Table of Contents

Volume 3, Issue 1

  January/February 2012

  Pages 1 - 110

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LANDES HIGHLIGHTS

Landes Highlights

Eva Riedmann
Pages 1 - 3
http://dx.doi.org/10.4161/nucl.19362
PDF




COMMENTARY

RS and RGG repeats as primitive proteins at the transition between the RNA and RNP worlds

Maarten Fornerod
Pages 4 - 5
http://dx.doi.org/10.4161/nucl.18631
Abstract | Full Text | PDF

For many experimental biologists in the field of nuclear cell biology, low complexity repeats in nuclear proteins constitute a nuisance. They are difficult to express, impossible to crystalize and have low but near ubiquitous unwanted affinities toward many biomolecules. Examples of such nuclear protein repeats are RS (Arg-Ser) repeats in splicing factors, RGG (Arg-Gly-Gly) repeats in hnRNP proteins and FG (Phe-Gly) repeats in nuclear pore components. Here, I would like to present a more positive perspective for at least a subset of repeats and suggest that they are excellent candidates to have constituted the first proteins emerging from an RNA world.




EXTRA VIEWS

Comparison between the CENP-A and histone H3 structures in nucleosomes

Hiroaki Tachiwana, Wataru Kagawa and Hitoshi Kurumizaka
Pages 6 - 11
http://dx.doi.org/10.4161/nucl.18372
Abstract | Full Text | PDF

Centromeres are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A (CENP-A nucleosome) and their inheritance is probably dictated by the architecture of the centromeric nucleosome. We previously determined the crystal structure of the human CENP-A nucleosome. CENP-A forms a histone octamer containing two each of histones H2A, H2B, H4 and CENP-A and the DNA is left-handedly wrapped around the histone octamer, as in canonical nucleosomes containing histone H3. In the CENP-A nucleosome structure, 13 base pairs of the DNA ends are detached from the histone surface and two CENP-A regions, the αN helix and loop 1, adopt different structures from those in the H3 nucleosome. In this Extra View article, we provide a detailed structural comparison between CENP-A and H3 in nucleosomes and describe their distinctions and similarities.

Modulation of chromatin access during adipocyte differentiation

Susanne Mandrup and Gordon Hager
Pages 12 - 15
http://dx.doi.org/10.4161/nucl.18928
Abstract | Full Text | PDF

Cellular development requires reprogramming of the genome to modulate the gene program of the undifferentiated cell and allow expression of the gene program unique to differentiated cells. A number of key transcription factors involved in this reprogramming of preadipocytes to adipocytes have been identified; however, it is not until recently that we have begun to understand how these factors act at a genome-wide scale. In a recent publication we have mapped the genome-wide changes in chromatin structure during differentiation of 3T3-L1 preadipocytes and shown that a major reorganization of the chromatin landscape occurs within few hours following the addition of the adipogenic cocktail. In addition, we have mapped the genome-wide profiles of several of the early adipogenic transcription factors and shown that they act in a highly cooperative manner to drive this dramatic remodeling process.

UPF1: A leader at the end of chromosomes

Claus M. Azzalin
Pages 16 - 21
http://dx.doi.org/10.4161/nucl.18929
Abstract | Full Text | PDF

The human helicase and ATPase up-frameshift suppressor 1 (UPF1), traditionally known as a major player in several RNA quality control mechanisms, is emerging as a crucial caretaker of the stability of the genome. Work from my laboratory has provided insight into the function of UPF1 during DNA metabolism and has revealed that this versatile enzyme sustains the proper replication of telomeres, the protective structures located at the ends of linear eukaryotic chromosomes. We have supplied direct evidence that telomere replication is not completed in cells with compromised UPF1 function, leading to the accumulation of DNA damage and telomere abnormalities. We also have isolated a number of factors that physically interact with UPF1 and might represent molecular links between UPF1 and telomeres. In this paper, I re-evaluate the functions of UPF1 in maintaining the stability of telomeres and of the genome at large and suggest a model that explains how UPF1 might be recruited and function during telomere replication.

Ribosome biogenesis factors working with a nuclear envelope SUN domain protein: New players in the solar system

Chihiro Horigome and Keiko Mizuta
Pages 22 - 28
http://dx.doi.org/10.4161/nucl.18930
Abstract | Full Text | PDF

The nucleolus, the most prominent structure observed in the nucleus, is often called a “ribosome factory.” Cells spend an enormous fraction of their resources to achieve the mass-production of ribosomes required by rapid growth. On the other hand, ribosome biogenesis is also tightly controlled, and must be coordinated with other cellular processes. Ribosomal proteins and ribosome biogenesis factors are attractive candidates for this link. Recent results suggest that some of them have functions beyond ribosome biogenesis. Here we review recent progress on ribosome biogenesis factors, Ebp2 and Rrs1, in yeast Saccharomyces cerevisiae. In this organism, Ebp2 and Rrs1 are found in the nucleolus and at the nuclear periphery. At the nuclear envelope, these proteins interact with a membrane-spanning SUN domain protein, Mps3, and play roles in telomere clustering and silencing along with the silent information regulator Sir4. We propose that a protein complex consisting Ebp2, Rrs1 and Mps3 is involved in a wide range of activities at the nuclear envelope.




REVIEWS

Open Access Article

Integrated regulation of PIKK-mediated stress responses by AAA+ proteins RUVBL1 and RUVBL2

Natsuko Izumi, Akio Yamashita and Shigeo Ohno
Pages 29 - 43
http://dx.doi.org/10.4161/nucl.18926
Abstract | Full Text | PDF

Proteins of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family are activated by various cellular stresses, including DNA damage, premature termination codon and nutritional status, and induce appropriate cellular responses. The importance of PIKK functions in the maintenance of genome integrity, accurate gene expression and the proper control of cell growth/proliferation is established. Recently, ATPase associated diverse cellular activities (AAA+) proteins RUVBL1 and RUVBL2 (RUVBL1/2) have been shown to be common regulators of PIKKs. The RUVBL1/2 complex regulates PIKK-mediated stress responses through physical interactions with PIKKs and by controlling PIKK mRNA levels. In this review, the functions of PIKKs in stress responses are outlined and the physiological significance of the integrated regulation of PIKKs by the RUVBL1/2 complex is presented. We also discuss a putative “PIKK regulatory chaperone complex” including other PIKK regulators, Hsp90 and the Tel2 complex.

Evolution of the lamin protein family: What introns can tell

Annette Peter and Reimer Stick
Pages 44 - 59
http://dx.doi.org/10.4161/nucl.18927
Abstract | Full Text | PDF

Lamins are the major components of the nuclear lamina, a filamentous layer found at the interphase between chromatin and the inner nuclear membrane. The lamina supports the nuclear envelope and provides anchorage sites for chromatin. Lamins and their associated proteins are required for most nuclear activities, mitosis, and for linking the nucleoskeleton to the network of cytoskeletal filaments. Mutations in lamins and their associated proteins give rise to a wide range of diseases, collectively called laminopathies. This review focuses on the evolution of the lamin protein family. Evolution from basal metazoans to man will be described on the basis of protein sequence comparisons and analyses of their gene structure. Lamins are the founding members of the family of intermediate filament proteins. How genes encoding cytoplasmic IF proteins could have arisen from the archetypal lamin gene progenitor, can be inferred from a comparison of the respective gene structures. The lamin/IF protein family seems to be restricted to the metazoans. In general, invertebrate genomes harbor only a single lamin gene encoding a B-type lamin. The archetypal lamin gene structure found in basal metazoans is conserved up to the vertebrate lineage. The completely different structure of lamin genes in Caenorhabditis and Drosophila are exceptions rather than the rule within their systematic groups. However, variation in the length of the coiled-coil forming central domain might be more common than previously anticipated. The increase in the number of lamin genes in vertebrates can be explained by two rounds of genome duplication. The origin of lamin A by exon shuffling might explain the processing of prelamin A to the mature non-isoprenylated form of lamin A. By alternative splicing the number of vertebrate lamin proteins has increased even further. Lamin C, an alternative splice form of the LMNA gene, is restricted to mammals. Amphibians and mammals express germline-specific lamins that differ in their protein structure from that of somatic lamins. Evidence is provided that there exist lamin-like proteins outside the metazoan lineage.




RESEARCH PAPERS

Open Access Article

Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina

Yanira Gonzalez, Akira Saito and Shelley Sazer
Pages 60 - 76
http://dx.doi.org/10.4161/nucl.18824
Abstract | Full Text | PDF

In animal cells the nuclear lamina, which consists of lamins and lamin-associated proteins, serves several functions: it provides a structural scaffold for the nuclear envelope and tethers proteins and heterochromatin to the nuclear periphery. In yeast, proteins and large heterochromatic domains including telomeres are also peripherally localized, but there is no evidence that yeast have lamins or a fibrous nuclear envelope scaffold. Nonetheless, we found that the Lem2 and Man1 proteins of the fission yeast Schizosaccharomyces pombe, evolutionarily distant relatives of the Lap2/Emerin/Man1 (LEM) sub-family of animal cell lamin-associated proteins, perform fundamental functions of the animal cell lamina. These integral inner nuclear membrane localized proteins, with nuclear localized DNA binding Helix-Extension-Helix (HEH) domains, impact nuclear envelope structure and integrity, are essential for the enrichment of telomeres at the nuclear periphery and by means of their HEH domains anchor chromatin, most likely transcriptionally repressed heterochromatin, to the nuclear periphery. These data indicate that the core functions of the nuclear lamina are conserved between fungi and animal cells and can be performed in fission yeast, without lamins or other intermediate filament proteins.

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe

Babett Steglich, Guillaume Filion, Bas van Steensel and Karl Ekwall
Pages 77 - 87
http://dx.doi.org/10.4161/nucl.18825
Abstract | Full Text | PDF

Metazoan chromatin at the nuclear periphery is generally characterized by lowly expressed genes and repressive chromatin marks and presents a sub-compartment with properties distinct from the nuclear interior. To test whether the S. pombe nuclear periphery behaves similarly, we used DNA adenine methyltransferase identification (DamID) to map the target loci of two inner nuclear membrane proteins, Ima1 and Man1. We found that peripheral chromatin shows low levels of RNA-Polymerase II and nucleosome occupancy, both characteristic of repressed chromatin regions. Consistently, lowly expressed genes preferentially associate with the periphery and highly expressed genes are depleted from it. When looking at peripheral intergenic regions (IGRs), we found that divergent IGRs are enriched compared with convergent IGRs, indicating that transcription preferentially points away from the periphery rather than toward it. Interestingly, we found that Ima1 and Man1 have common, but also separate target regions in the genome. Ima1-interacting loci were enriched for the RNAi components Dcr1 and Rdp1. This agrees with previous findings that Dcr1 is localized at the nuclear periphery. In contrast, Man1 target loci were bound by the heterochromatin protein Swi6, especially at subtelomeric regions. Subtelomeric chromatin was shown to form a unique chromatin type lacking both repressive and active chromatin features and containing low levels of the histone variant H2A.Z. Thus, we find that the fission yeast nuclear periphery shows similar properties to those of metazoan cells, despite the absence of a nuclear lamina. Our results point to a role of nuclear membrane proteins in organizing chromatin domains and loops.

Transient nuclear envelope rupturing during interphase in human cancer cells

Jesse D. Vargas, Emily M. Hatch, Daniel J. Anderson and Martin W. Hetzer
Pages 88 - 100
http://dx.doi.org/10.4161/nucl.18954
Abstract | PDF

Neoplastic cells are often characterized by specific morphological abnormalities of the nuclear envelope (NE), which have been used for cancer diagnosis for more than a century. The NE is a double phospholipid bilayer that encapsulates the nuclear genome, regulates all nuclear trafficking of RNAs and proteins and prevents the passive diffusion of macromolecules between the nucleoplasm and the cytoplasm. Whether there is a consequence to the proper functioning of the cell and loss of structural integrity of the nucleus remains unclear. Using live cell imaging, we characterize a phenomenon wherein nuclei of several proliferating human cancer cell lines become temporarily ruptured during interphase. Strikingly, NE rupturing was associated with the mislocalization of nucleoplasmic and cytoplasmic proteins and, in the most extreme cases, the entrapment of cytoplasmic organelles in the nuclear interior. In addition, we observed the formation of micronuclei-like structures during interphase and the movement of chromatin out of the nuclear space. The frequency of these NE rupturing events was higher in cells in which the nuclear lamina, a network of intermediate filaments providing mechanical support to the NE, was not properly formed. Our data uncover the existence of a NE instability that has the potential to change the genomic landscape of cancer cells.

Open Access Article

CENP-C facilitates the recruitment of M18BP1 to centromeric chromatin

Silvia Dambacher, Wen Deng, Matthias Hahn, Dennis Sadic, Jonathan Fröhlich, Alexander Nuber, Christian Hoischen, Stephan Diekmann, Heinrich Leonhardt and Gunnar Schotta
Pages 101 - 110
http://dx.doi.org/10.4161/nucl.18955
Abstract | Full Text | PDF

Centromeres are important structural constituents of chromosomes that ensure proper chromosome segregation during mitosis by providing defined sites for kinetochore attachment. In higher eukaryotes, centromeres have no specific DNA sequence and thus, they are rather determined through epigenetic mechanisms. A fundamental process in centromere establishment is the incorporation of the histone variant CENP-A into centromeric chromatin, which provides a binding platform for the other centromeric proteins. The Mis18 complex, and, in particular, its member M18BP1 was shown to be essential for both incorporation and maintenance of CENP-A.

 

Here we show that M18BP1 displays a cell cycle-regulated association with centromeric chromatin in mouse embryonic stem cells. M18BP1 is highly enriched at centromeric regions from late anaphase through to G1 phase. An interaction screen against 16 core centromeric proteins revealed a novel interaction of M18BP1 with CENP-C. We mapped the interaction domain in M18BP1 to a central region containing a conserved SANT domain and in CENP-C to the C-terminus. Knock-down of CENP-C leads to reduced M18BP1 association and lower CENP-A levels at centromeres, suggesting that CENP-C works as an important factor for centromeric M18BP1 recruitment and thus for maintaining centromeric CENP-A.