Research graph
References from Databases and prospects of dynamic gene regulation in eukaryotes: A mini review. Local targets link to admitted publications; unresolved targets remain external evidence.
The noncoding RNA revolution-trashing old rules to forge new ones
10.1016/j.cell.2014.03.008 · 2014 · External reference
Plant noncoding RNAs: hidden players in development and stress responses
10.1146/annurev-cellbio-100818-125218 · 2019 · External reference
Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases
10.1038/s41580-022-00476-9 · 2022 · External reference
Dicer-independent RNA-directed DNA methylation in Arabidopsis
10.1038/cr.2016.122 · 2016 · External reference
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
10.1038/nrg3683 · 2014 · External reference
RNA Pol IV and V in gene silencing: rebel polymerases evolving away from Pol II's rules
10.1016/j.pbi.2015.07.005 · 2015 · External reference
Combinatorial function of transcription factors and cofactors
10.1016/j.gde.2016.12.007 · 2017 · External reference
Eukaryotic core promoters and the functional basis of transcription initiation
10.1038/s41580-018-0028-8 · 2018 · External reference
Mysteries of gene regulation: promoters are not the sole triggers of gene expression
10.1016/j.csbj.2022.08.058 · 2022 · External reference
Epigenetic inheritance: concepts, mechanisms and perspectives
10.3389/fnmol.2018.00292 · 2018 · External reference
Epigenetic mechanisms of paternal stress in offspring development and diseases
2021 · External reference
Transgenerational inheritance or resetting of stress-induced epigenetic modifications: two sides of the same coin
10.3389/fpls.2015.00699 · 2015 · External reference
DNA methylation: roles in mammalian development
10.1038/nrg3354 · 2013 · External reference
Dynamics of DNA methylation and its functions in plant growth and development
10.3389/fpls.2021.596236 · 2021 · External reference
Regulation of chromatin by histone modifications
10.1038/cr.2011.22 · 2011 · External reference
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation
10.1038/s41588-020-00736-4 · 2020 · External reference
Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma
10.1186/s13148-018-0450-y · 2018 · External reference
DNA methylation and its basic function
10.1038/npp.2012.112 · 2013 · External reference
Dynamics and function of DNA methylation in plants
10.1038/s41580-018-0016-z · 2018 · External reference
Genome-wide evolutionary analysis of eukaryotic DNA methylation
10.1126/science.1186366 · 2010 · External reference
Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond
10.4161/15384101.2014.949201 · 2014 · External reference
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
10.1038/s41467-020-18035-1 · 2020 · External reference
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling
10.1186/s13059-019-1654-y · 2019 · External reference
FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin
10.1101/gr.5533506 · 2007 · External reference
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
10.1093/nar/gkab1113 · 2022 · External reference
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants
10.1093/nar/gky1081 · 2019 · External reference
An integrated encyclopedia of DNA elements in the human genome
10.1038/nature11247 · 2012 · External reference
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
10.1093/nar/gkab996 · 2022 · External reference
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors
10.1093/nar/gky822 · 2019 · External reference
GTRD: an integrated view of transcription regulation
10.1093/nar/gkaa1057 · 2021 · External reference
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
10.1093/nar/gkx1106 · 2018 · External reference
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
10.1093/nar/gkz1062 · 2020 · External reference
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
10.1093/nar/gkab1039 · 2022 · External reference
hTFtarget: a comprehensive database for regulations of human transcription factors and their targets
10.1016/j.gpb.2019.09.006 · 2020 · External reference
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
10.1093/nar/gky1094 · 2019 · External reference
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data
10.1093/nar/gkw965 · 2017 · External reference
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
2022 · External reference
PCSD: a plant chromatin state database
10.1093/nar/gkx919 · 2018 · External reference
PlantRegMap: charting functional regulatory maps in plants
2020 · External reference
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
10.1093/nar/gkw982 · 2017 · External reference
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
10.1093/nar/gkq1120 · 2011 · External reference
GRASSIUS: a platform for comparative regulatory genomics across the grasses
10.1104/pp.108.128579 · 2009 · External reference
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
10.1093/bib/bbn016 · 2008 · External reference
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
10.1093/nar/gkj143 · 2006 · External reference
UniBind: maps of high-confidence direct TF-DNA interactions across nine species
10.1186/s12864-021-07760-6 · 2021 · External reference
Mapping genome-wide transcription-factor binding sites using DAP-seq
10.1038/nprot.2017.055 · 2017 · External reference
From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases
10.3389/fgene.2020.00424 · 2020 · External reference
Systematic localization of common disease-associated variation in regulatory DNA
10.1126/science.1222794 · 2012 · External reference
Widespread long-range cis-regulatory elements in the maize genome
10.1038/s41477-019-0547-0 · 2019 · External reference
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli
10.1093/nar/10.9.2997 · 1982 · External reference
Sequence logos: a new way to display consensus sequences
10.1093/nar/18.20.6097 · 1990 · External reference
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
10.1093/nar/gku117 · 2014 · External reference
Determination and inference of eukaryotic transcription factor sequence specificity
10.1016/j.cell.2014.08.009 · 2014 · External reference
MEME-ChIP: motif analysis of large DNA datasets
10.1093/bioinformatics/btr189 · 2011 · External reference
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
10.1038/75556 · 2000 · External reference
Ontology, "The Gene Ontology resource: enriching a GOld mine
10.1093/nar/gkaa1113 · 2021 · External reference
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
10.1093/nar/gkac1000 · 2023 · External reference
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
10.1002/pro.3978 · 2021 · External reference
Conservation and divergence of methylation patterning in plants and animals
10.1073/pnas.1002720107 · 2010 · External reference
Molecular biology. Phylogeny of methylomes
10.1126/science.1190738 · 2010 · External reference
Human DNA methylomes at base resolution show widespread epigenomic differences
10.1038/nature08514 · 2009 · External reference
Global epigenomic reconfiguration during mammalian brain development
10.1126/science.1237905 · 2013 · External reference
Human body epigenome maps reveal noncanonical DNA methylation variation
10.1038/nature14465 · 2015 · External reference
The honey bee epigenomes: differential methylation of brain DNA in queens and workers
10.1371/journal.pbio.1000506 · 2010 · External reference
Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome
10.1093/bib/bbx019 · 2018 · External reference
The importance of DNA methylation of exons on alternative splicing
10.1261/rna.064865.117 · 2018 · External reference
DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress
10.1371/journal.pgen.1009710 · 2021 · External reference
Transposon age and non-CG methylation
10.1038/s41467-020-14995-6 · 2020 · External reference
Principles and challenges of genomewide DNA methylation analysis
10.1038/nrg2732 · 2010 · External reference
The CpG island searcher: a new WWW resource
2003 · External reference
CpGcluster: a distance-based algorithm for CpG-island detection
10.1186/1471-2105-7-446 · 2006 · External reference
An improved version of the DNA Methylation database (MethDB)
10.1093/nar/gkg093 · 2003 · External reference
PubMeth: a cancer methylation database combining text-mining and expert annotation
10.1093/nar/gkm788 · 2008 · External reference
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms
10.1093/nar/gkab937 · 2022 · External reference
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database
10.1093/nar/gkab1088 · 2022 · External reference
HeteroMeth: a database of Cell-to-cell heterogeneity in DNA methylation
10.1016/j.gpb.2018.07.002 · 2018 · External reference
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease
10.1093/nar/gkx985 · 2018 · External reference
MethBank 3.0: a database of DNA methylomes across a variety of species
10.1093/nar/gkx1139 · 2018 · External reference
NGSmethDB 2017: enhanced methylomes and differential methylation
10.1093/nar/gkw996 · 2017 · External reference
Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes
10.1093/database/baz130 · 2019 · External reference
scMethBank: a database for single-cell whole genome DNA methylation maps
10.1093/nar/gkab833 · 2022 · External reference
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
10.1038/nbt.2462 · 2013 · External reference
Widespread natural variation of DNA methylation within angiosperms
10.1186/s13059-016-1059-0 · 2016 · External reference
RNA degradome--its biogenesis and functions
10.1093/nar/gkr450 · 2011 · External reference
miRNA gene promoters are frequent targets of aberrant DNA methylation in human breast cancer
10.1371/journal.pone.0054398 · 2013 · External reference
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
10.1093/database/bav052 · 2015 · External reference
F. Consortium, and F. Drablos, "EpiFactors: a comprehensive database of human epigenetic factors and complexes
10.1093/database/bav067 · 2015 · External reference
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs
10.1186/s13072-020-00354-8 · 2020 · External reference
HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes
10.1093/nar/gkr1125 · 2012 · External reference
HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants
10.1093/database/baw014 · 2016 · External reference
SysPTM 2.0: an updated systematic resource for post-translational modification
10.1093/database/bau025 · 2014 · External reference
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes
2017 · External reference
Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes
10.1038/ng.3385 · 2015 · External reference
The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes
10.1186/s13148-021-01126-1 · 2021 · External reference
The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium
10.1038/s41467-019-10648-5 · 2019 · External reference
Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals
10.1016/j.csbj.2021.12.027 · 2022 · External reference
RiceENCODE: a comprehensive epigenomic database as a rice Encyclopedia of DNA Elements
10.1016/j.molp.2021.08.018 · 2021 · External reference
HHMD: the human histone modification database
10.1093/nar/gkp968 · 2010 · External reference
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae
10.1093/bioinformatics/btm236 · 2007 · External reference
The chromatin accessibility landscape of primary human cancers
10.1126/science.aav1898 · 2018 · External reference
ATACdb: a comprehensive human chromatin accessibility database
10.1093/nar/gkaa943 · 2021 · External reference
EIN2-directed histone acetylation requires EIN3-mediated positive feedback regulation in response to ethylene
10.1093/plcell/koaa029 · 2021 · External reference
Polycomb Repressive Complex 2 and KRYPTONITE regulate pathogen-induced programmed cell death in Arabidopsis
10.1093/plphys/kiab035 · 2021 · External reference
Integrated multi-omics framework of the plant response to jasmonic acid
10.1038/s41477-020-0605-7 · 2020 · External reference
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
10.1038/s41588-022-01089-w · 2022 · External reference
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
10.1038/ng.3539 · 2016 · External reference
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
10.1038/s41467-021-20940-y · 2021 · External reference
Long-range interactions between proximal and distal regulatory regions in maize
10.1038/s41467-019-10603-4 · 2019 · External reference
Synthesizing genome regulation data with vote-counting
10.1016/j.tig.2022.06.012 · 2022 · External reference
Transcription factor binding predicts histone modifications in human cell lines
10.1073/pnas.1412081111 · 2014 · External reference
10.1016/j.csbj.2021.12.015 · 2022 · Admitted local publication
10.1016/j.csbj.2020.11.006 · 2020 · Admitted local publication
Generating specificity in genome regulation through transcription factor sensitivity to chromatin
10.1038/s41576-022-00512-6 · 2022 · External reference
Structural insights into the interaction between transcription factors and the nucleosome
10.1016/j.sbi.2021.06.016 · 2021 · External reference
Cistrome and epicistrome features shape the regulatory DNA landscape
10.1016/j.cell.2016.08.063 · 2016 · External reference
Impact of cytosine methylation on DNA binding specificities of human transcription factors
2017 · External reference
Base-resolution methylation patterns accurately predict transcription factor bindings in vivo
10.1093/nar/gkv151 · 2015 · External reference
Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes
10.1016/j.celrep.2017.05.069 · 2017 · External reference
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo
10.1101/gr.146654.112 · 2013 · External reference
Transcription factors as readers and effectors of DNA methylation
10.1038/nrg.2016.83 · 2016 · External reference
Sensitivity of transcription factors to DNA methylation
10.1042/ebc20190033 · 2019 · External reference
Toward a mechanistic understanding of DNA methylation readout by transcription factors
2019 · External reference
Effects of cytosine methylation on transcription factor binding sites
10.1186/1471-2164-15-119 · 2014 · External reference
DNA methylation and methyl-CpG binding proteins: developmental requirements and function
10.1007/s00412-009-0221-9 · 2009 · External reference
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions
10.1186/s12859-022-04865-x · 2022 · External reference
Measuring quantitative effects of methylation on transcription factor-DNA binding affinity
10.1126/sciadv.aao1799 · 2017 · External reference
The interplay between DNA and histone methylation: molecular mechanisms and disease implications
10.15252/embr.202051803 · 2021 · External reference
Genome-scale DNA methylation maps of pluripotent and differentiated cells
10.1038/nature07107 · 2008 · External reference
The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase
10.1093/nar/gkg332 · 2003 · External reference
Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin
10.1016/s0960-9822(03)00432-9 · 2003 · External reference
Intragenic DNA methylation prevents spurious transcription initiation
10.1038/nature21373 · 2017 · External reference
Non-coding RNA: what is functional and what is junk?
10.3389/fgene.2015.00002 · 2015 · External reference
Overview of MicroRNA biogenesis, mechanisms of actions, and circulation
10.3389/fendo.2018.00402 · 2018 · External reference
Gene regulation by long non-coding RNAs and its biological functions
10.1038/s41580-020-00315-9 · 2021 · External reference
Non-coding RNAs: regulating disease progression and therapy resistance in hepatocellular carcinoma
10.3390/cancers12051243 · 2020 · External reference
Mechanisms of long non-coding RNAs in cancers and their dynamic regulations
10.3390/cancers12051245 · 2020 · External reference
An integrated expression atlas of miRNAs and their promoters in human and mouse
10.1038/nbt.3947 · 2017 · External reference
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data
10.1093/nar/gkr604 · 2011 · External reference
High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
10.1101/gr.242222.118 · 2019 · External reference
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
10.1101/gr.193607.115 · 2015 · External reference
Unique features of long non-coding RNA biogenesis and function
10.1038/nrg.2015.10 · 2016 · External reference
ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos
10.1038/nprot.2006.383 · 2006 · External reference
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
10.1101/gr.100552.109 · 2010 · External reference
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
10.1038/ng1473 · 2004 · External reference
Chromatin accessibility profiling by ATAC-seq
10.1038/s41596-022-00692-9 · 2022 · External reference
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
10.1101/pdb.prot5384 · 2010 · External reference
Dynamic regulation of nucleosome positioning in the human genome
10.1016/j.cell.2008.02.022 · 2008 · External reference
Nucleosome organization in the Drosophila genome
10.1038/nature06929 · 2008 · External reference
Hi-C 3.0: improved protocol for genome-wide chromosome conformation capture
10.1002/cpz1.198 · 2021 · External reference
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks
10.1007/978-1-61779-292-2_11 · 2012 · External reference
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
10.1038/nbt1414 · 2008 · External reference
RNA sequencing and analysis
10.1101/pdb.top084970 · 2015 · External reference
