scholarly journals A Hyperactive Transcriptional State Marks Genome Reactivation during Mitotic Exit

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 48-48
Author(s):  
Gerd A. Blobel ◽  
Chris C.S. Hsiung ◽  
Peng Huang ◽  
Cheryl Keller ◽  
Paul Ginart ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Transcriptional Control ◽  
Conflicts Of Interest ◽  
Large Fraction ◽  
Gene Activation ◽  
G1 Phase ◽  
Erythroid Precursor ◽  
Dividing Cells

Abstract The tremendous proliferative capacity of erythroid precursor cells underlies the production of over a million red blood cells per second in adult humans. During every mitosis the mammalian nucleus is disassembled and transcriptionally silent. Genome reactivation after mitosis is a key step in the propagation of transcriptional programs through cell generations, yet how this occurs remains largely unexplored. We carried out the first genome wide survey of transcription in cells emerging from mitosis using RNA polymerase II ChIP seq in purified populations at various post-mitotic time points. Using unsupervised approaches, we discover and classify genome reactivation patterns among genes. A surprisingly large fraction of genes (~25%) displays a post-mitotic spike in transcription. This spike represents the first complete round of transcription and accounts for the greatest gene-to-gene variance in temporal patterns of transcription in G1 phase. Another notable and contrasting pattern is gene activation late in the G1 phase. Single-molecule RNA FISH imaging demonstrates that the post-mitotic transcriptional spike represents the highest activity throughout the cell cycle and results in an increase in mature mRNAs, indicating that the phenomenon has the capacity to alter gene expression. Surprisingly, the post-mitotic transcriptional spike occurs independent of enhancer action and can be recapitulated with promoter sequences ectopically integrated into the genome. In contrast, late-G1 gene reactivation is distinct and requires enhancer function. Our findings uncover novel modes of transcriptional control during exit from mitosis with implications for our understanding of transitions in gene expression states in dividing cells. Disclosures No relevant conflicts of interest to declare.

Hematopoietic Transcriptional Regulation At The Mitosis-G1 Transition

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2440-2440
Author(s):  
Chris C.S. Hsiung ◽  
Arjun Raj ◽  
Gerd A. Blobel
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Gene Regulation ◽  
Cell Division ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Conflicts Of Interest ◽  
Specific Cell ◽  
Developmental Gene ◽  
Developmental Gene Regulation

Abstract Normal hematopoiesis involves the coordination of cell division and gene expression to produce physiologically appropriate cell numbers of various developmental stages across lineages. While studies have demonstrated intricate links between cell cycle progression and developmental gene regulation -- two cellular programs whose concomitant dysregulation is central to many malignant and non-malignant hematologic diseases -- researchers currently lack clear, general principles of how intrinsic properties of cell division could influence developmental gene regulation. In each round of division, mitosis imposes a striking disruption to gene expression: the nucleus is disassembled, bulk RNA synthesis ceases, and the transcription machinery and most transcription factors -- including repressive complexes -- are evicted from mitotic chromatin. Since hematopoietic lineage fidelity often requires the continued presence of repressive complexes to inhibit expression of developmentally inappropriate genes, we hypothesized that such repression may be inefficient during a narrow window immediately post-mitosis, resulting in transient aberrant transcription in a probabilistic manner. We tested for the presence of transient post-mitotic aberrant transcription at genes whose repression is known to depend on continued occupancy of repressive complexes. We used an experimentally tractable cell line, G1E cells, a rapidly dividing model of lineage-committed murine pro-erythroblasts that genetically lack the erythroid master regulator Gata1. Transduction with a Gata1-estrogen receptor fusion construct and treatment with estradiol restores Gata1 function, leading to recapitulation of early erythroid maturation events, including rapid repression of stemness-associated genes, such as Gata2 and c-Kit. We examined in fine temporal detail the post-mitotic transcriptional behavior of Gata2, c-Kit and other genes using population-based assays facilitated by drug-mediated cell cycle synchronization. In addition, we bypassed the use of synchronization drugs and their associated potential experimental artifacts by developing novel complementary methods to study the relationship between cell cycle status and transcription in asynchronous populations: 1. We harnessed single-molecule RNA fluorescence in situ hybridization technology to quantitatively assess transcription in individual cells at various cell cycle stages, and 2. We adapted a fluorescent protein cell cycle reporter to separate, using fluorescence-activated cell sorting, subpopulations of specific cell cycle stages for epigenomic and transcriptomic analyses. Together, our results revealed a post-mitotic pulse of increased RNA polymerase II recruitment and transcript synthesis most clearly exhibited by Gata2, c-Kit, and other genes whose repression is known to depend on co-repressor complexes in these cells. Our results support the notion that the mitosis-G1 transition presents a window of transcriptional plasticity. We are beginning to explore how this property of post-mitotic transcriptional control applies to hematopoietic cell types across the developmental spectrum and could contribute to functionally important variations in gene expression, such as in stem cell lineage commitment, experimental reprogramming, and non-genetic heterogeneity in malignancy. Disclosures: No relevant conflicts of interest to declare.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

scholarly journals A dual role for H2A.Z.1 in modulating the dynamics of RNA Polymerase II initiation and elongation

2020 ◽  
Author(s):  
Constantine Mylonas ◽  
Alexander L. Auld ◽  
Choongman Lee ◽  
Ibrahim I. Cisse ◽  
Laurie A. Boyer
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Embryonic Stem ◽  
Super Resolution ◽  
Fine Tuning ◽  
Transcriptional Initiation ◽  
Single Molecule Level

AbstractRNAPII pausing immediately downstream of the transcription start site (TSS) is a critical rate limiting step at most metazoan genes that allows fine-tuning of gene expression in response to diverse signals1–5. During pause-release, RNA Polymerase II (RNAPII) encounters an H2A.Z.1 nucleosome6–8, yet how this variant contributes to transcription is poorly understood. Here, we use high resolution genomic approaches2,9 (NET-seq and ChIP-nexus) along with live cell super-resolution microscopy (tcPALM)10 to investigate the role of H2A.Z.1 on RNAPII dynamics in embryonic stem cells (ESCs). Using a rapid, inducible protein degron system11 combined with transcriptional initiation and elongation inhibitors, our quantitative analysis shows that H2A.Z.1 slows the release of RNAPII, impacting both RNAPII and NELF dynamics at a single molecule level. We also find that H2A.Z.1 loss has a dramatic impact on nascent transcription at stably paused, signal-dependent genes. Furthermore, we demonstrate that H2A.Z.1 inhibits re-assembly and re-initiation of the PIC to reinforce the paused state and acts as a strong additional pause signal at stably paused genes. Together, our study suggests that H2A.Z.1 fine-tunes gene expression by regulating RNAPII kinetics in mammalian cells.

scholarly journals Trans-tail regulation-mediated suppression of cryptic transcription

2021 ◽  
Author(s):  
Jungmin Choi ◽  
Zae Young Ryoo ◽  
Dong-Hyung Cho ◽  
Hyun-Shik Lee ◽  
Hong-Yeoul Ryu
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Histone Deacetylases ◽  
Transcriptional Control ◽  
Molecular Techniques ◽  
Transcriptional Elongation ◽  
Post Translational Modifications ◽  
Phosphorylation Pattern ◽  
Cryptic Transcription ◽  
H3k79 Methylation

AbstractCrosstalk between post-translational modifications of histone proteins influences the regulation of chromatin structure and gene expression. Among such crosstalk pathways, the best-characterized example is H2B monoubiquitination-mediated H3K4 and H3K79 methylation, which is referred to as trans-tail regulation. Although many studies have investigated the fragmentary effects of this pathway on silencing and transcription, its ultimate contribution to transcriptional control has remained unclear. Recent advances in molecular techniques and genomics have, however, revealed that the trans-tail crosstalk is linked to a more diverse cascade of histone modifications and has various functions in cotranscriptional processes. Furthermore, H2B monoubiquitination sequentially facilitates H3K4 dimethylation and histone sumoylation, thereby providing a binding platform for recruiting Set3 complex proteins, including two histone deacetylases, to restrict cryptic transcription from gene bodies. The removal of both ubiquitin and SUMO, small ubiquitin-like modifier, modifications from histones also facilitates a change in the phosphorylation pattern of the RNA polymerase II C-terminal domain that is required for subsequent transcriptional elongation. Therefore, this review describes recent findings regarding trans-tail regulation-driven processes to elaborate on their contribution to maintaining transcriptional fidelity.

scholarly journals Global Modulation in DNA Epigenetics during Pro-Inflammatory Macrophage Activation

2019 ◽  
Author(s):  
Nikhil Jain ◽  
Tamar Shahal ◽  
Tslil Gabrieli ◽  
Noa Gilat ◽  
Dmitry Torchinsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Single Molecule ◽  
Transcriptional Control ◽  
Excision Repair ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Inflammatory Activation ◽  
Methylation Patterns

AbstractDNA methylation patterns create distinct gene expression profiles. These patterns are maintained after cell division, thus enabling the differentiation and maintenance of multiple cell types from the same genome sequence. The advantage of this mechanism for transcriptional control is that chemical-encoding allows to rapidly establish new epigenetic patterns “on-demand” through enzymatic methylation and de-methylation of DNA. Here we show that this feature is associated with the fast response of macrophages during their pro-inflammatory activation. By using a combination of mass spectroscopy and single-molecule imaging to quantify global epigenetic changes in the genomes of primary macrophages, we followed three distinct DNA marks (methylated, hydroxymethylated and unmethylated), involved in establishing new DNA methylation patterns during pro-inflammatory activation. The observed epigenetic modulation together with gene expression data generated for the involved enzymatic machinery, may suggest that de-methylation upon LPS-activation starts with oxidation of methylated CpGs, followed by excision-repair of these oxidized bases and their replacement with unmodified cytosine.

Cell-type-dependent gene activation by yeast transposon Ty1 involves multiple regulatory determinants

1987 ◽  
Vol 7 (9) ◽  
pp. 3205-3211
Author(s):  
M Company ◽  
B Errede
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Gene Activation ◽  
Distal Region ◽  
Control Site ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Negative Effects ◽  
Cis Acting ◽  
Transcriptional Control Region

Ty transposable element insertion mutations of Saccharomyces cerevisiae can cause cell-type-dependent activation of adjacent gene expression. Several cis-acting regulatory regions within Ty1 that are responsible for these effects were identified. A 211-base-pair (bp) region functions as an activator. This region includes the so-called U5 domain of delta and 145 bp of adjacent epsilon sequences. Unlike activation by the intact Ty1, activation by the 211-bp Ty1 subfragment is cell-type independent. The presence of a 112-bp fragment from a more distal region of Ty1 confers cell-type specificity to the activator. The 112-bp fragment includes sequences with homology to mammalian enhancers and to a yeast a/alpha control site. In addition, Ty1 regions that exert negative effects on gene expression were identified. These results demonstrate that the Ty1 transcriptional control region consists of multiple components with distinct regulatory functions.

FLT3ITD Target Enhancers Are Primed but Inaccessible in Fetal Hematopoietic Progenitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1228-1228
Author(s):  
Yanan Li ◽  
Riddhi M Patel ◽  
Emily Casey ◽  
Jeffrey A. Magee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Gene Activation ◽  
Chromatin Accessibility ◽  
Luciferase Reporter ◽  
Enhancer Activity ◽  
Target Gene Expression

The FLT3 Internal Tandem Duplication (FLT3ITD) is common somatic mutation in acute myeloid leukemia (AML). We have previously shown that FLT3ITD fails to induce changes in HSC self-renewal, myelopoiesis and leukemogenesis during fetal stages of life. FLT3ITD signal transduction pathways are hyperactivated in fetal progenitors, but FLT3ITD target genes are not. This suggests that postnatal-specific transcription factors may be required to help induce FLT3ITD target gene expression. Alternatively, repressive histone modifications may impose a barrier to FLT3ITD target gene activation in fetal HPCs that is relaxed during postnatal development. To resolve these possibilities, we used ATAC-seq, as well as H3K4me1, H3K27ac and H3K27me3 ChIP-seq, to identify cis-elements that putatively control FLT3ITD target gene expression in fetal and adult hematopoietic progenitor cells (HPCs). We identified many enhancer elements (ATAC-seq peaks with H3K4me1 and H3K27ac) that exhibited increased chromatin accessibility and activity in FLT3ITD adult HPCs relative to wild type adult HPCs. These elements were enriched near FLT3ITD target genes. HOMER analysis showed enrichment for STAT5, ETS, RUNX1 and IRF binding motifs within the FLT3ITD target enhancers, but motifs for temporally dynamic transcription factors were not identified. We cloned a subset of the enhancers and confirmed that they could synergize with their promoter to activate a luciferase reporter. For representative enhancers, STAT5 binding sites were required to activate the enhancer - as anticipated - and RUNX1 repressed enhancer activity. We tested whether accessibility or priming changed between fetal and adult stages of HPC development. FLT3ITD-dependent changes in chromatin accessibility were not observed in fetal HPCs, though the enhancers were primed early in development as evidenced by the presence of H3K4me1. Repressive H3K27me3 were not present at FLT3ITD target enhancers in either or adult HPCs. The data show that FLT3ITD target enhancers are demarcated early in hematopoietic development, long before they become responsive to FLT3ITD signaling. Repressive marks do not appear to create an epigenetic barrier to enhancer activation in the fetal stage. Instead, age-specific transcription factors are likely required to pioneer enhancer elements so that they can respond to STAT5 and other FLT3ITD effectors. Disclosures No relevant conflicts of interest to declare.

scholarly journals Cell-type-dependent gene activation by yeast transposon Ty1 involves multiple regulatory determinants.

1987 ◽  
Vol 7 (9) ◽  
pp. 3205-3211 ◽  
Author(s):  
M Company ◽  
B Errede
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Gene Activation ◽  
Distal Region ◽  
Control Site ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Negative Effects ◽  
Cis Acting ◽  
Transcriptional Control Region

Ty transposable element insertion mutations of Saccharomyces cerevisiae can cause cell-type-dependent activation of adjacent gene expression. Several cis-acting regulatory regions within Ty1 that are responsible for these effects were identified. A 211-base-pair (bp) region functions as an activator. This region includes the so-called U5 domain of delta and 145 bp of adjacent epsilon sequences. Unlike activation by the intact Ty1, activation by the 211-bp Ty1 subfragment is cell-type independent. The presence of a 112-bp fragment from a more distal region of Ty1 confers cell-type specificity to the activator. The 112-bp fragment includes sequences with homology to mammalian enhancers and to a yeast a/alpha control site. In addition, Ty1 regions that exert negative effects on gene expression were identified. These results demonstrate that the Ty1 transcriptional control region consists of multiple components with distinct regulatory functions.

scholarly journals PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency

2020 ◽  
Author(s):  
Paula Dobrinić ◽  
Aleksander T. Szczurek ◽  
Robert J. Klose
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Transcriptional Control ◽  
Target Genes ◽  
Gene Repression ◽  
Burst Frequency ◽  
Chromatin Domains ◽  
Time Resolved ◽  
Drive Gene

AbstractThe Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The interrelatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population, and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.

scholarly journals Histone lysine crotonylation regulates cell-fate determination of neural stem/progenitor cells by activating bivalent promoters

2020 ◽  
Author(s):  
Shang-Kun Dai ◽  
Pei-Pei Liu ◽  
Hong-Zhen Du ◽  
Xiao Liu ◽  
Ya-Jie Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Developmental Regulation ◽  
Gene Activation ◽  
Neuronal Cell ◽  
Wide Distribution ◽  
Histone Lysine ◽  
Neural Stem Progenitor Cells

AbstractHistone lysine crotonylation (Kcr), an evolutionarily conserved and widely expressed non-acetyl short-chain lysine acylation, plays important roles in transcriptional regulation and disease development. However, its genome-wide distribution, correlation with gene expression, and dynamic changes during developmental processes are largely unknown. In this study, we find that histone Kcr is mainly distributed in active promoters, has a ge-nome-wide positive correlation with transcriptional activity, and regulates transcription of genes participating in metabolism and proliferation. Moreover, elevated histone Kcr activates bivalent promoters to stimulate gene expression in neural stem/progenitor cells (NSPCs), through increasing chromatin openness and recruitment of RNA polymerase II (Pol II). Functionally, these activated genes remodel transcriptome and promote neuronal differentiation.Author summaryOverall, histone Kcr marks active promoters with high gene expression and modifies the local chromatin environment to allow gene activation, which influences neuronal cell fate. It may represent a unique active histone mark involved in neural developmental regulation.

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