Yeast study prompts rethink of DNA safekeeping

DNA replication is more prone to errors at times of stress leading to mutations that could cause disease.

Quelle: Sciencedaily

Frog eggs help researchers understand repair of DNA damages

The DNA replication process, which takes place every time a cell divides, also triggers repair of DNA damage, researchers have described in a new study. Scientists have studied extracts from frog eggs, whose proteins are very similar to those of human cells. The researchers hope the new research results can be used to develop more effective treatments for cancer in the long run.

Quelle: Sciencedaily

Key role found for enzymes in DNA replication and sensitivity to chemotherapeutic drugs

A new study shows that the TLK1 and TLK2 enzymes are critical for ensuring the copying of DNA. The research is based on previous studies that pointed to TLK1/2 as potential candidate targets in cancer therapy, and it provides new molecular details on their key functions in cancer cell proliferation. (Mehr in: Cancer News — ScienceDaily)

Rhythm of DNA replication exploited to kill cancer cells

Human cells divide and create new cells throughout life. In this process, a steady — even rhythmic — supply of DNA building blocks is needed to create new DNA. Now researchers have shown exactly how human cells regulate this process so it does not fail and cause illness. The researchers also show how they can manipulate the rhythm and suggest how this can be used in the future to kill cancer cells. (Mehr in: Cancer News — ScienceDaily)

The ‚DNA corrector‘ is more efficient in the most important regions of the genome

Error surveillance and repair mechanisms during DNA replication do not show the same competence in all regions of the human genome. Scientists have discovered that the mechanism that repairs errors in DNA is more efficient in the regions of genes that hold information for the production of proteins. (Mehr in: Cancer News — ScienceDaily)

Problems with DNA replication can cause epigenetic changes that may be inherited for several generations

Scientists reveal that a fault in the process that copies DNA during cell division can cause epigenetic changes that may be inherited for up-to five generations. They also identified the cause of these epigenetic changes, which is related to the loss of a molecular mechanism in charge of silencing genes. Their results will change the way we think about the impact of replication stress in cancer and during embryonic development, as well as its inter-generational inheritance. (Mehr in: Cancer News — ScienceDaily)

Squeezing life from DNA’s double helix

DNA replication begins when the double helix, caught in a vice of proteins, melts, scientists have discovered. (Mehr in: Cancer News — ScienceDaily)

Structure of key DNA replication protein solved

A research team has solved the three-dimensional structure of a key protein that helps damaged cellular DNA repair itself. Investigators say that knowing the chemical structure of the protein will likely help drug designers build novel anti-cancer agents. (Mehr in: Cancer News — ScienceDaily)

DNA Replication – Take a break

Before a cell divides, it must first handle a large-scale project: Its entire genetic material has to be duplicated so that each of the two daughter cells is equipped with a full copy after cell division. As errors in this DNA replication could lead to the death of the cell, the process is rigorously controlled. It takes place in two phases. Researchers at the Max Planck Institute of Biochemistry in Martinsried have now revealed in the journal Cell Reports that these two phases are strictly separated from one another by breaks, thereby preventing errors in the DNA replication. (Mehr in: Pressemitteilungen – idw – Informationsdienst Wissenschaft)

Enzyme with high potential for new cancer treatment identified

A team of researchers has identified an enzyme that separates DNA replication from repair. This discovery could be of tremendous significance in the treatment of tumors. (Mehr in: Cancer News — ScienceDaily)

Chromosomes: the importance of keeping the balance

The genetic material of cancer cells is unstable. For example, the number of chromosomes, which are the individual elements of packed DNA, is changed in so called aneuploidies. This imbalance in chromosomes, which often occurs early in tumor development, leads to cell stress and promotes disease. How this can happen is now shown by the discovery of a research team led by Zuzana Storchová at the Max Planck Institute of Biochemistry in Martinsried, reported in a groundbreaking study published in Nature Communications. An imbalance in an enzyme called MCM2-7 that is essential for DNA replication is likely to be responsible for this escalating genomic instability. (Mehr in: Pressemitteilungen – idw – Informationsdienst Wissenschaft)

Researchers connect haywire protein to breast cancer, leukemia

The cause of some cancers, including breast cancer and leukemia, is better understood, thanks to recent research. In the new study, the researchers found that too much of a key protein, called cyclin E, slows down DNA replication and introduces potentially harmful cancer-linked mutations when cells divide. (Mehr in: Cancer News — ScienceDaily)

A global assessment of cancer genomic alterations in epigenetic mechanisms

Muhammad A Shah, Emily L Denton, Cheryl H Arrowsmith, Mathieu Lupien and Matthieu Schapira

Abstract

Background

The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling are recurrently mutated in cancer patients.

Results

Here, we analyze mutational and transcriptional profiles from TCGA and the ICGC across a collection 441 chromatin factors and histones. Chromatin factors essential for rapid replication are frequently overexpressed, and those that maintain genome stability frequently mutated. We identify novel mutation hotspots such as K36M in histone H3.1, and uncover a general trend in which transcriptional profiles and somatic mutations in tumor samples favor increased transcriptionally repressive histone methylation, and defective chromatin remodeling.

Conclusions

This unbiased approach confirms previously published data, uncovers novel cancer-associated aberrations targeting epigenetic mechanisms, and justifies continued monitoring of chromatin-related alterations as a class, as more cancer types and distinct cancer stages are represented in cancer genomics data repositories.

Continue reading „A global assessment of cancer genomic alterations in epigenetic mechanisms“

Variation in cancer risk among tissues can be explained by the number of stem cell divisions

Tomasetti and Vogelstein show that the lifetime risk of cancers of many different types is strongly correlated with the total number of divisions of the normal self-renewing cells maintaining that tissue’s homeostasis. These results suggest that only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to bad luck, that is, random mutations arising during DNA replication in normal, noncancerous stem cells.

Tomasetti C, Vogelstein B (2015): Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science 2 January 2015: Vol. 347 no. 6217 pp. 78-81 DOI: 10.1126/science.1260825

Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci

3D-SIM-based DAPI intensity classification in the Barr body versus the entire nucleus of C2C12 cells. (A) Mid z-section of a DAPI-stained nucleus. The area below the dashed line illustrates the resolution level obtained by wide-field deconvolution microscopy, for comparison. Inset magnifications show the non-uniformly compacted structure of the Barr body resolvable with 3D-SIM (1) and an arbitrary autosomal region with CDCs (2). Scale bars: 5 μm, insets 1 μm. (B) X chromosome-specific painting (green) of Xi (left) and Xa territories (right) of the same nucleus in different z-sections. Note the high convergence between the painted Xi and the DAPI visualized Barr body (arrowheads). Scale bars: 2 μm, insets 1 μm. (C) 3D DAPI intensity classification exemplified for the nucleus shown in (A). Seven DAPI intensity classes displayed in false-color code ranging from class 1 (blue) representing pixels close to background intensity, largely representing the IC, up to class 7 (white) representing pixels with highest density, mainly associated with chromocenters. Framed areas of the Barr body (inset 1) and a representative autosomal region (inset 2) are shown on the right at resolution levels of 3D-SIM, deconvolution and conventional wide-field microscopy. The Xi territory pervaded by lower DAPI intensities becomes evident only at 3D-SIM resolution, whereas both wide-field and deconvolution microscopy imply a concentric increase of density in the Barr body. In the autosomal region, chromatin assigned to classes 2 to 3 lines compacted CDCs, represented by classes 4 to 6. (D) Left: average DAPI intensity classification profiles with standard deviations evaluated for entire nuclear volumes or the Barr body region only (dark grey bars). Right: over/underrepresentation of the average DAPI intensity class fraction sizes in the Barr body versus entire nuclear volumes (n = 12). Distribution differences on classes between Xi and entire nucleus P <0.001. 3D-SIM, three-dimensional structured illumination microscopy; CDC, chromatin domain cluster; DAPI, 4',6-diamidino-2-phenylindole; FISH, fluorescence in situ hybridization; IC, interchromatin compartment; Xa, active X chromosome; Xi, inactive X chromosome. Smeets et al. Epigenetics & Chromatin 2014 7:8   doi:10.1186/1756-8935-7-8
3D-SIM-based DAPI intensity classification in the Barr body versus the entire nucleus of C2C12 cells. (A) Mid z-section of a DAPI-stained nucleus. The area below the dashed line illustrates the resolution level obtained by wide-field deconvolution microscopy, for comparison. Inset magnifications show the non-uniformly compacted structure of the Barr body resolvable with 3D-SIM (1) and an arbitrary autosomal region with CDCs (2). Scale bars: 5 μm, insets 1 μm. (B) X chromosome-specific painting (green) of Xi (left) and Xa territories (right) of the same nucleus in different z-sections. Note the high convergence between the painted Xi and the DAPI visualized Barr body (arrowheads). Scale bars: 2 μm, insets 1 μm. (C) 3D DAPI intensity classification exemplified for the nucleus shown in (A). Seven DAPI intensity classes displayed in false-color code ranging from class 1 (blue) representing pixels close to background intensity, largely representing the IC, up to class 7 (white) representing pixels with highest density, mainly associated with chromocenters. Framed areas of the Barr body (inset 1) and a representative autosomal region (inset 2) are shown on the right at resolution levels of 3D-SIM, deconvolution and conventional wide-field microscopy. The Xi territory pervaded by lower DAPI intensities becomes evident only at 3D-SIM resolution, whereas both wide-field and deconvolution microscopy imply a concentric increase of density in the Barr body. In the autosomal region, chromatin assigned to classes 2 to 3 lines compacted CDCs, represented by classes 4 to 6. (D) Left: average DAPI intensity classification profiles with standard deviations evaluated for entire nuclear volumes or the Barr body region only (dark grey bars). Right: over/underrepresentation of the average DAPI intensity class fraction sizes in the Barr body versus entire nuclear volumes (n = 12). Distribution differences on classes between Xi and entire nucleus P Smeets et al. Epigenetics & Chromatin 2014 7:8 doi:10.1186/1756-8935-7-8

Daniel Smeets, Yolanda Markaki, Volker J Schmid, Felix Kraus, Anna Tattermusch, Andrea Cerase, Michael Sterr, Susanne Fiedler, Justin Demmerle, Jens Popken, Heinrich Leonhardt, Neil Brockdorff, Thomas Cremer1, Lothar Schermelleh and Marion Cremer

Abstract

Background

A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs).

Results

We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an ‘autosomal Barr body’ with less compacted chromatin and incomplete RNAP II exclusion.

Conclusions

3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform compaction of the Barr body at the nucleosome level. The localization of distinct Xist RNA foci at boundaries of the rudimentary ANC may be considered as snap-shots of a dynamic interaction with silenced genes. Enrichment of SAF-A within Xi territories and its close spatial association with Xist RNA suggests their cooperative function for structural organization of Xi.

Continue reading „Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci“