Series Summary for DCD000315SR

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

Case Control

10.1101/gr.203679.115

GSE75734

Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in non-mammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ~42% of zebrafish SEs from all cells and tissues analyzed were associated with orthologs that also were associated with SEs in mouse and human. Compared to their non-associated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous vertebrate gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish enhancer characterizations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.

True

mickael.dong

April 13, 2017, 4:56 a.m.

Nov. 7, 2018, 5:55 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD006854BS DCD000315SR tissue Shkumatava Lab, Institut Curie AB 90 Days-2 Years brain adult
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001774AA DCD013277BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS DCD001765AA
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002145SQ DCD002132TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004616DT: FASTQ
DCD008963DT: BIGNARROWPEAK GRCz10/danRer10
DCD009068DT: BIGWIG GRCz10/danRer10
DCD016563DT: BAM GRCz11/danRer11
DCD016752DT: BED GRCz10/danRer10
DCD016753DT: BIGNARROWPEAK GRCz10/danRer10
DCD016754DT: BIGNARROWPEAK GRCz10/danRer10
DCD016757DT: BAM GRCz10/danRer10
DCD017168DT: BED GRCz10/danRer10
DCD017170DT: BAM GRCz10/danRer10
DCD017171DT: BIGNARROWPEAK GRCz10/danRer10
DCD017172DT: BIGNARROWPEAK GRCz10/danRer10
DCD017175DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001773AA DCD013278BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS DCD001764AA
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002144SQ DCD002131TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004615DT: FASTQ
DCD008964DT: BIGNARROWPEAK GRCz10/danRer10
DCD009069DT: BIGWIG GRCz10/danRer10
DCD016564DT: BAM GRCz11/danRer11
DCD016758DT: BIGNARROWPEAK GRCz10/danRer10
DCD016759DT: BIGNARROWPEAK GRCz10/danRer10
DCD016760DT: BED GRCz10/danRer10
DCD016764DT: BAM GRCz10/danRer10
DCD017173DT: BIGNARROWPEAK GRCz10/danRer10
DCD017174DT: BED GRCz10/danRer10
DCD017176DT: BIGNARROWPEAK GRCz10/danRer10
DCD017177DT: BIGWIG GRCz10/danRer10
DCD017178DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001765AA DCD013286BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002136SQ DCD002123TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004607DT: FASTQ
DCD016985DT: BAM GRCz10/danRer10
DCD017007DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001764AA DCD013287BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002135SQ DCD002122TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004606DT: FASTQ
DCD016976DT: BAM GRCz10/danRer10
DCD017020DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage anatomical_term Hours Post Fertilization
DCD006855BS DCD000315SR tissue Shkumatava Lab, Institut Curie AB 90 Days-2 Years testis adult
Applied Assay ID Biosample Replicate Assay
DCD001776AA DCD013275BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002147SQ DCD002134TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004618DT: FASTQ
DCD008960DT: BIGNARROWPEAK GRCz10/danRer10
DCD009073DT: BIGWIG GRCz10/danRer10
DCD016510DT: BED GRCz11/danRer11
DCD016514DT: BAM GRCz11/danRer11
DCD016787DT: BIGNARROWPEAK GRCz10/danRer10
DCD016788DT: BED GRCz10/danRer10
DCD016789DT: BAM GRCz10/danRer10
DCD016961DT: BIGNARROWPEAK GRCz10/danRer10
DCD017211DT: BED GRCz10/danRer10
DCD017212DT: BAM GRCz10/danRer10
DCD017213DT: BIGNARROWPEAK GRCz10/danRer10
DCD017214DT: BIGNARROWPEAK GRCz10/danRer10
DCD017215DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001775AA DCD013276BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002146SQ DCD002133TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004617DT: FASTQ
DCD008961DT: BIGNARROWPEAK GRCz10/danRer10
DCD009071DT: BIGWIG GRCz10/danRer10
DCD016511DT: BED GRCz11/danRer11
DCD016512DT: BAM GRCz11/danRer11
DCD016783DT: BED GRCz10/danRer10
DCD016784DT: BIGNARROWPEAK GRCz10/danRer10
DCD016785DT: BAM GRCz10/danRer10
DCD016786DT: BIGNARROWPEAK GRCz10/danRer10
DCD017204DT: BIGNARROWPEAK GRCz10/danRer10
DCD017206DT: BED GRCz10/danRer10
DCD017208DT: BAM GRCz10/danRer10
DCD017209DT: BIGNARROWPEAK GRCz10/danRer10
DCD017210DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001767AA DCD013284BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002138SQ DCD002125TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004609DT: FASTQ
DCD016974DT: BAM GRCz10/danRer10
DCD017018DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001766AA DCD013285BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002137SQ DCD002124TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004608DT: FASTQ
DCD016997DT: BAM GRCz10/danRer10
DCD017010DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage anatomical_term Hours Post Fertilization
DCD006856BS DCD000315SR tissue Shkumatava Lab, Institut Curie AB 90 Days-2 Years heart adult
Applied Assay ID Biosample Replicate Assay
DCD001777AA DCD013274BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002148SQ DCD002135TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004619DT: FASTQ
DCD008965DT: BIGNARROWPEAK GRCz10/danRer10
DCD009070DT: BIGWIG GRCz10/danRer10
DCD016505DT: BIGNARROWPEAK GRCz11/danRer11
DCD016506DT: BIGNARROWPEAK GRCz11/danRer11
DCD016507DT: BED GRCz11/danRer11
DCD016508DT: BIGWIG GRCz11/danRer11
DCD016509DT: BAM GRCz11/danRer11
DCD016673DT: BIGNARROWPEAK GRCz10/danRer10
DCD016674DT: BIGNARROWPEAK GRCz10/danRer10
DCD016675DT: BED GRCz10/danRer10
DCD016677DT: BAM GRCz10/danRer10
DCD017070DT: BIGNARROWPEAK GRCz10/danRer10
DCD017071DT: BIGNARROWPEAK GRCz10/danRer10
DCD017072DT: BED GRCz10/danRer10
DCD017074DT: BIGWIG GRCz10/danRer10
DCD017075DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001768AA DCD013283BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002139SQ DCD002126TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004610DT: FASTQ
DCD016989DT: BAM GRCz10/danRer10
DCD017041DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage anatomical_term Hours Post Fertilization
DCD006857BS DCD000315SR tissue Shkumatava Lab, Institut Curie AB 90 Days-2 Years heart adult
Applied Assay ID Biosample Replicate Assay
DCD001779AA DCD013272BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002150SQ DCD002137TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004621DT: FASTQ
DCD008970DT: BIGNARROWPEAK GRCz10/danRer10
DCD009074DT: BIGWIG GRCz10/danRer10
DCD016468DT: BIGNARROWPEAK GRCz11/danRer11
DCD016469DT: BIGNARROWPEAK GRCz11/danRer11
DCD016470DT: BED GRCz11/danRer11
DCD016471DT: BIGWIG GRCz11/danRer11
DCD016472DT: BAM GRCz11/danRer11
DCD016808DT: BIGNARROWPEAK GRCz10/danRer10
DCD016809DT: BED GRCz10/danRer10
DCD016810DT: BAM GRCz10/danRer10
DCD016811DT: BIGNARROWPEAK GRCz10/danRer10
DCD017243DT: BAM GRCz10/danRer10
DCD017244DT: BIGNARROWPEAK GRCz10/danRer10
DCD017245DT: BIGNARROWPEAK GRCz10/danRer10
DCD017246DT: BED GRCz10/danRer10
DCD017247DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001778AA DCD013273BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002149SQ DCD002136TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004620DT: FASTQ
DCD008962DT: BIGNARROWPEAK GRCz10/danRer10
DCD009075DT: BIGWIG GRCz10/danRer10
DCD016463DT: BIGNARROWPEAK GRCz11/danRer11
DCD016464DT: BIGNARROWPEAK GRCz11/danRer11
DCD016465DT: BED GRCz11/danRer11
DCD016466DT: BIGWIG GRCz11/danRer11
DCD016467DT: BAM GRCz11/danRer11
DCD016804DT: BIGNARROWPEAK GRCz10/danRer10
DCD016805DT: BIGNARROWPEAK GRCz10/danRer10
DCD016806DT: BED GRCz10/danRer10
DCD016807DT: BAM GRCz10/danRer10
DCD017238DT: BAM GRCz10/danRer10
DCD017239DT: BED GRCz10/danRer10
DCD017240DT: BIGNARROWPEAK GRCz10/danRer10
DCD017241DT: BIGNARROWPEAK GRCz10/danRer10
DCD017242DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001770AA DCD013281BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002141SQ DCD002128TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004612DT: FASTQ
DCD016979DT: BAM GRCz10/danRer10
DCD017003DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001769AA DCD013282BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002140SQ DCD002127TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004611DT: FASTQ
DCD016980DT: BAM GRCz10/danRer10
DCD017008DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage anatomical_term Hours Post Fertilization
DCD006858BS DCD000315SR tissue Shkumatava Lab, Institut Curie AB 90 Days-2 Years intestine adult
Applied Assay ID Biosample Replicate Assay
DCD001781AA DCD013270BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002152SQ DCD002139TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004623DT: FASTQ
DCD008969DT: BIGNARROWPEAK GRCz10/danRer10
DCD009081DT: BIGWIG GRCz10/danRer10
DCD016591DT: BED GRCz11/danRer11
DCD016595DT: BAM GRCz11/danRer11
DCD016751DT: BED GRCz10/danRer10
DCD016756DT: BAM GRCz10/danRer10
DCD017166DT: BED GRCz10/danRer10
DCD017167DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001780AA DCD013271BR ChIP-seq_Shkumatava_Lab_H3K27ac_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002151SQ DCD002138TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004622DT: FASTQ
DCD008966DT: BIGNARROWPEAK GRCz10/danRer10
DCD009072DT: BIGWIG GRCz10/danRer10
DCD016589DT: BED GRCz11/danRer11
DCD016594DT: BAM GRCz11/danRer11
DCD016750DT: BED GRCz10/danRer10
DCD016755DT: BAM GRCz10/danRer10
DCD017165DT: BED GRCz10/danRer10
DCD017169DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001772AA DCD013279BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002143SQ DCD002130TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004614DT: FASTQ
DCD016982DT: BAM GRCz10/danRer10
DCD017027DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001771AA DCD013280BR ChIP-seq_Shkumatava_Lab_input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD002142SQ DCD002129TR Shkumatava Lab, Institut Curie Illumina HiSeq 2500 11/14/2016
DCD004613DT: FASTQ
DCD016977DT: BAM GRCz10/danRer10
DCD017013DT: BAM GRCz11/danRer11