Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF.

Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle.

Methyl Adenine Identification (MadID): High-Resolution Detection of Protein-DNA Interactions.

Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understand many essential biological processes. Methyl Adenine Identification (MadID) is a proximity methylation-based assay that allows the visualization, quantification, and identification of binding sites from DNA-interacting proteins in eukaryotic cells. Chromatin-binding proteins of interest are fused to the newly described bacterial methyltransferase M.

Imprinted MicroRNA Gene Clusters in the Evolution, Development, and Functions of Mammalian Placenta.

In mammals, the expression of a subset of microRNA (miRNA) genes is governed by genomic imprinting, an epigenetic mechanism that confers monoallelic expression in a parent-of-origin manner. Three evolutionarily distinct genomic intervals contain the vast majority of imprinted miRNA genes: the rodent-specific, paternally expressed C2MC located in intron 10 of the gene, the primate-specific, paternally expressed C19MC positioned at human Chr.19q13.

The 3D genome: From fundamental principles to disease and cancer.

In higher eukaryotes, the three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression, DNA repair and DNA replication regulations. Alteration of this 3D organization is detrimental to the organism and can give rise to a broad range of diseases such as cancers. Here, we review recent advances in the field.

[The intimate genome… in three dimensions].

Over the past decade, techniques based on chromosome conformation capture (3C) have accelerated our understanding of eukaryote's nuclear architecture. Coupled to high throughput sequencing and bioinformatics they have unveiled different organizational levels of the genome at an unprecedented scale. Initially performed using large populations of cells, a new variant of these techniques can be applied to single cell.

UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells.

Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair (TCR) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes.

The human TREX-2 complex is stably associated with the nuclear pore basket.

In eukaryotes, mRNA export involves many evolutionarily conserved factors that carry the nascent transcript to the nuclear pore complex (NPC). The THO/TREX complex couples transcription to mRNA export and recruits the mRNA export receptor NXF1 for the transport of messenger ribonucleoprotein particles (mRNP) to the NPC. The transcription and export complex 2 (TREX-2) was suggested to interact with NXF1 and to shuttle between transcription sites and the NPC.

Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output.

The tightly controlled deubiquitination activity of the human SAGA complex differentially modifies distinct gene regulatory elements.

The multisubunit SAGA coactivator complex facilitates access of general transcription factors to DNA through histone acetylation mediated by GCN5. USP22 (ubiquitin-specific protease 22) was recently described as a subunit of the human SAGA complex that removes ubiquitin from monoubiquitinated histone H2B and H2A in vitro. Here we demonstrate an allosteric regulation of USP22 through multiple interactions with different domains of other subunits of the SAGA deubiquitination module (ATXN7, ATXN7L3, and ENY2).

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.

The discovery of interchromosomal interactions in higher eukaryotes points to a functional interplay between genome architecture and gene expression, challenging the view of transcription as a one-dimensional process. However, the extent of interchromosomal interactions and the underlying mechanisms are unknown. Here we present the first genome-wide analysis of transcriptional interactions using the mouse globin genes in erythroid tissues.

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme.

Transcriptome studies have uncovered a plethora of noncoding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences.

The role of transcription factories in large-scale structure and dynamics of interphase chromatin.

The genome is spatially organized inside nuclei, with chromosomes and genes occupying preferential positions relative to each other and to various nuclear landmarks. What drives this organization is unclear, but recent findings suggest there are extensive intra- and inter-chromosomal communications between various genomic regions that appear to play important roles in genome function. Here we review transcription factories, distinct sub-nuclear foci where nascent transcription occurs.

Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes.

Imprinted genes are clustered in domains, and their allelic repression is mediated by imprinting control regions. These imprinting control regions are marked by DNA methylation, which is essential to maintain imprinting in the embryo. To explore how imprinting is regulated in placenta, we studied the Kcnq1 domain on mouse distal chromosome 7.

Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation.

Imprinted genes are expressed from only one of the parental chromosomes and are marked epigenetically by DNA methylation and histone modifications. The imprinting center 2 (IC2) on mouse distal chromosome 7 is flanked by several paternally repressed genes, with the more distant ones imprinted exclusively in the placenta. We found that most of these genes lack parent-specific DNA methylation, and genetic ablation of methylation does not lead to loss of their imprinting in the trophoblast (placenta).

Site-specific analysis of histone methylation and acetylation.

Covalent modifications on the nucleosomal histones are essential in chromatin regulation and gene expression. Patterns of histone modifications may be somatically maintained and can thereby maintain locus-specific repression/activity in defined lineages or throughout development. During recent years, histone acetylation and methylation have emerged as key players in the repression or activation of genes and chromosomal domains.

PrP-dependent cell adhesion in N2a neuroblastoma cells.

The cellular isoform of prion protein (PrP(C)) is a ubiquitous glycoprotein expressed by most tissues and with a biological function yet to be determined. Here, we have used a neuroblastoma cell model to investigate the involvement of PrP in cell adhesion. Incubation of single cell suspension induced cell-cell adhesion and formation of cell aggregates.