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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE304818 | GEO | 2025/08/27

REPOSITORIES: GEO

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

Project description:A subset of highly active chromosomal "hot zones" reproducibly positions adjacent to nuclear speckles (NS). Genes within these regions amplify their expression with NS proximity. However, gene expression changes inversely correlate with changes in NS distance genome-wide. We hypothesized the existence of additional gene expression "niches" away from but spatially correlated with NS. Here we report the identification of two dynamic perispeckle patterns of protein concentrations extending outwards from nuclear speckles and persisting even after NS are eliminated. Highly active chromosome regions which weakly associate with NS instead show close, NS-independent association with these perispeckle patterns. Additionally, transcripts from model intron-containing versus intronless genes associate differentially with these two patterns. While genes within speckle-associated genomic regions predominately are downregulated upon nuclear speckle depletion, genes associated with perispeckle patterns are biased towards upregulation. We suggest the interchromatin space (ICS) is partitioned into additional gene expression “niches”- surrounding and extending from nuclear speckles- that may be involved in mRNA and gene dynamics.

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

Project description:Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

Project description:Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

Project description:Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

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De novo LINE-1 retrotransposition in HepG2 cells preferentially targets gene poor regions of chromosome 13.

Project description:Long interspersed nuclear elements (Line-1 or L1s) account for ~17% of the human genome. While the majority of human L1s are inactive, ~80-100 elements remain retrotransposition competent and mobilize through RNA intermediates to different locations within the genome. De novo insertions of L1s account for polymorphic variation of the human genome and disruption of target loci at their new location. In the present study, fluorescence in situ hybridization and DNA sequencing were used to characterize retrotransposition profiles of L1(RP) in cultured human HepG2 cells. While expression of synthetic L1(RP) was associated with full-length and truncated insertions throughout the entire genome, a strong preference for gene-poor regions, such as those found in chromosome 13 was observed for full-length insertions. These findings shed light into L1 targeting mechanisms within the human genome and question the putative randomness of L1 retrotransposition.

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Project description:We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein (GapR) that selectively aids the initiation of chromosome replication and the initial steps of chromosome partitioning. The protein binds the chromosome origin of replication (Cori) and has higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. gapR gene expression is essential for normal rapid growth and sufficient GapR levels are required for the correct timing of chromosome replication. Whole genome ChIP-seq identified dynamic DNA-binding distributions for GapR, with the strongest associations at the partitioning (parABS) locus near Cori. Using molecular-genetic and fluorescence microscopy experiments, we showed that GapR also promotes the first steps of chromosome partitioning, the initial separation of the duplicated parS loci following replication from Cori. This separation occurs before the parABS-dependent partitioning phase. Therefore, this early separation, whose mechanisms is not known, coincides with the poorly defined mechanism(s) that establishes chromosome asymmetry: C. crescentus chromosomes are partitioned to distinct cell-poles which develop into replicating and non-replicating cell-types. We propose that GapR coordinates chromosome replication with asymmetry-establishing chromosome separation, noting that both roles are consistent with the phylogenetic restriction of GapR to asymmetrically dividing bacteria.

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