scholarly journals FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Emilia Dimitrova ◽  
Takashi Kondo ◽  
Angelika Feldmann ◽  
Manabu Nakayama ◽  
Yoko Koseki ◽  
...  
Keyword(s):  
Cpg Island ◽  
Es Cells ◽  
Cpg Islands ◽  
Embryonic Stem ◽  
Cell Lineage ◽  
Regulatory Elements ◽  
Lineage Commitment ◽  
Gene Promoters ◽  
Mouse Development ◽  
Developmental Genes

CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.

scholarly journals FBXL19 recruits CDK-Mediator to the CpG islands of developmental genes to prime them for activation during lineage commitment

2018 ◽  
Author(s):  
Emilia Dimitrova ◽  
Takashi Kondo ◽  
Angelika Feldmann ◽  
Manabu Nakayama ◽  
Yoko Koseki ◽  
...  
Keyword(s):  
Cpg Island ◽  
Es Cells ◽  
Cpg Islands ◽  
Embryonic Stem ◽  
Cell Lineage ◽  
Regulatory Elements ◽  
Lineage Commitment ◽  
Gene Promoters ◽  
Mouse Development ◽  
Developmental Genes

AbstractCpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.

scholarly journals CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions

2020 ◽  
Vol 48 (6) ◽  
pp. 2942-2955 ◽  
Author(s):  
Angelika Feldmann ◽  
Emilia Dimitrova ◽  
Alexander Kenney ◽  
Anna Lastuvkova ◽  
Robert J Klose
Keyword(s):  
Cpg Island ◽  
Gene Activation ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Gene Induction ◽  
Gene Promoters ◽  
Developmental Gene ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Distal Regulatory Elements

Abstract Appropriate developmental gene regulation relies on the capacity of gene promoters to integrate inputs from distal regulatory elements, yet how this is achieved remains poorly understood. In embryonic stem cells (ESCs), a subset of silent developmental gene promoters are primed for activation by FBXL19, a CpG island binding protein, through its capacity to recruit CDK-Mediator. How mechanistically these proteins function together to prime genes for activation during differentiation is unknown. Here we discover that in mouse ESCs FBXL19 and CDK-Mediator support long-range interactions between silent gene promoters that rely on FBXL19 for their induction during differentiation and gene regulatory elements. During gene induction, these distal regulatory elements behave in an atypical manner, in that the majority do not acquire histone H3 lysine 27 acetylation and no longer interact with their target gene promoter following gene activation. Despite these atypical features, we demonstrate by targeted deletions that these distal elements are required for appropriate gene induction during differentiation. Together these discoveries demonstrate that CpG-island associated gene promoters can prime genes for activation by communicating with atypical distal gene regulatory elements to achieve appropriate gene expression.

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

2020 ◽  
Author(s):  
Trisha A. Macrae ◽  
Miguel Ramalho-Santos
Keyword(s):  
Cell Fate ◽  
Es Cells ◽  
Embryonic Stem ◽  
Lineage Commitment ◽  
Mouse Development ◽  
Mammalian Embryo ◽  
Polycomb Repressive Complex 2 ◽  
Transcriptional Signature ◽  
Large Gene ◽  
Post Implantation

ABSTRACTPluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large gene-distal blankets in pre-implantation embryos to mark promoters of developmental genes. The factors that mediate this global redistribution of H3K27me3 are unknown. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion of Usp9x in post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of “stemness” and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.

scholarly journals Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding at cis-regulatory elements and TAD boundaries

2020 ◽  
Author(s):  
Shinichi Kadota ◽  
Jianhong Ou ◽  
Yuming Shi ◽  
Jiayu Sun ◽  
Eda Yildirim
Keyword(s):  
Nuclear Pore Complex ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Es Cells ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Temporal Organization ◽  
Nuclear Pore ◽  
Developmental Genes ◽  
Chromatin Architecture

ABSTRACTThe nuclear pore complex (NPC) components, nucleoporins (Nups), have been proposed to mediate spatial and temporal organization of chromatin during gene regulation. Nevertheless, we have little understanding on the molecular mechanisms that underlie Nup-mediated chromatin structure and transcription in mammals. Here, we show that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin occupancy and differential gene expression. This function of NUP153 is most prevalent at the developmental genes that show bivalent chromatin state. To dissect the functional relevance of NUP153-mediated CTCF and cohesin binding during transcriptional activation or silencing, we utilized epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We found that NUP153 binding at the cis-regulatory elements controls CTCF and cohesin binding and subsequent POL II pausing during the transcriptionally silent state. Furthermore, efficient and timely transcription initiation of IEGs relies on NUP153 and occurs around the nuclear periphery suggesting that NUP153 acts as an activator of IEG transcription. Collectively, these results uncover a key role for NUP153 in chromatin architecture and transcription by mediating CTCF and cohesin binding in mammalian cells. We propose that NUP153 links NPCs to chromatin architecture allowing developmental genes and IEGs that are poised to respond rapidly to developmental cues to be properly modulated.

scholarly journals E2F6 initiates stable epigenetic silencing of germline genes during embryonic development

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Thomas Dahlet ◽  
Matthias Truss ◽  
Ute Frede ◽  
Hala Al Adhami ◽  
Anaïs F. Bardet ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Cpg Island ◽  
Cpg Islands ◽  
Embryonic Stem ◽  
Epigenetic Silencing ◽  
Embryonic Cells ◽  
Mouse Development ◽  
Germline Genes

AbstractIn mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development.

scholarly journals An Orphan CpG Island Drives Expression of a let-7 miRNA Precursor with an Important Role in Mouse Development

Epigenomes ◽  
2019 ◽  
Vol 3 (1) ◽  
pp. 7 ◽  
Author(s):  
Martha Koerner ◽  
Kashyap Chhatbar ◽  
Shaun Webb ◽  
Justyna Cholewa-Waclaw ◽  
Jim Selfridge ◽  
...  
Keyword(s):  
Cpg Island ◽  
Mirna Family ◽  
Cpg Islands ◽  
Embryonic Stem ◽  
Mirna Precursor ◽  
Micro Rna ◽  
Mouse Development ◽  
Human Genes ◽  
Novel Transcripts ◽  
Precursor Rna

Most human genes are associated with promoters embedded in non-methylated, G + C-rich CpG islands (CGIs). Not all CGIs are found at annotated promoters, however, raising the possibility that many serve as promoters for transcripts that do not code for proteins. To test this hypothesis, we searched for novel transcripts in embryonic stem cells (ESCs) that originate within orphan CGIs. Among several candidates, we detected a transcript that included three members of the let-7 micro-RNA family: Let-7a-1, let-7f-1, and let-7d. Deletion of the CGI prevented expression of the precursor RNA and depleted the included miRNAs. Mice homozygous for this mutation were sub-viable and showed growth and other defects. The results suggest that despite the identity of their seed sequences, members of the let-7 miRNA family exert distinct functions that cannot be complemented by other members.

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

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trisha A. Macrae ◽  
Miguel Ramalho-Santos
Keyword(s):  
Cell Fate ◽  
Es Cells ◽  
Embryonic Stem ◽  
Lineage Commitment ◽  
Mouse Development ◽  
Mammalian Embryo ◽  
Polycomb Repressive Complex 2 ◽  
Transcriptional Signature ◽  
Disease States ◽  
Post Implantation

AbstractPluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of this global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion ofUsp9xin post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of “stemness” and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.

scholarly journals CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Anna Mantsoki ◽  
Guillaume Devailly ◽  
Anagha Joshi
Keyword(s):  
Cpg Island ◽  
Es Cells ◽  
Cpg Islands ◽  
Embryonic Stem ◽  
Sequence Motif ◽  
Chromatin Signature ◽  
Chip Sequencing ◽  
Mouse Es Cells ◽  
Developmental Factors ◽  
Subsequent Activation

Abstract In embryonic stem (ES) cells, developmental regulators have a characteristic bivalent chromatin signature marked by simultaneous presence of both activation (H3K4me3) and repression (H3K27me3) signals and are thought to be in a ‘poised’ state for subsequent activation or silencing during differentiation. We collected eleven pairs (H3K4me3 and H3K27me3) of ChIP sequencing datasets in human ES cells and eight pairs in murine ES cells and predicted high-confidence (HC) bivalent promoters. Over 85% of H3K27me3 marked promoters were bivalent in human and mouse ES cells. We found that (i) HC bivalent promoters were enriched for developmental factors and were highly likely to be differentially expressed upon transcription factor perturbation; (ii) murine HC bivalent promoters were occupied by both polycomb repressive component classes (PRC1 and PRC2) and grouped into four distinct clusters with different biological functions; (iii) HC bivalent and active promoters were CpG rich while H3K27me3-only promoters lacked CpG islands. Binding enrichment of distinct sets of regulators distinguished bivalent from active promoters. Moreover, a ‘TCCCC’ sequence motif was specifically enriched in bivalent promoters. Finally, this analysis will serve as a resource for future studies to further understand transcriptional regulation during embryonic development.

scholarly journals Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Paula Freire-Pritchett ◽  
Stefan Schoenfelder ◽  
Csilla Várnai ◽  
Steven W Wingett ◽  
Jonathan Cairns ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Target Gene ◽  
Target Genes ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Dna Looping ◽  
Lineage Commitment ◽  
Gene Promoters ◽  
Putative Target ◽  
Target Promoters

Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells.

scholarly journals Steroidogenic Factor-1 (SF-1)-Driven Differentiation of Murine Embryonic Stem (ES) Cells into a Gonadal Lineage

Endocrinology ◽  
2011 ◽  
Vol 152 (7) ◽  
pp. 2870-2882 ◽  
Author(s):  
Unmesh Jadhav ◽  
J. Larry Jameson
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Embryoid Body ◽  
Es Cells ◽  
Embryonic Stem ◽  
Cell Lineage ◽  
Culture Conditions ◽  
Steroidogenic Factor 1 ◽  
Lineage Differentiation ◽  
And Function

Steroidogenic factor 1 (SF-1) is essential for the development and function of steroidogenic tissues. Stable incorporation of SF-1 into embryonic stem cells (SF-1-ES cells) has been shown to prime the cells for steroidogenesis. When provided with exogenous cholesterol substrate, and after treatment with retinoic acid and cAMP, SF-1-ES cells produce progesterone but do not produce other steroids such as cortisol, estradiol, or testosterone. In this study, we explored culture conditions that optimize SF-1-mediated differentiation of ES cells into defined steroidogenic lineages. When embryoid body formation was used to facilitate cell lineage differentiation, SF-1-ES cells were found to be restricted in their differentiation, with fewer cells entering neuronal pathways and a larger fraction entering the steroidogenic lineage. Among the differentiation protocols tested, leukemia inhibitory factor (LIF) removal, followed by prolonged cAMP treatment was most efficacious for inducing steroidogenesis in SF-1-ES cells. In this protocol, a subset of SF-1-ES cells survives after LIF withdrawal, undergoes morphologic differentiation, and recovers proliferative capacity. These cells are characterized by induction of steroidogenic enzyme genes, use of de novo cholesterol, and production of multiple steroids including estradiol and testosterone. Microarray studies identified additional pathways associated with SF-1 mediated differentiation. Using biotinylated SF-1 in chromatin immunoprecipitation assays, SF-1 was shown to bind directly to multiple target genes, with induction of binding to some targets after steroidogenic treatment. These studies indicate that SF-1 expression, followed by LIF removal and treatment with cAMP drives ES cells into a steroidogenic pathway characteristic of gonadal steroid-producing cells.

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