Genomewide identification of nuclear matrix attachment regions: an analysis of methods

Androgen receptor: acting in the three-dimensional chromatin landscape of prostate cancer cells

Androgen receptor (AR) acts as a hormone-controlled transcription factor that conveys the messages of both natural and synthetic androgens to the level of genes and gene programs. Defective AR signaling leads to a wide array of androgen insensitivity disorders, and deregulated AR function, in particular overexpression of AR, is involved in the growth and progression of prostate cancer. Classic models of AR action view AR-binding sites as upstream regulatory elements in gene promoters or their proximity. However, recent wider genomic screens indicate that AR target genes are commonly activated through very distal chromatin-binding sites. This highlights the importance of long-range chromatin regulation of transcription by the AR, shifting the focus from the linear gene models to three-dimensional models of AR target genes and gene programs. The capability of AR to regulate promoters from long distances in the chromatin is particularly important when evaluating the role of AR in the regulation of genes in malignant prostate cells that frequently show striking genomic aberrations, especially gene fusions. Therefore, in addition to the mechanisms of DNA loop formation between the enhancer bound ARs and the transcription apparatus at the target core promoter, the mechanisms insulating distally bound ARs from promiscuously making contacts and activating other than their normal target gene promoters are critical for proper physiological regulation and thus currently under intense investigation. This review discusses the current knowledge about the AR action in the context of gene aberrations and the three-dimensional chromatin landscape of prostate cancer cells.

The sperm nucleus: chromatin, RNA, and the nuclear matrix

Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.

Exploring the effects of a dysfunctional nuclear matrix

The nuclear matrix has remained a contentious structure for decades; many believe that it is an artefact of harsh non-physiological procedures. However, its visualization using milder experimental techniques is leading to its general acceptance by the scientific community. It is a permanent network of core filaments underlying thicker fibres which is proposed to be a platform for numerous important nuclear activities such as transcription and DNA repair. Interestingly, A- and B-type lamin proteins and emerin are components of this nuclear structure; however, they are often referred to only as nuclear envelope proteins. The present mini-review intends to provide an overview of the nuclear matrix, mentioning both its constituents and functional significance. The impact of disease-causing mutations in both emerin and lamin proteins on the structure's ability to regulate and mediate nuclear processes is then discussed.

Progress and prospects: the design and production of plasmid vectors

Plasmid DNA (pDNA) expression vectors are fundamental to all forms of non-viral gene transfer. In this review, we discuss principles of pDNA design and production including the impact of bacterially derived sequences on transgene expression and minicircle approaches to minimize their effects. The impact of inclusion of DNA elements such as scaffold matrix attachment regions (S/MARs), transcription factor (TF)-binding sites and tissue-specific promoters are described. The benefits of eliminating CG dinucleotides (CpGs) from the pDNA are also considered.

The Role of Nuclear Matrix Attachment Regions in Plants

Regions of DNA that bind to the nuclear matrix, or nucleoskeleton, are known as Matrix Attachment Regions (MARs). MARs are thought to play an important role in higher-order structure and chromatin organization within the nucleus. MARs are also thought to act as boundaries of chromosomal domains that act to separate regions of gene-rich, decondensed euchromatin from highly repetitive, condensed heterochromatin. Herein I will present evidence that MARs do indeed act as domain boundaries and can prevent the spread of silencing into active genes. Many fundamental questions remain unanswered about how MARs function in the nucleus. New findings in epigenetics indicate that MARs may also play an important role in the organization of genes and the eventual transport of their mRNAs through the nuclear pore.

Differential nuclear scaffold/matrix attachment marks expressed genes

It is well established that nuclear architecture plays a key role in poising regions of the genome for transcription. This may be achieved using scaffold/matrix attachment regions (S/MARs) that establish loop domains. However, the relationship between changes in the physical structure of the genome as mediated by attachment to the nuclear scaffold/matrix and gene expression is not clearly understood. To define the role of S/MARs in organizing our genome and to resolve the often contradictory loci-specific studies, we have surveyed the S/MARs in HeLa S3 cells on human chromosomes 14–18 by array comparative genomic hybridization. Comparison of LIS (lithium 3,5-diiodosalicylate) extraction to identify SARs and 2 m NaCl extraction to identify MARs revealed that approximately one-half of the sites were in common. The results presented in this study suggest that SARs 5′ of a gene are associated with transcript presence whereas MARs contained within a gene are associated with silenced genes. The varied functions of the S/MARs as revealed by the different extraction methods highlights their unique functional contribution.

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

The folding of chromatin into topologically constrained loop domains is essential for genomic function. We have identified genomic anchors that define the organization of chromatin loop domains across the human major histocompatibility complex (MHC). This locus contains critical genes for immunity and is associated with more diseases than any other region of the genome. Classical MHC genes are expressed in a cell type-specific pattern and can be induced by cytokines such as interferon-gamma (IFNG). Transcriptional activation of the MHC was associated with a reconfiguration of chromatin architecture resulting from the formation of additional genomic anchors. These findings suggest that the dynamic arrangement of genomic anchors and loops plays a role in transcriptional regulation.

The KLAB Toolbox: a suite of in-house software applications for epigenetic analysis

Systems biology presents a new paradigm for elucidating the processes required to organize and sustain life. We now have access to whole genome sequences, gene expression data for multiple cell types, and databases for regulatory elements governing these genes. These resources make it feasible to identify conserved genomic sequences across multiple species, transcription factors regulating the expression of genes with similar expression patterns within a given cell type and to compare expression levels of specific genes between normal and diseased cellular states. In order to utilize this wealth of information, new computational tools that integrate these datasets in a genome-wide context are required. Using the protamine cluster as an example, we present a series of in-house applications that we have developed to integrate, contextualize and visualize datasets across multiple hierarchies.

Real-time PCR quantification using a variable reaction efficiency model

The quantitative real-time polymerase chain reaction (PCR) remains a cornerstone technique in gene expression analysis and sequence characterization. Despite the importance of the approach to experimental biology, the confident assignment of reaction efficiency to the early cycles of real-time PCR reactions remains problematic. Considerable noise may be generated when few cycles in the amplification are available to estimate peak efficiency. An alternate approach that uses data from beyond the log-linear amplification phase is explored in this article with the aim of reducing noise and adding confidence to efficiency estimates. PCR reaction efficiency is regressed to estimate the per-cycle profile of an asymptotically departed peak efficiency even when this is not closely approximated in the measurable cycles. The process can be repeated over replicates to develop a robust estimate of peak reaction efficiency. This leads to an estimate of the maximum reaction efficiency that may be considered primer design specific. Using a series of biological scenarios, we demonstrate that this approach can provide an accurate estimate of initial template concentration.

Anchoring the genome

Although the principles governing chromosomal architecture are largely unresolved, there is evidence that higher-order chromatin folding is mediated by the anchoring of specific DNA sequences to the nuclear matrix. These genome anchors are also crucial regulators of gene expression and DNA replication, and play a role in pathogenesis.

Scaffold/matrix attachment regions (S/MARs): relevance for disease and therapy

There is increasing awareness that processes, such as development, aging and cancer, are governed, to a considerable extent, by epigenetic processes, such as DNA and histone modifications. The sites of these modifications in turn reflect their position and role in the nuclear architecture. Since epigenetic changes are easier to reverse than mutations, drugs that remove or add the chemical tags are at the forefront of research for the treatment of cancerous and inflammatory diseases. This review will use selected examples to develop a unified view that might assist the systematic development of novel therapeutic regimens.