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Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

https://doi.org/10.1093/molbev/msv210
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolution by Gene Duplication
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Floral and insect-induced volatile formation in Arabidopsis lyrata ssp. petraea, a perennial, outcrossing relative of A. thaliana
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Improved plant transformation vectors for fluorescent protein tagging
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Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
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Animal Transcription Networks as Highly Connected, Quantitative Continua
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Gene Duplication and the Evolution of Plant MADS-box Transcription Factors
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Complexes of MADS-box proteins are sufficient to convert leaves into floral organs
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Effect of natural genetic variation on enhancer selection and function
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
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High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
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Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
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Transposable elements and the evolution of regulatory networks
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Regulation of transcription in plants: mechanisms controlling developmental switches
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Evolution of transcription factor binding in metazoans — mechanisms and functional implications
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Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants
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Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
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Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to be 157 Mb and thus 25 % Larger than the Arabidopsis Genome Initiative Estimate of 125 Mb
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Mechanisms of Recent Genome Size Variation in Flowering Plants
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The selfing syndrome: a model for studying the genetic and evolutionary basis of morphological adaptation in plants
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Structural determinants of DNA recognition by plant MADS-domain transcription factors
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PLAZA 3.0: an access point for plant comparative genomics
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Rapid Evolution of cis-Regulatory Sequences via Local Point Mutations
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Multiple whole-genome alignments without a reference organism
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cis -Regulatory and Protein Evolution in Orthologous and Duplicate Genes
inferredcites →https://doi.org/10.1105/tpc.111.088914openalex-snapshot
POD1 Regulates Pollen Tube Guidance in Response to Micropylar Female Signaling and Acts in Early Embryo Patterning inArabidopsis
inferredcites →https://doi.org/10.1105/tpc.112.103010openalex-snapshot
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inferredcites →https://doi.org/10.1105/tpc.113.113209openalex-snapshot
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inferredcites →https://doi.org/10.1105/tpc.114.127001openalex-snapshot
Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis
inferredcites →https://doi.org/10.1105/tpc.2.8.755openalex-snapshot
Early Flower Development in Arabidopsis
inferredcites →https://doi.org/10.1111/j.1365-313x.2011.04521.xopenalex-snapshot
Journey through the past: 150 million years of plant genome evolution
inferredcites →https://doi.org/10.1111/nyas.12466openalex-snapshot
The causes and molecular consequences of polyploidy in flowering plants
inferredcites →https://doi.org/10.1111/tpj.12434openalex-snapshot
Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species
inferredcites →https://doi.org/10.1126/science.1185244openalex-snapshot
Orchestration of Floral Initiation by APETALA1
inferredcites →https://doi.org/10.1146/annurev-genom-082410-101412openalex-snapshot
The Repatterning of Eukaryotic Genomes by Random Genetic Drift
inferredcites →https://doi.org/10.1146/annurev.genom.7.080505.115623openalex-snapshot
Transcriptional Regulatory Elements in the Human Genome
inferredcites →https://doi.org/10.1186/1471-2229-9-5openalex-snapshot
In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana
inferredcites →https://doi.org/10.1186/1746-4811-7-11openalex-snapshot
ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r41openalex-snapshot
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
inferredcites →https://doi.org/10.1371/journal.pbio.0030314openalex-snapshot
Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
inferredcites →https://doi.org/10.1371/journal.pbio.1000090openalex-snapshot
Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower
inferredcites →https://doi.org/10.1371/journal.pbio.1001420openalex-snapshot
Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1002384openalex-snapshot
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1004226openalex-snapshot
The Functional Consequences of Variation in Transcription Factor Binding
inferredcites →https://doi.org/10.3732/ajb.93.1.1openalex-snapshot
Floral development in three species of Impatiens (Balsaminaceae)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants
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ChIP-Hub provides an integrative platform for exploring plant regulome
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Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence
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Evolutionary causes and consequences of gene duplication
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Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs
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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
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Identification and functional validation of super-enhancers in Arabidopsis thaliana
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The analysis of Gene Regulatory Networks in plant evo-devo
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A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors
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The release of sexual conflict after sex loss is associated with evolutionary changes in gene expression
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Extensive genome evolution distinguishes maize within a stable tribe of grasses
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Floral Organogenesis: When Knowing Your ABCs Is Not Enough
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Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data
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Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize
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Factors determining chromosomal localization of transposable elements in plants
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MADS evolution : insights into evolutionary changes in transcription factors and their binding sites
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Insight Into the Multiple Branches Traits of a Mutant in Larix olgensis by Morphological, Cytological, and Transcriptional Analyses
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Jasmonic acid negatively regulates branch growth in pear
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The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation
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Genome-Wide Identification and Expression Profiling of MYC Transcription Factor Family in Toona sinensis Under Abiotic and Hormonal Stresses
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Unwinding BRAHMA Functions in Plants
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Comprehensive Evolutionary Analysis of the SMXL Gene Family in Rosaceae: Further Insights into Its Origin, Expansion, Diversification, and Role in Regulating Pear Branching
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