Early replication timing of the chicken α-globin gene domain correlates with its open chromatin state in cells of different lineages

The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold attachment factor A (SAF-A), also known as Heteronuclear Ribonucleoprotein Protein U (HNRNPU), contributes to the formation of open chromatin structure. Here we demonstrate that SAF-A promotes the normal progression of DNA replication, and enables resumption of replication after inhibition. We report that cells depleted for SAF-A show reduced origin licensing in G1 phase, and consequently reduced origin activation frequency in S phase. Replication forks progress slowly in cells depleted for SAF-A, also contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed that the boundaries between early- and late- replicating domains are blurred in cells depleted for SAF-A. Associated with these defects, SAF-A-depleted cells show elevated gH2A phosphorylation and tend to enter quiescence. Overall we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.

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Spatial Organization of the Chicken α-Globin Gene Domain in Cells of Different Origins

Molecular Biology ◽

10.1007/s11008-005-0105-x ◽

2005 ◽

Vol 39 (6) ◽

pp. 851-856

Author(s):

E. S. Ioudinkova ◽

A. V. Petrov ◽

Y. S. Vassetzky ◽

S. V. Razin

Keyword(s):

Spatial Organization ◽

Globin Gene ◽

Different Origins ◽

Globin Gene Domain ◽

In Cells

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Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data

BMC Genomics ◽

10.1186/s12864-021-07373-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Henriette Miko ◽

Yunjiang Qiu ◽

Bjoern Gaertner ◽

Maike Sander ◽

Uwe Ohler

Keyword(s):

Time Series ◽

Histone Modifications ◽

Gene Activation ◽

Expectation Maximization Algorithm ◽

Chromatin State ◽

Open Chromatin ◽

Multiple Time ◽

Enhancer Activity ◽

Chromatin States ◽

Multiple Time Points

Abstract Background Co-localized combinations of histone modifications (“chromatin states”) have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points (“chromatin state trajectories”) have previously been analyzed at promoter and enhancers separately. With the advent of time series Hi-C data it is now possible to connect promoters and enhancers and to analyze chromatin state trajectories at promoter-enhancer pairs. Results We present TimelessFlex, a framework for investigating chromatin state trajectories at promoters and enhancers and at promoter-enhancer pairs based on Hi-C information. TimelessFlex extends our previous approach Timeless, a Bayesian network for clustering multiple histone modification data sets at promoter and enhancer feature regions. We utilize time series ATAC-seq data measuring open chromatin to define promoters and enhancer candidates. We developed an expectation-maximization algorithm to assign promoters and enhancers to each other based on Hi-C interactions and jointly cluster their feature regions into paired chromatin state trajectories. We find jointly clustered promoter-enhancer pairs showing the same activation patterns on both sides but with a stronger trend at the enhancer side. While the promoter side remains accessible across the time series, the enhancer side becomes dynamically more open towards the gene activation time point. Promoter cluster patterns show strong correlations with gene expression signals, whereas Hi-C signals get only slightly stronger towards activation. The code of the framework is available at https://github.com/henriettemiko/TimelessFlex. Conclusions TimelessFlex clusters time series histone modifications at promoter-enhancer pairs based on Hi-C and it can identify distinct chromatin states at promoter and enhancer feature regions and their changes over time.

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Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription

Genes ◽

10.3390/genes12070961 ◽

2021 ◽

Vol 12 (7) ◽

pp. 961

Author(s):

Kanwal Tariq ◽

Ann-Kristin Östlund Farrants

Keyword(s):

Stress Responses ◽

Ribosomal Gene ◽

Chromatin Remodelling ◽

Chromatin State ◽

Rrna Gene ◽

Open Chromatin ◽

Histone Chaperones ◽

Embryonic Cells ◽

Cell Type ◽

Chromatin States

Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.

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The upstream area of the chicken α-globin gene domain is transcribed in both directions in the same cells

FEBS Letters ◽

10.1016/j.febslet.2005.07.051 ◽

2005 ◽

Vol 579 (21) ◽

pp. 4746-4750 ◽

Cited By ~ 6

Author(s):

Victoria Borunova ◽

Olga V. Iarovaia ◽

Yegor S. Vassetzky ◽

Sergey V. Razin

Keyword(s):

Globin Gene ◽

Globin Gene Domain

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Long-Distance Control of Origin Choice and Replication Timing in the Human β-Globin Locus Are Independent of the Locus Control Region

Molecular and Cellular Biology ◽

10.1128/mcb.20.15.5581-5591.2000 ◽

2000 ◽

Vol 20 (15) ◽

pp. 5581-5591 ◽

Cited By ~ 75

Author(s):

Daniel M. Cimbora ◽

Dirk Schübeler ◽

Andreas Reik ◽

Joan Hamilton ◽

Claire Francastel ◽

...

Keyword(s):

Gene Expression ◽

Control Region ◽

Globin Gene ◽

Replication Timing ◽

S Phase ◽

Chromatin Conformation ◽

Erythroid Cells ◽

Long Distance ◽

Targeted Deletion ◽

Globin Gene Expression

ABSTRACT DNA replication in the human β-globin locus is subject to long-distance regulation. In murine and human erythroid cells, the human locus replicates in early S phase from a bidirectional origin located near the β-globin gene. This Hispanic thalassemia deletion removes regulatory sequences located over 52 kb from the origin, resulting in replication of the locus from a different origin, a shift in replication timing to late S phase, adoption of a closed chromatin conformation, and silencing of globin gene expression in murine erythroid cells. The sequences deleted include nuclease-hypersensitive sites 2 to 5 (5′HS2-5) of the locus control region (LCR) plus an additional 27-kb upstream region. We tested a targeted deletion of 5′HS2-5 in the normal chromosomal context of the human β-globin locus to determine the role of these elements in replication origin choice and replication timing. We demonstrate that the 5′HS2-5-deleted locus initiates replication at the appropriate origin and with normal timing in murine erythroid cells, and therefore we conclude that 5′HS2-5 in the classically defined LCR do not control replication in the human β-globin locus. Recent studies also show that targeted deletion of 5′HS2-5 results in a locus that lacks globin gene expression yet retains an open chromatin conformation. Thus, the replication timing of the locus is closely correlated with nuclease sensitivity but not globin gene expression.

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The coordinate replication of the human beta-globin gene domain reflects its transcriptional activity and nuclease hypersensitivity

Molecular and Cellular Biology ◽

10.1128/mcb.8.11.4958-4965.1988 ◽

1988 ◽

Vol 8 (11) ◽

pp. 4958-4965

Author(s):

V Dhar ◽

D Mager ◽

A Iqbal ◽

C L Schildkraut

Keyword(s):

Cell Lines ◽

Dna Sequences ◽

Globin Gene ◽

K562 Cells ◽

Globin Genes ◽

Beta Globin ◽

Beta Globin Gene ◽

Hypersensitive Sites ◽

Flanking Sequences ◽

Globin Gene Domain

The temporal order of replication of DNA sequences in the chromosomal domain containing the human beta-globin gene cluster and its flanking sequences (140 kilobases) was measured and compared in two different human cell lines. In human erythroleukemia (K562) cells, in which embryonic and fetal globin genes are transcribed, all of the sequences we examined from the beta-globin domain replicated early during S phase, while in HeLa cells, in which globin genes are transcriptionally silent, these sequences replicated late during S. Potential sites of initiation of DNA replication within this domain were identified. The beta-globin gene domain was also found to differ with respect to the nuclease sensitivity of the chromatin in these two cell lines. In K562 cells, hypersensitive sites for endogenous nucleases and DNase I were present in the chromatin near the earliest-replicating segments in the beta-globin domain.

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CTCF-dependent enhancer blockers at the upstream region of the chicken -globin gene domain

Nucleic Acids Research ◽

10.1093/nar/gkh301 ◽

2004 ◽

Vol 32 (4) ◽

pp. 1354-1362 ◽

Cited By ~ 42

Author(s):

V. Valadez-Graham

Keyword(s):

Globin Gene ◽

Upstream Region ◽

Globin Gene Domain

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Coexpression of gamma and beta globin mRNA in cells containing a single human beta globin locus: results from studies using single-cell reverse transcription polymerase chain reaction [published erratum appears in Blood 1994 Aug 15;84(4):1357]

Blood ◽

10.1182/blood.v83.5.1412.1412 ◽

1994 ◽

Vol 83 (5) ◽

pp. 1412-1419 ◽

Cited By ~ 8

Author(s):

T Furukawa ◽

G Zitnik ◽

K Leppig ◽

T Papayannopoulou ◽

G Stamatoyannopoulos

Keyword(s):

Polymerase Chain Reaction ◽

Reverse Transcription ◽

Single Cells ◽

Globin Gene ◽

Erythroid Cell ◽

Beta Globin ◽

Chain Reaction ◽

Globin Mrna ◽

Polymerase Chain ◽

In Cells

Abstract We developed a method detecting globin gene expression in single cells using reverse transcription polymerase chain reaction. epsilon and gamma globin cDNAs are coamplified by an epsilon gamma primer set whereas gamma and beta globin cDNAs are coamplified by a gamma beta primer set and the individual globin cDNAs are distinguished by restriction enzyme digestion. Analysis of RNA preparations from human fetal liver, neonatal red blood cells (RBCs), or adult RBCs showed the expected mRNA species for each stage of human development. Analysis of single cells from a human erythroleukemia line coexpressing gamma and beta globin chains showed heterogeneity in gamma and beta mRNA contents. The method was subsequently used to test whether only one or more than one globin genes are expressed in cells that contain a single human beta globin locus. We found that about 50% of single cells from MEL x fetal erythroid cell hybrids containing a single human beta globin locus coexpressed gamma and beta globin mRNA. This finding is best explained by assuming that both gamma and beta genes are simultaneously transcribed from the same beta globin locus implying that the LCR can simultaneously interact with more than one globin gene promoter.

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N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

Science ◽

10.1126/science.aay6018 ◽

2020 ◽

Vol 367 (6477) ◽

pp. 580-586 ◽

Cited By ~ 46

Author(s):

Jun Liu ◽

Xiaoyang Dou ◽

Chuanyuan Chen ◽

Chuan Chen ◽

Chang Liu ◽

...

Keyword(s):

Messenger Rna ◽

Embryonic Stem ◽

Chromatin Accessibility ◽

Chromatin State ◽

Open Chromatin ◽

Dependent Manner ◽

Nuclear Exosome ◽

Regulatory Rnas ◽

Nuclear Degradation ◽

Long Interspersed Element

N6-methyladenosine (m6A) regulates stability and translation of messenger RNA (mRNA) in various biological processes. In this work, we show that knockout of the m6A writer Mettl3 or the nuclear reader Ythdc1 in mouse embryonic stem cells increases chromatin accessibility and activates transcription in an m6A-dependent manner. We found that METTL3 deposits m6A modifications on chromosome-associated regulatory RNAs (carRNAs), including promoter-associated RNAs, enhancer RNAs, and repeat RNAs. YTHDC1 facilitates the decay of a subset of these m6A-modified RNAs, especially elements of the long interspersed element-1 family, through the nuclear exosome targeting–mediated nuclear degradation. Reducing m6A methylation by METTL3 depletion or site-specific m6A demethylation of selected carRNAs elevates the levels of carRNAs and promotes open chromatin state and downstream transcription. Collectively, our results reveal that m6A on carRNAs can globally tune chromatin state and transcription.

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