TAF4b promotes oocyte survival and proper ovarian chromatin state in the mouse

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

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Rewiring of chromatin state and gene expression by transposable elements

Development Growth & Differentiation ◽

10.1111/dgd.12735 ◽

2021 ◽

Author(s):

Hitoshi Ohtani ◽

Yuka W. Iwasaki

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

Chromatin State

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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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Annotation of chromatin states in 66 complete mouse epigenomes during development

Communications Biology ◽

10.1038/s42003-021-01756-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Arjan van der Velde ◽

Kaili Fan ◽

Junko Tsuji ◽

Jill E. Moore ◽

Michael J. Purcaro ◽

...

Keyword(s):

Target Genes ◽

Cell Types ◽

Developmental Trajectory ◽

Phase Iii ◽

Chromatin State ◽

Mammalian Development ◽

Chromatin States ◽

Transcription Start Sites ◽

Repressive Mark ◽

Distinct Cell

AbstractThe morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development.

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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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