Altered chromatin states drive cryptic transcription in aging mammalian stem cells

Chromatin plasticity is thought to be fundamental to the pluripotency of embryonic stem cells. Hmgn proteins modulate chromatin structure and are highly expressed during early development and in neural stem/progenitor cells of the developing and adult brain. Here, we show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of Hmgn2 is associated with the disruption of active chromatin states at specific classes of gene. The levels of H3K4me3, H3K9ac, H3K27ac and H3K122ac are considerably reduced at the pluripotency genes Nanog and Oct4, which impacts transcription. At endodermal/mesodermal lineage-specific genes, the loss of Hmgn2 leads to a switch from a bivalent to a repressive chromatin configuration. However, at the neuronal lineage genes Neurog1 and Ascl1, no epigenetic changes are observed and their bivalent states are retained. We conclude that Hmgn proteins play important roles in maintaining chromatin plasticity in stem cells, and are essential for maintaining stem cell identity and pluripotency.

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Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells

Frontiers in Genetics ◽

10.3389/fgene.2018.00731 ◽

2019 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Sharmi Banerjee ◽

Hongxiao Zhu ◽

Man Tang ◽

Wu-chun Feng ◽

Xiaowei Wu ◽

...

Keyword(s):

Stem Cells ◽

Neural Stem Cells ◽

Chromatin States ◽

Regulatory Modules ◽

Transcriptional Regulatory

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

Nucleic Acids Research ◽

10.1093/nar/gkx167 ◽

2017 ◽

Vol 45 (10) ◽

pp. 5770-5784 ◽

Cited By ~ 28

Author(s):

Juri Kazakevych ◽

Sergi Sayols ◽

Berith Messner ◽

Christina Krienke ◽

Natalia Soshnikova

Keyword(s):

Stem Cells ◽

Intestinal Stem Cells ◽

Dynamic Changes ◽

Chromatin States

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DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells

10.1101/2020.02.03.931741 ◽

2020 ◽

Cited By ~ 1

Author(s):

F. Ferrari ◽

L. Arrigoni ◽

H. Franz ◽

L. Butenko ◽

E. Trompouki ◽

...

Keyword(s):

Stem Cells ◽

Neuronal Differentiation ◽

Cellular Differentiation ◽

Neural Progenitors ◽

Methyltransferase Activity ◽

Enhancer Activity ◽

Chromatin States ◽

Genome Wide ◽

A Genome

ABSTRACTBackgroundDuring cellular differentiation, the chromatin landscape changes dynamically and contributes to the activation of cell-type specific transcriptional programs. Disruptor of telomeric silencing 1-like (DOT1L) is a histone methyltransferase that mediates mono-, di- and trimethylation of lysine 79 of histone H3 (H3K79me1, 2, 3). Its enzymatic activity is critical for driving cellular differentiation into cardiomyocytes, chondrocytes and neurons, from embryonic or other type of stem cells in physiological settings. Ectopic localization of DOT1L in MLL-rearranged leukemias is causative for leukemogenesis and relapse. Little is known about the causal relevance of DOT1L methyltransferase activity in the global chromatin context and how its enzymatic function affects transcriptional and global chromatin states. Recent reports conducted in leukemia cell models have suggested that deposition of H3K79me2 may be critical to preserve histone H3K27 acetylation (ac) and enhancer activity, and to sustain expression of highly transcribed genes. If and to what extent DOT1L affects chromatin states and enhancer activity during physiological differentiation processes is currently unknown.ResultsWe measure global changes of seven histone modifications during the differentiation process via high-throughput and quantitative ChIP-seq in an in-vitro neuronal differentiation model of mouse embryonic stem cells (mESC). We observe that H3K27ac globally decreases, whereas H3K79me2 globally increases during differentiation, while other modifications remain globally unaltered. Pharmacological inhibition of DOT1L in mESC and mESC-derived neural progenitors results in decreased expression of highly transcribed genes and increased expression of normally repressed genes. Acute DOT1L inhibition primes neural progenitors towards a mature differentiation state. Transcriptional downregulation associates with decreased accessibility of enhancers specifically bound by the master regulator SOX2.ConclusionsIn-vitro neuronal differentiation couples with a genome-wide accumulation of H3K79me2, never described previously in mammalian cells. Acute inhibition of DOT1L is sufficient to initiate a defined transcriptional program, which biases the transcriptome of neural progenitor cells towards neuronal differentiation. H3K79me2 is not generally causative for maintaining transcriptional levels at a genome-wide scale. In contrast, DOT1L inactivation reduces the chromatin accessibility of enhancers bound by SOX2 in-vivo, thereby reducing the expression level of a restricted number of genes. Our work establishes that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.

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Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters

10.21203/rs.3.rs-82156/v1 ◽

2020 ◽

Author(s):

Brenna McCauley ◽

Luyang Sun ◽

Ruofan Yu ◽

Dena Leeman ◽

Yun Huang ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem ◽

Human Mesenchymal Stem Cells ◽

Chromatin State ◽

Hematopoietic Stem ◽

Chromatin Signature ◽

Promoter Sequences ◽

Cryptic Transcription ◽

Cryptic Promoters

Abstract Suppressing spurious cryptic transcription by a repressive intragenic chromatin state featuring trimethylated lysine 36 on histone H3 (H3K36me3) and DNA methylation is critical for maintaining self-renewal capacity in mouse embryonic stem cells. In yeast and nematodes, such cryptic transcription is elevated with age, and reducing the levels of age-associated cryptic transcription extends yeast lifespan. Whether cryptic transcription is also increased during mammalian aging is unknown. We show for the first time an age-associated elevation in cryptic transcription in several stem cell populations, including murine hematopoietic stem cells (mHSCs) and neural stem cells (NSCs) and human mesenchymal stem cells (hMSCs). Using DECAP-seq, we mapped and quantified age-associated cryptic transcription in hMSCs aged in vitro. Regions with significant age-associated cryptic transcription have a unique chromatin signature: decreased H3K36me3 and increased H3K4me1, H3K4me3, and H3K27ac with age. Furthermore, genomic regions undergoing such age-dependent chromatin changes resemble known promoter sequences and are bound by the promoter-associated protein TBP even in young cells. Hence, the more permissive chromatin state at intragenic cryptic promoters likely underlies the increase of cryptic transcription in aged mammalian stem cells.

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Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells

Blood ◽

10.1182/blood-2009-07-235176 ◽

2010 ◽

Vol 115 (2) ◽

pp. 247-256 ◽

Cited By ~ 74

Author(s):

Holger Weishaupt ◽

Mikael Sigvardsson ◽

Joanne L. Attema

Keyword(s):

Stem Cells ◽

T Cells ◽

Hematopoietic Stem Cells ◽

Cell Fate ◽

Developmental Plasticity ◽

Cell Function ◽

Hematopoietic Stem ◽

Chromatin States ◽

Stem And Progenitor Cells ◽

Epigenetic Signatures

Abstract Heritable epigenetic signatures are proposed to serve as an important regulatory mechanism in lineage fate determination. To investigate this, we profiled chromatin modifications in murine hematopoietic stem cells, lineage-restricted progenitors, and CD4+ T cells using modified genome-scale mini-chromatin immunoprecipitation technology. We show that genes involved in mature hematopoietic cell function associate with distinct chromatin states in stem and progenitor cells, before their activation or silencing upon cellular maturation. Many lineage-restricted promoters are associated with bivalent histone methylation and highly combinatorial histone modification patterns, which may determine their selective priming of gene expression during lineage commitment. These bivalent chromatin states are conserved in mammalian evolution, with a particular overrepresentation of promoters encoding key regulators of hematopoiesis. After differentiation into progenitors and T cells, activating histone modifications persist at transcriptionally repressed promoters, suggesting that these transcriptional programs might be reactivated after lineage restriction. Collectively, our data reveal the epigenetic framework that underlies the cell fate options of hematopoietic stem cells.

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CRYPTIC TRANSCRIPTION IS ASSOCIATED WITH AGE IN MAMMALIAN STEM CELLS

Innovation in Aging ◽

10.1093/geroni/igz038.3493 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

pp. S963-S963

Author(s):

Brenna McCauley ◽

Luyang Sun ◽

Weiwei Dang

Keyword(s):

Stem Cells ◽

Chromatin Structure ◽

Chromatin State ◽

Open Chromatin ◽

Rna Pol Ii ◽

Cellular Processes ◽

Transcriptional Dysregulation ◽

Cryptic Transcription ◽

First Time ◽

Key Pathways

Abstract Aging is a multifaceted process that challenges organisms with stresses resulting from the dysregulation of cellular processes. Unsurprisingly, given how tightly regulated it is under normal conditions, transcription is one of the key pathways disrupted during aging. Indeed, dysregulation of transcription contributes to the activation of transposable elements, the loss of cellular identity, and decreased stem cell potency with age. Our previous work identified intragenic cryptic transcription (CT) as a novel type of age-associated transcriptional dysregulation that limits the lifespan of yeast and worms. Continuing this work, we show for the first time that CT increases with age in mammalian stem cells. Increased CT is associated with disrupted chromatin structure, particularly with the reduction of H3K36me3, a histone modification known to inhibit CT throughout eukaryotes. We propose that an age-associated reduction in H3K36me3 in actively transcribed gene bodies drives disruption of chromatin structure in these regions, resulting in an open chromatin state. This open chromatin state is permissive for the entry of RNA Pol II, which can then initiate transcription from within the gene body. These aberrant cryptic transcripts may contribute to the pathological load of mammalian aging.

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CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Nucleic Acids Research ◽

10.1093/nar/gkz908 ◽

2019 ◽

Vol 47 (21) ◽

pp. 11181-11196 ◽

Cited By ~ 6

Author(s):

Christopher T Clarkson ◽

Emma A Deeks ◽

Ralph Samarista ◽

Hulkar Mamayusupova ◽

Victor B Zhurkin ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Symmetry Breaking ◽

Embryonic Stem ◽

Ctcf Binding ◽

Chromatin Domains ◽

Chromatin States ◽

Linker Length ◽

Binding Factor ◽

Nucleosome Array

Abstract The CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we investigate chromatin boundaries in mouse embryonic stem cells, defined by the regions with decreased Nucleosome Repeat Length (NRL) for ∼20 nucleosomes near CTCF sites, affecting up to 10% of the genome. We found that the nucleosome-depleted region (NDR) near CTCF is asymmetrically located >40 nucleotides 5′-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA and the presence of cohesin is correlated with the decrease of NRL near CTCF, and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation, a subset of preserved, common CTCF sites maintains asymmetric nucleosome pattern and small NRL. The sites which lost CTCF upon differentiation are characterized by nucleosome rearrangement 3′-downstream, with unchanged NDR 5′-upstream of CTCF motifs. Boundaries of topologically associated chromatin domains frequently contain several inward-oriented CTCF motifs whose effects, described above, add up synergistically.

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