{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Masomeh Askari"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16210"],"description":["Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Recent studies have revealed that prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation during later stages of prophase I. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating permissive chromatin at meiotic gene promoters before meiosis, thereby controlling the timely activation of meiotic genetic program during later meiosis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - CUT&Tag libraries were prepared as described by Henikoff et al. (2020) (DOI: 10.17504/protocols.io.x54v9mkmzg3e/v5). Briefly, ~80,000 cells were bound to Concanavalin A-coated magnetic beads and incubated sequentially with primary and secondary antibodies, followed by pAG-Tn5 tagmentation at 55 °C for 1 h. DNA was released with SDS–Proteinase K treatment, PCR-amplified using NEBNext 2× PCR master mix (11 cycles, 98 °C 10 s / 60 °C 10 s), and purified with AMPure XP beads. Final libraries were quantified and assessed for quality before sequencing.","Nucleic Acid Extraction - Following tagmentation and reverse crosslinking, DNA was purified using AMPure XP beads (Beckman Coulter, A63880) according to the manufacturer’s instructions, and eluted in 22 µl Tris-HCl (pH 8.5).","Sequencing - CUT&Tag libraries were sequenced as paired-end 79 bp × 79 bp reads using the Illumina NextSeq 550 platform at the Karolinska Institute Genomics Core Facility. Sequencing data were demultiplexed and converted to FASTQ format using bcl2fastq (v2.20). Raw reads were adapter- and quality-trimmed with fastp (v0.24.0) and aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.4) with parameters --local --very-sensitive --no-unal --no-mixed --no-discordant. Only uniquely mapped reads were retained for downstream analysis. Performer: Karolinska Institute Genomics Core Facility Hardware: Illumina NextSeq 550","Sample Collection - FACS-purified spermatogonia (SpG) were isolated from adult mouse testes. Cells were collected and counted prior to CUT&Tag library preparation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Processed bigWig files were generated from aligned BAMs using deepTools (v3.5.1). Coverage was normalized using spike-in-free scaling factors (10,000 / spike-in read count) to enable cross-sample comparison."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["CUT&RUN"],"species":["Mus musculus"],"pubmed_authors":["Masomeh Askari"],"additional_accession":[]},"is_claimable":false,"name":"Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice","description":"Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Recent studies have revealed that prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation during later stages of prophase I. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating permissive chromatin at meiotic gene promoters before meiosis, thereby controlling the timely activation of meiotic genetic program during later meiosis.","dates":{"release":"2025-11-20T00:00:00Z","modification":"2026-05-27T14:54:22.34Z","creation":"2025-11-20T20:29:55.619Z"},"accession":"E-MTAB-16210","cross_references":{"ENA":["ERP185437"],"EFO":["EFO_0002944","EFO_0009973","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}