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GEO Series: GSE75164

Title: Sperm is epigenetically programmed to regulate gene transcription in embryo

Summary

Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in embryos. We observe that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks, at fertilization, deregulates gene expression in the resulting embryos in a paternal chromatin dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits.


Contributors: Charles Bradshaw, Marta Teperek, Angela Simeone, Vincent Gaggioli, Kei Miiyamoto, George Allen, Serap Erkek, Taejoon Kwon, Edward Marcotte, Philip Zegermann, Charles Bradshaw, Antoine Peters, John Gurdon, Jerome Jullien

Experiment Type: 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin

Experiment Reagents: Tg(CMV:mRFP), Tg(Mmu.kdm5bdel), Tg(Mmu.kdm6bdel).

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE + spermatozoon - NF10.5-11.5 (control) GSM1944440  GSM1944442  GSM1944444  GSM1944446  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CMV:mRFP) oocyte stage VI stage VI oocyte
Intracytoplasmic sperm injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
   WE + kdm5b + spermatozoon - NF10.5-11.5 DEG GSM1944417  GSM1944419  GSM1944422  GSM1944424  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Mmu.kdm5bdel) kdm5b.L oocyte stage VI stage VI oocyte
Intracytoplasmic sperm injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
   WE + kdm6b + spermatozoon - NF10.5-11.5 DEG GSM1944439  GSM1944441  GSM1944443  GSM1944445  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Mmu.kdm6bdel) kdm6b.L oocyte stage VI oocyte
Intracytoplasmic sperm injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
input spermatid - adult GSM1944490  GSM1944492  GSM1944494  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
   H3K27me3 spermatid - adult (1) GSM1944504  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage H3f3a Ab25
   H3K27me3 spermatid - adult (2) GSM1944503  GSM1944505  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage H3f3a Ab24
   H3K4me2 spermatid - adult GSM1944491  GSM1944493  GSM1944495  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage H3f3a Ab3
   H3K9me3 spermatid - adult GSM1944500  GSM1944501  GSM1944502  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage H3f3a Ab26
input spermatozoon - adult GSM1944473  GSM1944475  GSM1944477  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage  
   H3K27me3 spermatozoon - adult (1) GSM1944488  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage H3f3a Ab25
   H3K27me3 spermatozoon - adult (2) GSM1944487  GSM1944489  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage H3f3a Ab24
   H3K4me2 spermatozoon - adult GSM1944474  GSM1944476  GSM1944478  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage H3f3a Ab3
   H3K9me3 spermatozoon - adult GSM1944484  GSM1944485  GSM1944486  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage H3f3a Ab26
input spermatozoon - adult (MBD-Seq) GSM1944461  GSM1944462  GSM1944463  MBD-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage  
   spermatozoon - adult (MBD-Seq) GSM1944464  GSM1944465  GSM1944466  MBD-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage  
input spermatozoon - adult H3K4me3 GSM1944480  GSM1944482  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage  
   H3K4me3 spermatozoon - adult GSM1944479  GSM1944481  GSM1944483  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage Tri-Methyl H3f3a Ab19
input spermatid - adult H3K4me3 GSM1944496  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
   H3K4me3 spermatid - adult (1) GSM1944497  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage H3f3a Ab27
   H3K4me3 spermatid - adult (2) GSM1944498  GSM1944499  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage Tri-Methyl H3f3a Ab19
WE + spermatid - NF10.5-11.5 (control) GSM1944426  GSM1944428  GSM1944429  GSM1944431  GSM1944435  GSM1944437  GSM1944438  GSM1944449  GSM1944450  GSM1944451  GSM1944453  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CMV:mRFP) oocyte stage VI stage VI oocyte
Intracytoplasmic spermatid injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
   WE + kdm5b + spermatid - NF10.5-11.5 DEG GSM1944425  GSM1944427  GSM1944430  GSM1944432  GSM1944433  GSM1944434  GSM1944436  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Mmu.kdm5bdel) kdm5b.L oocyte stage VI stage VI oocyte
Intracytoplasmic spermatid injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
   WE + kdm6b + spermatid - NF10.5-11.5 DEG GSM1944447  GSM1944448  GSM1944452  GSM1944454  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Mmu.kdm6bdel) kdm6b.L oocyte stage VI oocyte
Intracytoplasmic spermatid injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
input spermatid - adult (MBD-Seq) GSM1944467  GSM1944468  GSM1944469  MBD-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
   spermatid - adult (MBD-Seq) GSM1944470  GSM1944471  GSM1944472  MBD-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
WE + UV + spermatid - NF10.5-11.5 (PE) GSM1944401  GSM1944410  GSM1944411  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
UV light   mature egg stage nucleus
Intracytoplasmic spermatid injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
WE + UV + spermatid - NF10.5-11.5 (SE) GSM1944403  GSM1944405  GSM1944407  GSM1944409  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
UV light   mature egg stage nucleus
Intracytoplasmic spermatid injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
WE + UV + spermatozoon - NF10.5-11.5 (PE) GSM1944400  GSM1944412  GSM1944413  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
Intracytoplasmic sperm injection   mature egg stage egg
UV light   mature egg stage nucleus
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
WE + UV + spermatozoon - NF10.5-11.5 (SE) GSM1944402  GSM1944404  GSM1944406  GSM1944408  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
Intracytoplasmic sperm injection   mature egg stage egg
UV light   mature egg stage nucleus
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
WE + spermatozoon - NF10.5-11.5 GSM1944418  GSM1944420  GSM1944421  GSM1944423  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CMV:mRFP) oocyte stage VI stage VI oocyte
Intracytoplasmic sperm injection   mature egg stage egg
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 11.5  
spermatid - adult GSM1944414  GSM1944415  GSM1944416  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
spermatid - adult (MNase-Seq) GSM1944458  GSM1944459  GSM1944460  MNase-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage  
spermatozoon - adult (MNase-Seq) GSM1944455  GSM1944456  GSM1944457  MNase-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatozoon adult frog stage  
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