Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

[1]  Yue Liu,et al.  A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data , 2017, Functional & Integrative Genomics.

[2]  Jinsheng Lai,et al.  Dynamic and Antagonistic Allele-Specific Epigenetic Modifications Controlling the Expression of Imprinted Genes in Maize Endosperm. , 2017, Molecular plant.

[3]  Kang Zhang,et al.  Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum , 2016, Scientific Reports.

[4]  N. Provart,et al.  ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium , 2016, Nucleic Acids Res..

[5]  Dewei Zheng,et al.  Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton1[OPEN] , 2016, Plant Physiology.

[6]  F. Ali,et al.  Response and Tolerance Mechanism of Cotton Gossypium hirsutum L. to Elevated Temperature Stress: A Review , 2016, Front. Plant Sci..

[7]  Q. He,et al.  Glutathione S-Transferase Gene Family in Gossypium raimondii and G. arboreum: Comparative Genomic Study and their Expression under Salt Stress , 2016, Front. Plant Sci..

[8]  M. Guiltinan,et al.  Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor , 2015, BMC Plant Biology.

[9]  Xiaoyun Liu,et al.  Regulation of Histone Methylation and Reprogramming of Gene Expression in the Rice Inflorescence Meristem , 2015, Plant Cell.

[10]  Lei Fang,et al.  Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement , 2015, Nature Biotechnology.

[11]  He Zhang,et al.  Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution , 2015, Nature Biotechnology.

[12]  Xun Xu,et al.  Genome sequence of the cultivated cotton Gossypium arboreum , 2014, Nature Genetics.

[13]  M. Fromm,et al.  H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis thaliana. , 2014, Molecular plant.

[14]  Ping Zheng,et al.  CottonGen: a genomics, genetics and breeding database for cotton research , 2013, Nucleic Acids Res..

[15]  X. Liu,et al.  Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. , 2013, Molecular plant.

[16]  V. Colot,et al.  Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation , 2013 .

[17]  Chao-jun Zhang,et al.  mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage , 2013, PloS one.

[18]  John Z. Yu,et al.  The draft genome of a diploid cotton Gossypium raimondii , 2012, Nature Genetics.

[19]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[20]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[21]  A. Berr,et al.  Histone modifications in transcriptional activation during plant development. , 2011, Biochimica et biophysica acta.

[22]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[23]  M. Lauria,et al.  Epigenetic control of gene regulation in plants. , 2011, Biochimica et biophysica acta.

[24]  Chao-jun Zhang,et al.  Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). , 2011, Genomics.

[25]  X. Deng,et al.  The epigenome and plant development. , 2011, Annual review of plant biology.

[26]  Wen-Hsiung Li,et al.  Coordinated histone modifications are associated with gene expression variation within and between species. , 2011, Genome research.

[27]  Andrew J. Bannister,et al.  Regulation of chromatin by histone modifications , 2011, Cell Research.

[28]  C. Luo,et al.  ANCORP: a high-resolution approach that generates distinct chromatin state models from multiple genome-wide datasets. , 2010, The Plant journal : for cell and molecular biology.

[29]  B. Haas,et al.  Advancing RNA-Seq analysis , 2010, Nature Biotechnology.

[30]  S. Salzberg,et al.  NIH Public Access Author Manuscript , 2006 .

[31]  G. Pavesi,et al.  Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing , 2010, Briefings Bioinform..

[32]  Julia A. Lasserre,et al.  Histone modification levels are predictive for gene expression , 2010, Proceedings of the National Academy of Sciences.

[33]  Y. Qi,et al.  Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids[W] , 2010, Plant Cell.

[34]  Xing Wang Deng,et al.  Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis[W] , 2009, The Plant Cell Online.

[35]  F. Denoeud,et al.  Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.

[36]  Songgang Li,et al.  High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression[W] , 2008, The Plant Cell Online.

[37]  Yong Zhang,et al.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..

[38]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[39]  S. Henikoff,et al.  Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. , 2003, Genetics.

[40]  H. Woodrow,et al.  : A Review of the , 2018 .

[41]  Hui Li,et al.  Genome-Wide Analysis of Histone Modifications : H 3 K 4 me 2 , H 3 K 4 me 3 , H 3 K 9 ac , and H 3 K 27 ac in Oryza sativa L . Japonica , 2013 .

[42]  P. Reich,et al.  Biomass allocation to leaves, stems and roots: meta-analyses of interspecific variation and environmental control. , 2012, The New phytologist.

[43]  Y. Qi,et al.  Genome-wide and Organ-specific Landscapes of Epigenetic Modifications and Their Relationships to Mrna and Small Rna Transcriptomes in Maize , 2022 .