H3K4me2 functions as a repressive epigenetic mark in plants

Position-specific intron retention is mediated by the histone methyltransferase SDG725

(2018) Gang Wei et al.   BMC BIOLOGY

Chromatin-remodeling factor OsINO80 is involved in regulation of gibberellin biosynthesis and is crucial for rice plant growth and development

(2018) Chao Li et al.   Journal of Integrative Plant Biology

SIP1 participates in regulation of flowering time in rice by recruiting OsTrx1 to Ehd1

(2018) Pengfei Jiang et al.   NEW PHYTOLOGIST

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Identification of H3K4me1-associated proteins at mammalian enhancers

(2017) Andrea Local et al.   NATURE GENETICS

SET DOMAIN GROUP701 encodes a H3K4-methytransferase and regulates multiple key processes of rice plant development

(2017) Kunpeng Liu et al.   NEW PHYTOLOGIST

CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality

(2017) Helen Hoffmeister et al.   NUCLEIC ACIDS RESEARCH

ATX3 , ATX4 , and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development

(2017) Li-Qun Chen et al.   PLANT PHYSIOLOGY

An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS

(2016) Ryan Rickels et al.   MOLECULAR CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways

(2016) Feng Tan et al.   PLANT PHYSIOLOGY

Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription

(2016) Saravanan Ramakrishnan et al.   Nature Communications

SET DOMAIN GROUP 708, a histone H3 lysine 36-specific methyltransferase, controls flowering time in rice (Oryza sativa )

(2015) Bing Liu et al.   NEW PHYTOLOGIST

CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data

(2015) Jiawei Wang et al.   PLANT JOURNAL

ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes?

(2014) Michael Fromm et al.   CURRENT OPINION IN PLANT BIOLOGY

ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1) is required for cell production, patterning, and morphogenesis in root development

(2014) Selene Napsucialy-Mendivil et al.   JOURNAL OF EXPERIMENTAL BOTANY

Trithorax Group Protein Oryza sativa Trithorax1 Controls Flowering Time in Rice via Interaction with Early heading date3

(2014) S. C. Choi et al.   PLANT PHYSIOLOGY

Disruption of FAT10–MAD2 binding inhibits tumor progression

(2014) Steven Setiawan Theng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

(2013) D. Hu et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

(2013) Zhou Du et al.   Molecular Plant

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome

(2012) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

(2012) Jing-Quan Lim et al.   GENOME BIOLOGY

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

The COMPASS Family of H3K4 Methylases in Drosophila

(2011) M. Mohan et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice

(2011) Pengfei Sui et al.   PLANT JOURNAL

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana

(2010) Karin van Dijk et al.   BMC PLANT BIOLOGY

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Analysis of H3K4 Methylation Defines MLL Family Member Targets and Points to a Role for MLL1-Mediated H3K4 Methylation in the Regulation of Transcriptional Initiation by RNA Polymerase II

(2009) P. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

The need for speed

(2009) Paul Flicek   GENOME BIOLOGY

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

(2008) M. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

The Highly Similar Arabidopsis Homologs of Trithorax ATX1 and ATX2 Encode Proteins with Divergent Biochemical Functions

(2008) A. Saleh et al.   PLANT CELL

ARABIDOPSIS TRITHORAX1 Dynamically Regulates FLOWERING LOCUS C Activation via Histone 3 Lysine 4 Trimethylation

(2008) S. Pien et al.   PLANT CELL

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL