, focusing on the differentiation and functional diversification of the vegetative cell and the male germ cell, which are crucial for the success of double fertilization.

CURRENT OPINION IN PLANT BIOLOGY (2021)

Article Biology

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidonsis

Michael Borg et al.

Summary: The alternation between morphologically distinct haploid and diploid life forms in plants and algae is controlled by epigenetic modifications such as the loss of H3K9me2 and global loss of H3K27me3. These events lead to significant changes in chromatin accessibility and transcriptional reprogramming, guiding the transition between generations in flowering plants.
Article Biochemistry & Molecular Biology

Integrated analysis of multimodal single-cell data

Yuhan Hao et al.

Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.
Article Biotechnology & Applied Microbiology

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

Michael Hagemann-Jensen et al.

NATURE BIOTECHNOLOGY (2020)

Article Plant Sciences

Transcriptomics of Arabidopsis sperm cells at single-cell resolution

Chandra Shekhar Misra et al.

PLANT REPRODUCTION (2019)

Review Biochemistry & Molecular Biology

Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC

Silvia Costa et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2019)

Article Biotechnology & Applied Microbiology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim et al.

NATURE BIOTECHNOLOGY (2019)

Article Plant Sciences

The embryonic transcriptome of Arabidopsis thaliana

Falko Hofmann et al.

PLANT REPRODUCTION (2019)

Article Genetics & Heredity

Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis

James Walker et al.

NATURE GENETICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Embryonic epigenetic reprogramming by a pioneer transcription factor in plants

Zeng Tao et al.

NATURE (2017)

Article Plant Sciences

Sperm cells are passive cargo of the pollen tube in plant fertilization

Jun Zhang et al.

NATURE PLANTS (2017)

Article Multidisciplinary Sciences

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

John Arne Dahl et al.

NATURE (2016)

Review Biochemistry & Molecular Biology

Chromatin remodeling and bivalent histone modifications in embryonic stem cells

Arigela Harikumar et al.

EMBO REPORTS (2015)

Article Biochemical Research Methods

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

Christian Schmidt et al.

NATURE METHODS (2015)

Article Cell Biology

Germline and Pluripotent Stem Cells

Wolf Reik et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Multidisciplinary Sciences

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

Julie Brind'Amour et al.

NATURE COMMUNICATIONS (2015)

Review Biochemistry & Molecular Biology

Chromatin dynamics during spermiogenesis

Christina Rathke et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2014)

Review Biochemistry & Molecular Biology

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

Edith Heard et al.

Review Plant Sciences

Embryo and endosperm, partners in seed development

Clement Lafon-Placette et al.

CURRENT OPINION IN PLANT BIOLOGY (2014)

Article Cell Biology

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

Benjamin R. Carone et al.

DEVELOPMENTAL CELL (2014)

Article Biochemical Research Methods

Full-length RNA-seq from single cells using Smart-seq2

Simone Picelli et al.

NATURE PROTOCOLS (2014)

Article Cell Biology

Epigenetic Regulation in Plant Responses to the Environment

David C. Baulcombe et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

Review Cell Biology

A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants

Xiaoqi Feng et al.

DEVELOPMENTAL CELL (2013)

Review Cell Biology

A double take on bivalent promoters

Philipp Voigt et al.

GENES & DEVELOPMENT (2013)

Article Biochemistry & Molecular Biology

Asymmetrically Modified Nucleosomes

Philipp Voigt et al.

Article Biochemistry & Molecular Biology

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

Joseph P. Calarco et al.

Editorial Material Developmental Biology

The ABC model of flower development: then and now

John L. Bowman et al.

DEVELOPMENT (2012)

Article Biochemical Research Methods

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell et al.

NATURE PROTOCOLS (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Multidisciplinary Sciences

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

Christian A. Ibarra et al.

SCIENCE (2012)

Review Plant Sciences

Male gametogenesis and germline specification in flowering plants

David Twell

SEXUAL PLANT REPRODUCTION (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Zygotic Resetting of the HISTONE 3 Variant Repertoire Participates in Epigenetic Reprogramming in Arabidopsis

Mathieu Ingouff et al.

CURRENT BIOLOGY (2010)

Review Cell Biology

Epigenetic Transitions in Germ Cell Development and Meiosis

Satya K. Kota et al.

DEVELOPMENTAL CELL (2010)

Review Multidisciplinary Sciences

Epigenetic Reprogramming in Plant and Animal Development

Suhua Feng et al.

SCIENCE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

R. Keith Slotkin et al.

Article Biochemistry & Molecular Biology

ANXUR1 and 2, Sister Genes to FERONIA/SIRENE, Are Male Factors for Coordinated Fertilization

Saori Miyazaki et al.

CURRENT BIOLOGY (2009)

Article Developmental Biology

Disruption of the pollen-expressed FERONIA homologs ANXUR1 and ANXUR2 triggers pollen tube discharge

Aurelien Boisson-Dernier et al.

DEVELOPMENT (2009)

Article Multidisciplinary Sciences

Distinctive chromatin in human sperm packages genes for embryo development

Saher Sue Hammoud et al.

NATURE (2009)

Article Multidisciplinary Sciences

Resetting of FLOWERING LOCUS C expression after epigenetic repression by vernalization

Candice C. Sheldon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Cell Biology

Chromatin signatures of pluripotent cell lines

V Azuara et al.

NATURE CELL BIOLOGY (2006)

Article Biochemistry & Molecular Biology

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

BE Bernstein et al.

Article Developmental Biology

Interaction of polycomb-group proteins controlling flowering in Arabidopsis

Y Chanvivattana et al.

DEVELOPMENT (2004)

Article Biochemistry & Molecular Biology

The human genome browser at UCSC

WJ Kent et al.

GENOME RESEARCH (2002)

Article Multidisciplinary Sciences

B and C floral organ identity functions require SEPALLATA MADS-box genes

S Pelaz et al.

NATURE (2000)