H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots

[1]  C. Dean,et al.  The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2 , 2020, Proceedings of the National Academy of Sciences.

[2]  L. Hennig,et al.  Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis , 2020, Genome Biology.

[3]  Tomás C. Moyano,et al.  Local changes in chromatin accessibility and transcriptional networks underlying the nitrate response in Arabidopsis roots. , 2019, Molecular plant.

[4]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[5]  Geo Pertea,et al.  Transcriptome assembly from long-read RNA-seq alignments with StringTie2 , 2019, Genome Biology.

[6]  J. Altmüller,et al.  Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem , 2019, Journal of experimental botany.

[7]  E. Meshorer,et al.  Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency. , 2019, Developmental cell.

[8]  Sandy L. Klemm,et al.  Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.

[9]  Chenlong Li,et al.  Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings , 2019, Plant direct.

[10]  Jennifer I. C. Benichou,et al.  Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq , 2018, Plant Methods.

[11]  Xing Fu,et al.  Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants , 2018, Nature Genetics.

[12]  Marko Bajic,et al.  Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type‐specific transcription factor networks , 2018, The Plant journal : for cell and molecular biology.

[13]  R. Klose,et al.  Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes , 2018, bioRxiv.

[14]  R. Deal,et al.  Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq. , 2018, Methods in molecular biology.

[15]  H. Bourbon,et al.  Genome Regulation by Polycomb and Trithorax: 70 Years and Counting , 2017, Cell.

[16]  Margaret Woodhouse,et al.  Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules , 2017, Plant Cell.

[17]  F. Romero-Campero,et al.  H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity , 2017, Genome Biology.

[18]  M. Tolstorukov,et al.  Enhancer regions show high histone H3.3 turnover that changes during differentiation , 2016, eLife.

[19]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[20]  F. Turck,et al.  The age of multiplexity: recruitment and interactions of Polycomb complexes in plants. , 2016, Current opinion in plant biology.

[21]  Chongsheng He,et al.  Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements , 2016, PLoS genetics.

[22]  G. V. James,et al.  Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2 , 2015, PLoS Genetics.

[23]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[24]  L. Hennig,et al.  Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. , 2015, The Plant journal : for cell and molecular biology.

[25]  M. Calonje,et al.  PRC1 is taking the lead in PcG repression. , 2015, The Plant journal : for cell and molecular biology.

[26]  L. Hennig,et al.  The polycomb group protein regulatory network. , 2015, Annual review of plant biology.

[27]  B. Snel,et al.  The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history , 2015, BMC Evolutionary Biology.

[28]  Alyssa C. Frazee,et al.  Ballgown bridges the gap between transcriptome assembly and expression analysis , 2015, Nature Biotechnology.

[29]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[30]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[31]  M. Calonje PRC1 marks the difference in plant PcG repression. , 2014, Molecular plant.

[32]  F. Turck,et al.  VAL- and AtBMI1-Mediated H2Aub Initiate the Switch from Embryonic to Postgerminative Growth in Arabidopsis , 2013, Current Biology.

[33]  L. Hennig,et al.  Arabidopsis MSI1 connects LHP1 to PRC2 complexes , 2013, The EMBO journal.

[34]  X. Zhou,et al.  Dense Chromatin Activates Polycomb Repressive Complex 2 to Regulate H3 Lysine 27 Methylation , 2012, Science.

[35]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[36]  P. Angrand,et al.  A human Polycomb isoform lacking the Pc box does not participate to PRC1 complexes but forms protein assemblies and represses transcription , 2012, Epigenetics.

[37]  Lucy J. Colwell,et al.  A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence , 2012, Proceedings of the National Academy of Sciences.

[38]  D. Zilberman,et al.  EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development , 2012, PLoS genetics.

[39]  L. Hennig,et al.  Distinct modes of DNA accessibility in plant chromatin , 2012, Nature Communications.

[40]  J. C. del Pozo,et al.  Regulation of the new Arabidopsis imprinted gene AtBMI1C requires the interplay of different epigenetic mechanisms. , 2012, Molecular plant.

[41]  A. Truax,et al.  ChIP and Re-ChIP assays: investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind. , 2012, Methods in molecular biology.

[42]  R. Kingston,et al.  Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. , 2011, Genes & development.

[43]  D. Reinberg,et al.  L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. , 2011, Molecular cell.

[44]  O. Clarenz,et al.  Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation , 2011, PLoS genetics.

[45]  Arp Schnittger,et al.  Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition , 2011, PLoS genetics.

[46]  M. Koch,et al.  Keeping Cell Identity in Arabidopsis Requires PRC1 RING-Finger Homologs that Catalyze H2A Monoubiquitination , 2010, Current Biology.

[47]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[48]  F. Turck,et al.  Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part A: ChIP-chip molecular methods. , 2010, Methods in molecular biology.

[49]  M. Ramalho-Santos,et al.  Open chromatin in pluripotency and reprogramming , 2010, Nature Reviews Molecular Cell Biology.

[50]  David S. Lapointe,et al.  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data , 2010, BMC Bioinformatics.

[51]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[52]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[53]  W. Shen,et al.  Polycomb Silencing of KNOX Genes Confines Shoot Stem Cell Niches in Arabidopsis , 2008, Current Biology.

[54]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[55]  Sébastien Lê,et al.  FactoMineR: An R Package for Multivariate Analysis , 2008 .

[56]  Z. R. Sung,et al.  EMBRYONIC FLOWER1 Participates in Polycomb Group–Mediated AG Gene Silencing in Arabidopsis[W] , 2008, The Plant Cell Online.

[57]  Jo Handelsman,et al.  EPIGENETIC REGULATION OF CELLULAR MEMORY BY THE POLYCOMB AND TRITHORAX GROUP PROTEINS , 2008 .

[58]  V. Gaudin,et al.  The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation , 2007, Nature Structural &Molecular Biology.

[59]  Vincent Colot,et al.  Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27 , 2007, PLoS genetics.

[60]  U. Grossniklaus,et al.  Different Polycomb group complexes regulate common target genes in Arabidopsis , 2006, EMBO reports.

[61]  Yi Zhang,et al.  Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. , 2005, Molecular cell.

[62]  M. Vidal,et al.  Role of histone H2A ubiquitination in Polycomb silencing , 2004, Nature.

[63]  K. Nakahigashi,et al.  Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. , 2003, Plant & cell physiology.

[64]  Hur-Song Chang,et al.  EMF Genes Maintain Vegetative Development by Repressing the Flower Program in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.007831. , 2003, The Plant Cell Online.

[65]  Brigitte Wild,et al.  Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.

[66]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[67]  V. Gaudin,et al.  Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. , 2001, Development.

[68]  P. Adler,et al.  Drosophila genes Posterior Sex Combs and Suppressor two of zeste encode proteins with homology to the murine bmi-1 oncogene , 1991, Nature.