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Series GSE109344 Query DataSets for GSE109344
Status Public on Feb 11, 2019
Title Reprogramming of meiotic chromatin architecture during primate spermatogenesis
Organisms Macaca mulatta; Mus musculus
Experiment type Other
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Chromatin organization undergoes drastic reprogramming during gametogenesis . However, the three-dimensional chromatin structure and its reprogramming remain largely unknown, with even less known for primates. Here, by using a low-input Hi-C method we developed recently, we examined re-organization of 3D chromatin architecture during spermatogenesis in rhesus monkey (Macaca mulatta). Interestingly, we found that topologically associating domains (TADs) are partially dissolved in spermatogonia and are further depleted at the pachytene stage, before they gradually become consolidated in round spermatids and mature sperm. Strikingly, in local regions, pachytene chromatin is uniquely characterized by highly refined compartments that alternate between transcribing regions (Refined-A) and non-transcribed regions (Refined-B). Refined A/B occurs genomewide except for the X chromosome, which is inactivated at this stage. Interestingly, such chromatin organization remains intact upon transcription inhibition but is disrupted in spermatocytes deficient in SYCP2, a core component of synaptonemal complex. Strikingly, this is accompanied by the restoration of TADs in these mutant cells, suggesting that synaptonemal complex may restrict TADs and permit the emergence of strong local compartments. Taken together, these data reveal extensive reprogramming of higher-order meiotic chromatin architecture during mammalian gametogenesis.
Overall design Rhesus monkey spermatogonia (SPA), pachytene spermatocytes (PAC), round spermatids (RS) and sperm were obtained, together with fibroblast as control. Mouse PAC were treated with amantin to test the effect of trancription inhibition. Sycp2 KO or Top6bl KO mouse PAC-like cells were used to explore the contribution of synaptonemal complex towards higher order chromatin organization. HiC, STEM-seq and RNA-seq were performed in these cells at various stages during spermatogenesis.
Contributor(s) Wang Y, Zhang Y, Du Z, Wang H, Wu X, Xie W
Citation(s) 30735655
Submission date Jan 18, 2018
Last update date Apr 08, 2019
Contact name Wei Xie
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
Platforms (3)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24522 HiSeq X Ten (Macaca mulatta)
Samples (35)
GSM2940099 Hi-C_monkey_fibroblast_rep1
GSM2940100 Hi-C_monkey_fibroblast_rep2
GSM2940101 Hi-C_monkey_PAC_rep1
BioProject PRJNA430777
SRA SRP131117

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109344_RAW.tar 163.7 Mb (http)(custom) TAR (of BEDGRAPH)
GSE109344_monkey_fibro_allValidPairs.txt.gz 14.7 Gb (ftp)(http) TXT
GSE109344_monkey_fibro_pac_rs_gene.fpkm.txt.gz 348.5 Kb (ftp)(http) TXT
GSE109344_monkey_fibroblast_rep12_allValidPairs.txt.gz 7.8 Gb (ftp)(http) TXT
GSE109344_monkey_pac_allValidPairs.txt.gz 19.5 Gb (ftp)(http) TXT
GSE109344_monkey_pac_rep12_allValidPairs.txt.gz 7.6 Gb (ftp)(http) TXT
GSE109344_monkey_rs_allValidPairs.txt.gz 15.3 Gb (ftp)(http) TXT
GSE109344_monkey_rs_rep12_allValidPairs.txt.gz 8.7 Gb (ftp)(http) TXT
GSE109344_monkey_spa_allValidPairs.txt.gz 14.3 Gb (ftp)(http) TXT
GSE109344_monkey_spa_rep12_allValidPairs.txt.gz 4.5 Gb (ftp)(http) TXT
GSE109344_monkey_sperm_allValidPairs.txt.gz 11.0 Gb (ftp)(http) TXT
GSE109344_monkey_sperm_rep12_allValidPairs.txt.gz 3.9 Gb (ftp)(http) TXT
GSE109344_mouse_mutant_exp.fpkm.txt.gz 325.3 Kb (ftp)(http) TXT
GSE109344_mouse_pac_amanitin_hic_allValidPairs.txt.gz 5.8 Gb (ftp)(http) TXT
GSE109344_mouse_pac_wt_allValidPairs.txt.gz 6.2 Gb (ftp)(http) TXT
GSE109344_mouse_pac_wt_mutant_gene.fpkm.txt.gz 268.3 Kb (ftp)(http) TXT
GSE109344_mouse_top6blko_pac_like_hic_allValidPairs.txt.gz 3.1 Gb (ftp)(http) TXT
GSE109344_new_mouse_SYCP2_KO_PAC_HiC_allValidPairs.txt.gz 3.6 Gb (ftp)(http) TXT
GSE109344_new_mouse_sycp2ko_pac_like_hic_allValidPairs.txt.gz 3.7 Gb (ftp)(http) TXT
GSE109344_new_mouse_top6bl_KO_LEPL_HiC_allValidPairs.txt.gz 2.8 Gb (ftp)(http) TXT
GSE109344_new_mouse_top6bl_KO_ZYGL_HiC_allValidPairs.txt.gz 3.1 Gb (ftp)(http) TXT
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Processed data provided as supplementary file

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