{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Antonio Lentini"],"organism":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14392"],"description":["Sex-chromosome dosage represents a challenge for heterogametic species to maintain correct proportion of gene products across chromosomes in each sex. While therian mammals (XX/XY system) achieve near-perfect balance of X-chromosome mRNAs through X-upregulation and X-inactivation, birds (ZW/ZZ system) have been found to lack efficient compensation at RNA level, challenging the necessity of resolving major gene-dosage discrepancies in avian cells. Through allele-resolved multiome analyses, we comprehensively examined dosage compensation in female (ZW), male (ZZ), and rare intersex (ZZW) chicken. Remarkably, this revealed that females exhibit upregulation of their single Z through increased transcriptional burst frequency similar to mammalian X-upregulation, and that Z-protein levels are further balanced via enhanced translation efficiency in females. Global analyses of transcriptional kinetics elements in birds demonstrate remarkable conservation of the genomic encoding of burst kinetics between mammals and birds. Our study uncovers new mechanisms for achieving sex-chromosome dosage compensation and highlights the importance of gene-dosage balance across diverse species."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Triplicate pellets of 10^6 cells were collected for all conditions, flash frozen and stored at −80 °C before use.  Immunoprecipitation was performed using the EpiFinder™ Genome kit (Epigenica, EpGe001) according to the manufacturer's instructions. In brief, native frozen cell pellets were lysed and MNase digested to mono- to tri-nucleosome fragments and ligated with double-stranded DNA adaptors in a one-pot reaction.","Sequencing - Fragment size distribution and library quality were assessed on a Bioanalyzer instrument using a high sensitivity dsDNA chip and concentration was determined using a Qubit's high sensitivity dsDNA kit on a Qubit 3.0 fluorometer. Libraries were combined and sequenced on an MGI DNBSEQ-G400RS instrument platform with paired-end settings.","Sample Collection - Pellets of 1 million chicken embryonic fibroblast cells were collected by centrifugation at 300g for 5min. To eliminate serum-containing medium residues, the pellets were washed 3 times in 1x PBS before a final centrifugation at 300g for 5min. Finally, the supernatant was completely removed without disturbing the cell pellets and the samples were placed in -80°C until further processing.","Library Construction - Barcoded samples were then pooled and aliquoted into individual ChIP reactions with Protein A (Dynabeads; Thermofisher) for the following antibodies: H3K4me3 [Millipore; 04-745], H3K27ac [Active Motif; 39034], H3K9ac [Active Motif; 39137-AF], H4K16ac [Millipore; 07-329]. Upon incubation overnight with rotation  at 4 °C and washing steps, ChIP DNA was isolated and set up in sequential reactions of adaptor fill-in, in vitro transcription, RNA 3′ adapter ligation, reverse transcription and PCR amplification to generate final libraries for each ChIP."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quality evaluation, mapping, scaling the data to input, and the creation of bigWig files was done using the minute workflow (v. 0.6.0; settings: fragment_size: 400, max_barcode_errors: 1, mapping_quality: 0).","Sequence Alignment - Raw ChIP-seq data was converted to FASTQ format and demultiplexed using mgikit (v. 0.1.4; settings: -m 1), allowing for up to one mismatch in the barcodes. Each FASTQ file of the demultiplexed samples were concatenated across the four lanes, creating the sample-specific FASTQ files for further processing. The mapping was done using the GRCg6a reference genome, and low mapping regions were excluded."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-G400"],"study_type":["ChIP-seq"],"species":["Gallus gallus"],"pubmed_authors":["Antonio Lentini","Björn Reinius","Natali Papanicolaou"],"additional_accession":[]},"is_claimable":false,"name":"Multi-layer dosage compensation of the avian Z chromosome (MINUTE-ChIP)","description":"Sex-chromosome dosage represents a challenge for heterogametic species to maintain correct proportion of gene products across chromosomes in each sex. While therian mammals (XX/XY system) achieve near-perfect balance of X-chromosome mRNAs through X-upregulation and X-inactivation, birds (ZW/ZZ system) have been found to lack efficient compensation at RNA level, challenging the necessity of resolving major gene-dosage discrepancies in avian cells. Through allele-resolved multiome analyses, we comprehensively examined dosage compensation in female (ZW), male (ZZ), and rare intersex (ZZW) chicken. Remarkably, this revealed that females exhibit upregulation of their single Z through increased transcriptional burst frequency similar to mammalian X-upregulation, and that Z-protein levels are further balanced via enhanced translation efficiency in females. Global analyses of transcriptional kinetics elements in birds demonstrate remarkable conservation of the genomic encoding of burst kinetics between mammals and birds. Our study uncovers new mechanisms for achieving sex-chromosome dosage compensation and highlights the importance of gene-dosage balance across diverse species.","dates":{"release":"2025-06-30T00:00:00Z","modification":"2024-08-27T16:48:11.449Z","creation":"2024-08-27T16:48:11.449Z"},"accession":"E-MTAB-14392","cross_references":{"ENA":["ERP163588"],"Biostudies":["E-MTAB-14393","E-MTAB-14391","E-MTAB-14390"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}