Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy

Gehre, Maja; Bunina, Daria; Sidoli, Simone; Lübke, Marlena J.; Diaz, Nichole; Trovato, Matteo; Garcia, Benjamin A.; Zaugg, Judith B.; Noh, Kyung‐Min

doi:10.1038/s41588-020-0586-5

Cited by 38 publications

(58 citation statements)

References 65 publications

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“…Laboratory of Kyung-Min Noh (Gehre et al, 2020) Oligonucleotides See (Bolger et al, 2014) http://www.usadellab.org/cms/index.php? page=trimmomatic ; RRID:SCR_011848 Snakemake 5.0 https://doi.org/10.1093/bioinformatics/ bts480 (Kö ster and Rahmann, 2012) https://snakemake.readthedocs.io/; RRID:SCR_003475 Deeptools 2.5.0 https://doi.org/10.1093/nar/gku365 (Ramírez et al, 2014) https://deeptools.readthedocs.io/en/ develop/; RRID:SCR_016366…”

Section: Continuedmentioning

confidence: 99%

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

et al. 2020

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Section: Continuedmentioning

confidence: 99%

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

et al. 2020

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“…Bowtie2 was used to map reads to mm10. ChIP-seq signal enrichment was analyzed and obtained by bamCompare from Deeptools [ 101 , 102 ]. ChIP signal heatmap and line plot were also generated by computeMatrix and plotHeatmap form Deeptools.…”

Section: Methodsmentioning

confidence: 99%

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Zhang

et al. 2021

Genome Biol

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Background Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera assays, unlike mouse naïve PSCs. However, the molecular mechanisms underlying the lower developmental competency of primed PSCs remain elusive. Results We examine the regulation of telomere maintenance, retrotransposon activity, and genomic stability of primed PSCs and compare them with naïve PSCs. Surprisingly, primed PSCs only minimally maintain telomeres and show fragile telomeres, associated with declined DNA recombination and repair activity, in contrast to naïve PSCs that robustly elongate telomeres. Also, we identify LINE1 family integrant L1Md_T as naïve-specific retrotransposon and ERVK family integrant IAPEz to define primed PSCs, and their transcription is differentially regulated by heterochromatic histones and Dnmt3b. Notably, genomic instability of primed PSCs is increased, in association with aberrant retrotransposon activity. Conclusions Our data suggest that fragile telomere, retrotransposon-associated genomic instability, and declined DNA recombination repair, together with reduced function of cell cycle and mitochondria, increased apoptosis, and differentiation properties may link to compromised developmental potency of primed PSCs, noticeably distinguishable from naïve PSCs.

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“…However, H3.3 deposition also occurs at telomeres and pericentric heterochromatin, where it is catalyzed by the chaperone dimer, Atrx/Daxx [86,87]. A study using a H3.3K4A mutant has suggested that the Lysine 4 residue of histone H3.3 is required for ESC differentiation and transcription accuracy [88].…”

Section: H33mentioning

confidence: 99%

Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin

Morrison

Thakur

2021

IJMS

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Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin—open chromatin structure associated with active transcription; heterochromatin—less accessible chromatin associated with silencing; centromeric chromatin—the site of spindle binding in chromosome segregation.

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Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy

Cited by 38 publications

References 65 publications

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin

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