Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation

Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome

(2021) J. Yuyang Lu et al.   CELL RESEARCH

GAGA factor: a multifunctional pioneering chromatin protein

(2021) Darya Chetverina et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

(2021) Anjali Kaushal et al.   Nature Communications

Chromatin architecture transitions from zebrafish sperm through early embryogenesis

(2021) Candice L. Wike et al.   GENOME RESEARCH

CTCF looping is established during gastrulation in medaka embryos

(2021) Ryohei Nakamura et al.   GENOME RESEARCH

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

(2021) Sergio Martin Espinola et al.   NATURE GENETICS

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

(2021) Elizabeth Ing-Simmons et al.   NATURE GENETICS

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

(2021) Marissa M Gaskill et al.   eLife

Three-dimensional folding dynamics of the Xenopus tropicalis genome

(2021) Longjian Niu et al.   NATURE GENETICS

The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

(2021) William Jordan et al.   Epigenetics & Chromatin

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

(2021) Martin Franke et al.   Nature Communications

CTCF is a barrier for 2C-like reprogramming

(2021) Teresa Olbrich et al.   Nature Communications

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

(2021) Jingyue Duan et al.   eLife

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

(2021) Andrew J. Modzelewski et al.   CELL

Awakening of the zygotic genome by pioneer transcription factors

(2021) Wataru Kobayashi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

On transposons and totipotency

(2020) Maria-Elena Torres-Padilla   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

(2020) James D.P. Rhodes et al.   Cell Reports

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

(2020) Máté Pálfy et al.   PLoS Genetics

Parental-to-embryo switch of chromosome organization in early embryogenesis

(2020) Samuel Collombet et al.   NATURE

Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA

(2020) Ke Zhang et al.   MOLECULAR CELL

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development

(2019) Bo Fu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

(2019) Marina Veil et al.   GENOME RESEARCH

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

(2019) Mélanie Eckersley-Maslin et al.   GENES & DEVELOPMENT

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

(2019) Julien Pontis et al.   Cell Stem Cell

Genome–lamina interactions are established de novo in the early mouse embryo

(2019) Máté Borsos et al.   NATURE

The maternal-to-zygotic transition revisited

(2019) Nadine L. Vastenhouw et al.   DEVELOPMENT

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ecdysone-Induced 3D Chromatin Reorganization Involves Active Enhancers Bound by Pipsqueak and Polycomb

(2019) Irene Gutierrez-Perez et al.   Cell Reports

Zygotic genome activation in the chicken: a comparative review

(2019) Deivendran Rengaraj et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The multiscale effects of polycomb mechanisms on 3D chromatin folding

(2019) Thierry Cheutin et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals

(2019) George E. Gentsch et al.   Nature Communications

3D genome organisation in Drosophila

(2019) Charlotte Moretti et al.   Briefings in Functional Genomics

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos

(2019) Zhenhai Du et al.   MOLECULAR CELL

Key role for CTCF in establishing chromatin structure in human embryos

(2019) Xuepeng Chen et al.   NATURE

Long noncoding RNAs exchange during zygotic genome activation in goat†

(2018) Mingtian Deng et al.   BIOLOGY OF REPRODUCTION

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

Mechanisms regulating zygotic genome activation

(2018) Katharine N. Schulz et al.   NATURE REVIEWS GENETICS

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

Conservation and innovation in the DUX4-family gene network

(2017) Jennifer L Whiddon et al.   NATURE GENETICS

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Lineage specification in the mouse preimplantation embryo

(2016) Claire Chazaud et al.   DEVELOPMENT

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Chromatin-linked determinants of zygotic genome activation

(2012) Olga Østrup et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos

(2012) James M. Moore et al.   PLoS One

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE