Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming

The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.

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The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development

10.1242/prelights.23770 ◽

2020 ◽

Author(s):

Sergio Menchero

Keyword(s):

Mouse Development ◽

Chromatin Reprogramming

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Chromatin reprogramming of male somatic cell-derived Xist and Tsix in ES hybrid cells

Cytogenetic and Genome Research ◽

10.1159/000071581 ◽

2002 ◽

Vol 99 (1-4) ◽

pp. 106-114 ◽

Cited By ~ 16

Author(s):

H. Kimura ◽

M. Tada ◽

S. Hatano ◽

M. Yamazaki ◽

N. Nakatsuji ◽

...

Keyword(s):

Somatic Cell ◽

Hybrid Cells ◽

Chromatin Reprogramming

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HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype

Reproduction ◽

10.1530/rep-20-0636 ◽

2021 ◽

Author(s):

Rowena Smith ◽

Susan J Pickering ◽

Anna Kopakaki ◽

Kj Thong ◽

Richard A Anderson ◽

...

Keyword(s):

Mouse Models ◽

Sperm Chromatin ◽

Zygote Formation ◽

Loss Of Function ◽

Phenotype Correlation ◽

Male Pronucleus ◽

Histone H3.3 ◽

Chromatin Reprogramming ◽

Histone Exchange

Elucidating the mechanisms underpinning fertilisation is essential to optimising IVF procedures. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. HIRA is the main H3.3 chaperone governing this protamine-to-histone exchange. Failure of this step results in abnormally fertilised zygotes containing only 1 pronucleus (1PN), in contrast to normal two-pronuclei (2PN) zygotes. 1PN zygotes are frequently observed in IVF treatments, but the genotype-phenotype correlation remains elusive. We investigated the maternal functions of two other molecules of the Hira complex, Cabin1 and Ubn1, in mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed an abnormal 1PN zygote phenotype. We then studied human 1PN zygotes and found that the HIRA complex was absent in 1PN zygotes that lacked the male pronucleus. This shows that the role of the HIRA complex in male pronucleus formation potentially has coherence from mice to humans. Furthermore, rescue experiments in mouse showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of HIRA. We have demonstrated that HIRA complex regulates male pronucleus formation in mice and is implicated in humans, that both CABIN1 and UBN1 components of the HIRA complex are equally essential for male pronucleus formation, and that rescue is feasible.

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Chromatin Reprogramming via Contact Guidance-Induced Nuclear Deformation Promotes Stem Cell Differentiation

10.21203/rs.3.rs-155599/v1 ◽

2021 ◽

Author(s):

Xinlong Wang ◽

Vasundhara Agrawal ◽

Yue Li ◽

Ranya Virk ◽

Priyam Patel ◽

...

Keyword(s):

Stem Cells ◽

Osteogenic Differentiation ◽

Cell Fate ◽

Nuclear Architecture ◽

Human Mesenchymal Stem Cells ◽

Stem Cell Differentiation ◽

Contact Guidance ◽

Live Cells ◽

Nuclear Deformation ◽

Chromatin Reprogramming

Abstract Efficient manipulation of cell fate is important for regenerative engineering applications. Lineage-specific differentiation of stem cells is particularly challenging due to their inherent plasticity. Engineered topographies may alter cellular plasticity through contact guidance. However, the ability to rationally design topographies to regulate phenotypic outcomes has been hindered in part by the lack of tools to quantify nanoscale chromatin structure reorganization in live cells. Herein we use micropillars, molecular, and nanostructural quantification tools to investigate how nuclear morphology in human mesenchymal stem cells (hMSCs) affects chromatin conformation and osteogenic differentiation. We show that micropillar-induced contact guidance is transduced via the cytoskeleton and impacts nuclear architecture, lamin A/C multimerization, histone modifications, and the 3-D conformation of chromatin within packing domains, a key regulator of transcriptional responsiveness. Micropillars repressed expression of genes associated with developmental processes and enhanced lineage-specific responsiveness, thereby decreasing cell plasticity and off-target differentiation, and facilitating osteogenic differentiation of hMSCs. Altogether, these findings reveal that chromatin reprogramming through contact guidance-induced nuclear deformation can be an efficient way to manipulate cell fate.

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LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Nature Communications ◽

10.1038/s41467-020-20883-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Run Jin ◽

Samantha Klasfeld ◽

Yang Zhu ◽

Meilin Fernandez Garcia ◽

Jun Xiao ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Cell Fate ◽

Chromatin Accessibility ◽

Binding Motifs ◽

Chromatin Remodelers ◽

Pioneer Transcription Factor ◽

Chromatin Reprogramming

AbstractMaster transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY ‘unlocks’ chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.

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Histone H3.3 Hira chaperone complex contributes to zygote formation in mice and humans

10.1101/2020.06.18.159954 ◽

2020 ◽

Author(s):

Rowena Smith ◽

Sue Pickering ◽

Anna Kopakaki ◽

K Joo Thong ◽

Richard A Anderson ◽

...

Keyword(s):

Sperm Chromatin ◽

Proof Of Concept ◽

Loss Of Function ◽

Male Pronucleus ◽

Histone H3.3 ◽

Infertile Couples ◽

Chaperone Complex ◽

Chromatin Reprogramming ◽

Histone Exchange

AbstractElucidating the underlining mechanisms underpinning successful fertilisation is imperative in optimising IVF treatments, and may lead to a specific diagnosis and therefore potential treatment for some infertile couples. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. This step is critical for the formation of the male pronucleus, without which the zygote contains only 1 pronucleus (1PN), in contrast to normally fertilised zygotes with two-pronuclei (2PN). 1PN zygotes are a frequently observed phenomenon in IVF treatments, therefore aberrant mechanism of action controlling paternal chromatin repackaging may be an important cause of abnormal fertilisation. Hira is the main H3.3 chaperone that governs this protamine-to-histone exchange. In this study, we investigated the maternal functions of two other molecules of the Hira complex, Cabin1 and Ubn1 in the mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed abnormal 1PN zygote phenotypes, similar to the phenotype of Hira mutants. We then studied human 1PN zygotes, and found that the Hira complex was absent in 1PN zygotes which were lacking the male pronucleus. This result confirms that the role of the Hira complex in male pronucleus formation has coherence from mice to humans. Furthermore, rescue experiments showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of Hira in the mouse oocytes. In summary, we have provided evidence of the role of Hira complex in regulating male pronucleus formation in both mice and humans, that both Cabin1 and Ubn1 components of the Hira complex are equally essential for male pronucleus formation, and that this can be rescued. We present a proof-of-concept experiment that could potentially lead to a personalised IVF therapy for oocyte defects.

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LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

10.1101/2020.03.16.994418 ◽

2020 ◽

Cited By ~ 1

Author(s):

Run Jin ◽

Samantha Klasfeld ◽

Meilin Fernandez Garcia ◽

Jun Xiao ◽

Soon-Ki Han ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Cell Fate ◽

Chromatin Accessibility ◽

Binding Motifs ◽

Chromatin Remodelers ◽

Pioneer Transcription Factor ◽

Chromatin Reprogramming

ABSTRACTMaster transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet no bonafide pioneer transcription factor has - been identified in this kingdom. Here we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds in a sequence-specific manner and with high affinity to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1, where it co-occupies DNA with histones. Moreover, the LFY DNA contact helix shares defining properties with those of strong nucleosome binding pioneer factors. At the AP1 locus, LFY unlocks chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later and require activity of additional, non-pioneer transcription, factors. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between plant and animal pioneer transcription factors. Further analyses aimed at elucidating the defining characteristics of pioneer transcription factors will allow harnessing these for enhanced cell fate reprogramming.

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