Conservation and divergence of canonical and non-canonical imprinting in murids DOI Creative Commons
Julien Richard Albert, Toshihiro Kobayashi, Azusa Inoue

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: March 14, 2023

Abstract Background Genomic imprinting affects gene expression in a parent-of-origin manner and has profound impact on complex traits including growth behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified this murid. To systematically identify genomic imprints rat, we use low input methods for genome-wide analyses of DNA methylation profile embryonic extraembryonic tissues at allele-specific resolution. Results We 14 26 these tissues, respectively, with 10 both tissues. Comparative mouse reveal that orthologous associated canonical are conserved embryo proper Muridae family. However, only 3 paternally expressed tissue murids, all which non-canonical H3K27me3 imprints. The discovery 8 novel unique consistent more rapid evolution imprinting. Meta-analysis reveals multiple mechanisms by species-specific may be established, deposition oocyte, appearance ZFP57 binding motifs, insertion endogenous retroviral promoters. Conclusions In summary, provide an expanded list loci extent conservation expression, potential responsible

Language: Английский

The transcription factor GABPA is a master regulator of naive pluripotency DOI Creative Commons
Chengjie Zhou, Meng Wang, Chunxia Zhang

et al.

Nature Cell Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Abstract The establishment of naive pluripotency is a continuous process starting with the generation inner cell mass (ICM) that then differentiates into epiblast (EPI). Recent studies have revealed key transcription factors (TFs) for ICM formation, but which TFs initiate EPI specification remains unknown. Here, using targeted rapid protein degradation system, we show GABPA not only regulator major ZGA, also master specifier required by regulating 47% genes during E3.5 to E4.5 transition. Chromatin binding dynamics analysis suggests controls formation at least partly gene promoters occupied regulators TFAP2C and SOX2 establish E4.5. Our study uncovers as regulator, supports notion mammalian requires dynamic stepwise multi-TF regulatory network.

Language: Английский

Citations

1
Dynamics of replication timing during mammalian development DOI Creative Commons
Tsunetoshi Nakatani

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Recent developments in low-input genomics techniques have greatly advanced the analysis of order which DNA is replicated genome - that is, replication timing (RT) and its interrelationships with other processes. RT correlates or anticorrelates genomic-specific parameters such as gene expression, chromatin accessibility, histone modifications, 3D structure genome, but significance how they influence each relate to biological processes remains unclear. In this review I discuss results recent analyses RT, time at it remodeled consolidated during embryogenesis, influences development differentiation, regulatory mechanisms factors involved.

Language: Английский

Citations

1
Epigenome dynamics in early mammalian embryogenesis DOI

Adam Burton,

Maria‐Elena Torres‐Padilla

Nature Reviews Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

Citations

1
Multigenerational epigenetic inheritance: Transmitting information across generations DOI
Nick Burton, Eric Lieberman Greer

Seminars in Cell and Developmental Biology, Journal Year: 2021, Volume and Issue: 127, P. 121 - 132

Published: Aug. 21, 2021

Language: Английский

Citations

56
Features and mechanisms of canonical and noncanonical genomic imprinting DOI Open Access
Courtney W. Hanna, Gavin Kelsey

Genes & Development, Journal Year: 2021, Volume and Issue: 35(11-12), P. 821 - 834

Published: June 1, 2021

Genomic imprinting is the monoallelic expression of a gene based on parent origin and consequence differential epigenetic marking between male female germlines. Canonically, genomic mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in methylation-independent imprinting, termed “noncanonical imprinting.” In this review, we compare contrast what currently known about underlying mechanisms, role endogenous retroviral elements, conservation canonical noncanonical imprinting.

Language: Английский

Citations

51
Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages DOI Creative Commons
Daniel Andergassen, Zachary D. Smith, Helene Kretzmer

et al.

Developmental Cell, Journal Year: 2021, Volume and Issue: 56(21), P. 2995 - 3005.e4

Published: Nov. 1, 2021

Highlights•Comprehensive inventory of epigenetic mechanisms that regulate parent-specific imprints•Extraembryonic ectoderm uses broader array imprinting than the epiblast•G9a-mediated pathway controls ERV-driven promoters non-canonical imprinted genes•Polycomb silences secondary X chromosome targets in extraembryonic ectodermSummaryGenomic and inactivation (XCI) require to encode allele-specific expression, but how these specific tasks are accomplished at single loci or across chromosomal scales remains incompletely understood. Here, we systematically disrupt essential pathways within polymorphic embryos order examine canonical genomic as well XCI. We find DNA methylation Polycomb group repressors indispensable for autosomal imprinting, albeit distinct gene sets. Moreover, relies on a spectrum mechanisms, including targeting maternal endogenous retrovirus (ERV)-driven by H3K9 methyltransferase G9a. further identify Polycomb-dependent -independent clusters chromosome, which appear reflect domains Xist-mediated suppression. From our data, assemble comprehensive maintain eutherian mammals, an expanded view placental lineage.Graphical abstract

Language: Английский

Citations

49
Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing DOI Creative Commons
Kentaro Mochizuki, Jafar Sharif, Kenjiro Shirane

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 2, 2021

Silencing of a subset germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these are generally hypomethylated in the blastocyst, implicating alternative repressive pathways before implantation. Indeed, embryonic stem cells (ESCs), an overlapping set genes, including "genome-defence" (GGD) upregulated following deletion H3K9 methyltransferase SETDB1 or subunits non-canonical PRC1 complex PRC1.6. Here, we show that pre-implantation embryos and naïve ESCs (nESCs), promoters bound by PRC1.6 DNA-binding MGA/MAX/E2F6 enriched for RING1B-dependent H2AK119ub1 H3K9me3. Accordingly, repression nESCs shows greater dependence on than DNAme. In contrast, GGD hypermethylated epiblast-like (EpiLCs) their silencing SETDB1, PRC1.6/RING1B DNAme, with H3K9me3 DNAme establishment MGA binding. Thus, initially repressed PRC1.6, subsequently engaged post-implantation embryos.

Language: Английский

Citations

45
The Molecular and Nuclear Dynamics of X-Chromosome Inactivation DOI Open Access
François Dossin, Édith Heard

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: unknown, P. a040196 - a040196

Published: July 26, 2021

François Dossin1,2 and Edith Heard1 1European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany Correspondence: edith.heard{at}embl.org ↵2 Present address: Genome Integrity, Immunity Cancer Department of Immunology, Genomes Genetics, Institut Pasteur, 75015 Paris, France.

Language: Английский

Citations

42
Histone Mono-Ubiquitination in Transcriptional Regulation and Its Mark on Life: Emerging Roles in Tissue Development and Disease DOI Creative Commons
Liat Oss‐Ronen,

Tzlil Sarusi,

Idan Cohen

et al.

Cells, Journal Year: 2022, Volume and Issue: 11(15), P. 2404 - 2404

Published: Aug. 4, 2022

Epigenetic regulation plays an essential role in driving precise transcriptional programs during development and homeostasis. Among epigenetic mechanisms, histone mono-ubiquitination has emerged as important post-transcriptional modification. Two major events are the of H2A at lysine 119 (H2AK119ub), placed by Polycomb repressive complex 1 (PRC1), H2B 120 (H2BK120ub), heteromeric RNF20/RNF40 complex. Both these play fundamental roles shaping chromatin landscape cellular identity. In this review we summarize current understandings molecular concepts behind mono-ubiquitination, focusing on their recently identified tissue pathologies.

Language: Английский

Citations

32
Revisiting chromatin packaging in mouse sperm DOI

Qiangzong Yin,

Chih-Hsiang Yang, Olga Strelkova

et al.

Genome Research, Journal Year: 2023, Volume and Issue: 33(12), P. 2079 - 2093

Published: Dec. 1, 2023

Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact hydrodynamic head, it has been proposed that chromatin architecture helps program gene expression early embryo. Scores of genome-wide surveys have reported patterns accessibility, nucleosome localization, histone modification, chromosome folding. Here, we revisit these studies light recent reports obtained from mouse epididymis are contaminated with low levels cell-free chromatin. absence proper lysis, readily recapitulate multiple prominent chromatin, suggesting profiles primarily reflect contaminating Removal DNA, appropriate lysis conditions, together required reveal a state distinct most previous reports. Using ATAC-seq explore relatively accessible loci, identify landscape open loci associated development transcriptional control. Histone modification folding also strongly support hypothesis prior suffer contamination, but technical challenges reliably preserving head prevent us confidently assaying true localization for epigenetic marks. Together, our knowledge mammalian remains largely incomplete, motivate future efforts more accurately characterize genome organization mature sperm.

Language: Английский

Citations

19