-
Mitotic checkpoint defects: en route to cancer and drug resistance Chromosome Res. (IF 3.413) Pub Date : 2021-01-06 Sinjini Sarkar, Pranab Kumar Sahoo, Sutapa Mahata, Ranita Pal, Dipanwita Ghosh, Tanuma Mistry, Sushmita Ghosh, Tanmoy Bera, Vilas D. Nasare
Loss of mitosis regulation is a common feature of malignant cells that leads to aberrant cell division with inaccurate chromosome segregation. The mitotic checkpoint is responsible for faithful transmission of genetic material to the progeny. Defects in this checkpoint, such as mutations and changes in gene expression, lead to abnormal chromosome content or aneuploidy that may facilitate cancer development
-
Cyclic DNA remethylation following active demethylation at euchromatic regions in mouse embryonic stem cells Chromosome Res. (IF 3.413) Pub Date : 2020-11-17 Musashi Kubiura-Ichimaru, Takamasa Ito, Louis Lefebvre, Masako Tada
DNA methylation is an essential epigenetic mark that regulates normal mammalian embryonic development. DNA methylation profiles are not always static, especially during germline development. In zygotes, DNA is typically highly methylated but, during preimplantation, DNA methylation is erased globally. Then, at the start of post-implantation development in mouse embryos, DNA again becomes dramatically
-
Multiple and independent rearrangements revealed by comparative cytogenetic mapping in the dysploid Leptostachyus group ( Phaseolus L., Leguminosae) Chromosome Res. (IF 3.413) Pub Date : 2020-11-16 Maria Eduarda Ferraz, Artur Fonsêca, Andrea Pedrosa-Harand
Polyploidy and dysploidy have been reported as the main events in karyotype evolution of plants. In the genus Phaseolus L. (2n = 22), a small monophyletic group of three species, the Leptostachyus group, presents a dysploid karyotype with 2n = 20. It was shown in Phaseolus leptostachyus that the dysploidy was caused by a nested chromosome fusion (NCF) accompanied by several translocations, suggesting
-
CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites Chromosome Res. (IF 3.413) Pub Date : 2020-10-18 Michi Miura, Honglin Chen
CUT&RUN is a powerful tool to study protein-DNA interactions in vivo. DNA fragments cleaved by the targeted micrococcal nuclease identify the footprints of DNA-binding proteins on the chromatin. We performed CUT&RUN on human lung carcinoma cell line A549 maintained in a multi-well cell culture plate to profile RNA polymerase II. Long (> 270 bp) DNA fragments released by CUT&RUN corresponded to the
-
Analysis of Holhymenia histrio genome provides insight into the satDNA evolution in an insect with holocentric chromosomes. Chromosome Res. (IF 3.413) Pub Date : 2020-09-19 Vanessa Bellini Bardella,Diogo Milani,Diogo Cavalcanti Cabral-de-Mello
Satellite DNAs (satDNA) are fast-evolving repetitive sequences organized in large tandem arrays, with characteristic enrichment in heterochromatin. Knowledge about evolutionary dynamics of this genome fraction is mostly restricted to its characterization in species with monocentric chromosomes, i.e., localized centromeres. In holocentric species, with non-localized centromeres, satDNAs have been largely
-
Using telomeric chromosomal aberrations to evaluate clastogen-induced genomic instability in mammalian cells. Chromosome Res. (IF 3.413) Pub Date : 2020-09-17 Alejandro D Bolzán
Telomeres, the specialized nucleoproteic complexes localized at the physical ends of linear eukaryotic chromosomes, play a fundamental role in maintaining chromosomal stability and integrity, being one of the leading guardians of genome stability. In recent years, the identification and analysis of chromosomal aberrations involving telomeres has proven to be a unique tool to evaluate misrepaired and
-
Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res. (IF 3.413) Pub Date : 2020-09-17 Ivona Kubalová,Markéta Schmidt Černohorská,Martina Huranová,Klaus Weisshart,Andreas Houben,Veit Schubert
Expansion microscopy (ExM) is a method to magnify physically a specimen with preserved ultrastructure. It has the potential to explore structural features beyond the diffraction limit of light. The procedure has been successfully used for different animal species, from isolated macromolecular complexes through cells to tissue slices. Expansion of plant-derived samples is still at the beginning, and
-
Impacts of genomic networks governed by human-specific regulatory sequences and genetic loci harboring fixed human-specific neuro-regulatory single nucleotide mutations on phenotypic traits of modern humans. Chromosome Res. (IF 3.413) Pub Date : 2020-09-09 Gennadi V Glinsky
Recent advances in identification and characterization of human-specific regulatory DNA sequences set the stage for the assessment of their global impact on physiology and pathology of modern humans. Gene set enrichment analyses (GSEA) of 8405 genes linked with 35,074 human-specific neuro-regulatory single-nucleotide changes (hsSNCs) revealed numerous significant associations with morphological structures
-
The Bre1/Rad6 machinery: writing the central histone ubiquitin mark on H2B and beyond. Chromosome Res. (IF 3.413) Pub Date : 2020-09-07 Zhi-Heng Deng,Hua-Song Ai,Cheng-Piao Lu,Jia-Bin Li
Mono-ubiquitination on H2B (H2Bub1) is an evolutionarily conserved histone post-translational modification implicated in various important physiological processes including DNA replication, transcription activation, and DNA damage repair. The Bre1/Rad6 ubiquitination machinery is currently considered to be the sole writer of H2Bub1, but the mechanistic basis by which it operates is unclear. Recently
-
Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignancies. Chromosome Res. (IF 3.413) Pub Date : 2020-08-20 Ali Naderi
Deletions of chromosome 1p36 are common in malignancies; however, there is limited information regarding the biological and prognostic implications of 1p36 in cancer. Steroid Receptor–Associated and Regulated Protein (SRARP) is a tumor suppressor on chromosome 1p36.13 that its inactivation predicts poor cancer outcome, indicating that the 1p36.13 segment requires further studies. Therefore, a comprehensive
-
Mechanisms driving acentric chromosome transmission. Chromosome Res. (IF 3.413) Pub Date : 2020-07-25 Brandt Warecki,William Sullivan
The kinetochore-microtubule association is a core, conserved event that drives chromosome transmission during mitosis. Failure to establish this association on even a single chromosome results in aneuploidy leading to cell death or the development of cancer. However, although many chromosomes lacking centromeres, termed acentrics, fail to segregate, studies in a number of systems reveal robust alternative
-
Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). Chromosome Res. (IF 3.413) Pub Date : 2020-07-11 Ana Rafaela da S Oliveira,Lívia do Vale Martins,Fernanda de O Bustamante,María Muñoz-Amatriaín,Timothy Close,Antônio F da Costa,Ana Maria Benko-Iseppon,Andrea Pedrosa-Harand,Ana Christina Brasileiro-Vidal
Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced
-
A novel method of male sex identification of human ancient skeletal remains. Chromosome Res. (IF 3.413) Pub Date : 2020-07-03 María Teresa Navarro-Romero,María de Lourdes Muñoz,Enrique Alcala-Castañeda,Eladio Terreros-Espinosa,Eduardo Domínguez-de-la-Cruz,Normand García-Hernández,Miguel Ángel Moreno-Galeana
Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in
-
Correction to: Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. Chromosome Res. (IF 3.413) Pub Date : 2020-05-19 M A Sader,Y Dias,Z P Costa,C Munhoz,H Penha,H Bergès,M L C Vieira,A Pedrosa-Harand
The article "Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH," written by Mariela A. Sader, Yhanndra Dias, Zirlane P. da Costa, Carla Munhoz, Helen Penha, Hélène Bergès, Maria Lucia C. Vieira, and Andrea Pedrosa-Harand, was originally published with incorrect values in Figure 4.
-
Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an "ancestral amniote super-sex chromosome"? Chromosome Res. (IF 3.413) Pub Date : 2020-05-01 Worapong Singchat,Siwapech Sillapaprayoon,Narongrit Muangmai,Sudarath Baicharoen,Chantra Indananda,Prateep Duengkae,Surin Peyachoknagul,Rebecca E O'Connor,Darren K Griffin,Kornsorn Srikulnath
Sex chromosomes in some amniotes share linkage homologies with distantly related taxa in regions orthologous to squamate reptile chromosome 2 (SR2) and the snake W sex chromosome. Thus, the SR2 and W chromosomes may formerly have been part of a larger ancestral amniote super-sex chromosome. Comparison of various sex chromosomal linkage homologies in Toxicofera with those in other amniotes offers an
-
Intragenic meiotic recombination in Schizosaccharomyces pombe is sensitive to environmental temperature changes. Chromosome Res. (IF 3.413) Pub Date : 2020-04-17 Simon D Brown,Charlotte Audoynaud,Alexander Lorenz
Changes in environmental temperature influence cellular processes and their dynamics, and thus affect the life cycle of organisms that are unable to control their cell/body temperature. Meiotic recombination is the cellular process essential for producing healthy haploid gametes by providing physical links (chiasmata) between homologous chromosomes to guide their accurate segregation. Additionally
-
A universal chromosome identification system for maize and wild Zea species. Chromosome Res. (IF 3.413) Pub Date : 2020-03-26 Guilherme T Braz,Lívia do Vale Martins,Tao Zhang,Patrice S Albert,James A Birchler,Jiming Jiang
Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification
-
Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Res. (IF 3.413) Pub Date : 2020-01-13 Qing Hu,Elizabeth G Maurais,Peter Ly
Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began
-
Structural variant identification and characterization. Chromosome Res. (IF 3.413) Pub Date : 2020-01-06 Parithi Balachandran,Christine R Beck
Abstract Structural variant (SV) differences between human genomes can cause germline and mosaic disease as well as inter-individual variation. De-regulation of accurate DNA repair and genomic surveillance mechanisms results in a large number of SVs in cancer. Analysis of the DNA sequences at SV breakpoints can help identify pathways of mutagenesis and regions of the genome that are more susceptible
-
Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res. (IF 3.413) Pub Date : 2019-11-27 David C Klein,Sarah J Hainer
Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly
-
Genomic methods for measuring DNA replication dynamics. Chromosome Res. (IF 3.413) Pub Date : 2019-12-17 Michelle L Hulke,Dashiell J Massey,Amnon Koren
Abstract Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding
-
Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells. Chromosome Res. (IF 3.413) Pub Date : 2019-12-03 Solmaz Khosravi,Takayoshi Ishii,Steven Dreissig,Andreas Houben
The 3D organization of chromatin plays an important role in genome stability and many other pivotal biological programs. Therefore, the establishment of imaging methods, which enable us to study the dynamics of chromatin in living cells, is necessary. Although primary live cell imaging methods were a breakthrough, there is a need to develop more specific labeling techniques. With the discovery of programmable
-
Probing the function of long noncoding RNAs in the nucleus. Chromosome Res. (IF 3.413) Pub Date : 2020-02-06 Sajal Medha K Akkipeddi,Anthony J Velleca,Dawn M Carone
The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds
-
Seq'ing identity and function in a repeat-derived noncoding RNA world. Chromosome Res. (IF 3.413) Pub Date : 2020-03-07 Rachel J O'Neill
Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts
-
Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosome Res. (IF 3.413) Pub Date : 2020-01-30 Xinying Song,Rongrong Song,Jiawen Zhou,Wenkai Yan,Tao Zhang,Haojie Sun,Jin Xiao,Yufeng Wu,Mengli Xi,Qunfeng Lou,Haiyan Wang,Xiue Wang
Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes
-
Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. Chromosome Res. (IF 3.413) Pub Date : 2019-07-18 M A Sader,Y Dias,Z P Costa,C Munhoz,H Penha,H Bergès,M L C Vieira,Andrea Pedrosa-Harand
Passiflora edulis, the yellow passion fruit, is the main crop from the Passiflora genus, which comprises 525 species with its diversity center in South America. Genetic maps and a BAC (bacterial artificial chromosome) genomic library are available, but the nine chromosome pairs of similar size and morphology (2n = 18) hamper chromosome identification, leading to different proposed karyotypes. Thus
-
DNA double-strand breaks: a potential therapeutic target for neurodegenerative diseases. Chromosome Res. (IF 3.413) Pub Date : 2019-11-09 Nidheesh Thadathil,Roderick Hori,Jianfeng Xiao,Mohammad Moshahid Khan
The complexity of neurodegeneration restricts the ability to understand and treat the neurological disorders affecting millions of people worldwide. Therefore, there is an unmet need to develop new and more effective therapeutic strategies to combat these devastating conditions and that will only be achieved with a better understanding of the biological mechanism associated with disease conditions
-
Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini. Chromosome Res. (IF 3.413) Pub Date : 2019-08-15 Hirohisa Hirai,Yuriko Hirai,Toshifumi Udono,Kiyoaki Matsubayashi,Anthony J Tosi,Akihiko Koga
African great apes have large constitutive heterochromatin (C-band) blocks in subtelomeric regions of the majority of their chromosomes, but humans lack these. Additionally, the chimpanzee meiotic cell division process demonstrates unique partial terminal associations in the first meiotic prophase (pachytene). These are likely formed as a result of interaction among subtelomeric C-band blocks. We thus
-
A database of amphibian karyotypes. Chromosome Res. (IF 3.413) Pub Date : 2019-07-23 Riddhi D Perkins,Julio Rincones Gamboa,Michelle M Jonika,Johnathan Lo,Amy Shum,Richard H Adams,Heath Blackmon
One of the first characteristics that we learn about the genome of many species is the number of chromosomes it is divided among. Despite this, many questions regarding the evolution of chromosome number remain unanswered. Testing hypotheses of chromosome number evolution using comparative approaches requires trait data to be readily accessible and associated with currently accepted taxonomy. The lack
-
Global epigenetic changes of histone modification under environmental stresses in rice root. Chromosome Res. (IF 3.413) Pub Date : 2019-07-06 Aqwin Polosoro,Wening Enggarini,Nobuko Ohmido
Abiotic stresses are non-living factors with negative morphological and physiological effects on living organisms. Substantial evidence exists that gene expression changes during plant cell growth are regulated by chromatin reconfiguration and histone modification. Several types of histone modifications are dramatically transformed in stress-responsive gene regions under drought stress conditions.
-
Comparative meiosis and cytogenomic analysis in euploid and aneuploid hybrids of Urochloa P. Beauv. Chromosome Res. (IF 3.413) Pub Date : 2019-09-04 Mara Jane da Rocha,Raquel Bezerra Chiavegatto,Ana Gabriela Damasceno,Laiane Corsini Rocha,Fausto Souza Sobrinho,Vânia Helena Techio
The genus Urochloa includes most of the important grasses and hybrids currently used as pastures in the tropical regions. Cytogenetic analyzes have identified some aneuploid hybrids that provide new perspectives for genetic breeding. The objective was to analyze the meiotic behavior in euploid (2n = 4x = 36) and aneuploid (2n = 4x = 36 + 2) hybrids of U. ruziziensis x U. decumbens and U. ruziziensis
-
Characterization of chromatin at structurally abnormal inactive X chromosomes reveals potential evidence of a rare hybrid active and inactive isodicentric X chromosome. Chromosome Res. (IF 3.413) Pub Date : 2019-11-27 Brian P Chadwick
X chromosome structural abnormalities are relatively common in Turner syndrome patients, in particular X isochromosomes. Reports over the last five decades examining asynchronous DNA replication between the normal X and isochromosome have clearly established that the structurally abnormal chromosome is the inactive X chromosome (Xi). Here the organization of chromatin at a deleted X chromosome, an
-
Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Chromosome Res. (IF 3.413) Pub Date : 2019-11-16 Tiago Ribeiro,Emanuelle Vasconcelos,Karla G B Dos Santos,Magdalena Vaio,Ana Christina Brasileiro-Vidal,Andrea Pedrosa-Harand
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach to study the organization and diversification of repetitive
-
The maize B chromosome is capable of expressing microRNAs and altering the expression of microRNAs derived from A chromosomes. Chromosome Res. (IF 3.413) Pub Date : 2019-11-11 Yen-Hua Huang,Shu-Fen Peng,Yao-Pin Lin,Ya-Ming Cheng
Supernumerary B chromosomes (Bs) are nonessential chromosomes that are considered genetically inert. However, the maize B carries control elements that direct its behavior, such as that of nondisjunction, during the second pollen mitosis, and affects normal A chromosomes during cell division. Recently, the maize B has been found to contain transcriptionally active sequences and to affect the transcription
-
Correction to: Implications of sequence variation on the evolution of rRNA. Chromosome Res. (IF 3.413) Pub Date : 2019-06-28 Matthew M Parks,Chad M Kurylo,Jake E Batchelder,C Theresa Vincent,Scott C Blanchard
The article Implications of sequence variation on the evolution of rRNA, written by Matthew M. Parks, Chad M. Kurylo, Jake E. Batchelder, C. Theresa Vincent and Scott C. Blanchard, was originally published electronically on the publisher's internet portal (currently SpringerLink).
-
Hybrids between Brassica napus and B. nigra show frequent pairing between the B and A/C genomes and resistance to blackleg. Chromosome Res. (IF 3.413) Pub Date : 2019-07-08 Roman Gaebelein,Dima Alnajar,Birger Koopmann,Annaliese S Mason
High frequencies of homoeologous and even non-homologous chromosome recombination in Brassica hybrids can transfer useful traits between genomes, but also destabilise synthetic allopolyploids. We produced triploid hybrids (2n = 3x = ABC) from the cross B. napus (rapeseed, 2n = 4x = AACC) × B. nigra (black mustard, 2n = 2x = BB) by embryo rescue and allohexaploid hybrids (2n = 6x = AABBCC = 54) by chromosome
-
The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies. Chromosome Res. (IF 3.413) Pub Date : 2019-05-24 Pedro M Fonseca,Rafael D Moura,Gabriel L Wallau,Elgion L S Loreto
The Drosophila genus is one of the main model organisms in evolutionary studies, including those investigating the role of transposable elements (TE) in genomic evolution both at the nucleotide and chromosome levels. D. incompta is a species with restricted ecology, using Cestrum (Solanaceae) flowers as unique sources for oviposition, feeding and development. In the present study, we deeply characterise
-
MiR-153 regulates cardiomyocyte apoptosis by targeting Nrf2/HO-1 signaling. Chromosome Res. (IF 3.413) Pub Date : 2019-05-01 Xianting Zhu,Yuling Zhao,Wei Hou,Ling Guo
MicroRNAs (miRNAs) play various roles in the regulation of human disease, including cardiovascular diseases. MiR-153 has been previously shown to be involved in regulating neuron survival during cerebral ischemia/reperfusion (I/R) injury. However, whether miR-153 is involved in I/R-induced cardiomyocyte apoptosis remains to be elucidated. In this study, we aimed to explore the role of miR-153 in the
-
Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex. Chromosome Res. (IF 3.413) Pub Date : 2019-04-24 Katherine Kennedy,Rachael Thomas,Jessica Durrant,Tao Jiang,Alison Motsinger-Reif,Matthew Breen
Canine histiocytic malignancies (HM) are rare across the general dog population, but overrepresented in certain breeds, such as Bernese mountain dog and flat-coated retriever. Accurate diagnosis relies on immunohistochemical staining to rule out histologically similar cancers with different prognoses and treatment strategies (e.g., lymphoma and hemangiosarcoma). HM are generally treatment refractory
-
Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res. (IF 3.413) Pub Date : 2019-03-11 Jiming Jiang
Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. This review
-
A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Res. (IF 3.413) Pub Date : 2019-02-17 Brendan M Smalec,Thomas N Heider,Brianna L Flynn,Rachel J O'Neill
A common feature of eukaryotic centromeres is the presence of large tracts of tandemly arranged repeats, known as satellite DNA. However, these centromeric repeats appear to experience rapid evolution under forces such as molecular drive and centromere drive, seemingly without consequence to the integrity of the centromere. Moreover, blocks of heterochromatin within the karyotype, including the centromere
-
Implications of sequence variation on the evolution of rRNA. Chromosome Res. (IF 3.413) Pub Date : 2019-02-06 Matthew M Parks,Chad M Kurylo,Jake E Batchelder,C Theresa Vincent,Scott C Blanchard
The evolution of the multi-copy family of ribosomal RNA (rRNA) genes is unique in regard to its genetics and genome evolution. Paradoxically, rRNA genes are highly homogenized within and between individuals, yet they are globally distinct between species. Here, we discuss the implications for models of rRNA gene evolution in light of our recent discoveries that ribosomes bearing rRNA sequence variants
-
Ribosomal DNA-connecting ribosome biogenesis and chromosome biology. Chromosome Res. (IF 3.413) Pub Date : 2019-01-22 Lev Porokhovnik,Jennifer L Gerton
Ribosomal DNA, the topic of this special issue, has long fascinated biologists. The RNA products of the ribosomal DNA are the ribosomal RNAs that are part of the ribosome. In this special issue, we focus on the sequence, molecular organization, repair, stability, copy number, and peculiar genetics of this region of the genome. The locus can impact not only the translational capability of cells, but
-
The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis. Chromosome Res. (IF 3.413) Pub Date : 2019-01-19 Joanna Stachecka,Joanna Nowacka-Woszuk,Pawel A Kolodziejski,Izabela Szczerbal
Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene's nuclear positioning for its activity during in vitro adipogenesis in the pig. We used an established system
-
Ribosomal DNA and the nucleolus in the context of genome organization. Chromosome Res. (IF 3.413) Pub Date : 2019-01-19 Tamara A Potapova,Jennifer L Gerton
The nucleolus constitutes a prominent nuclear compartment, a membraneless organelle that was first documented in the 1830s. The fact that specific chromosomal regions were present in the nucleolus was recognized by Barbara McClintock in the 1930s, and these regions were termed nucleolar organizing regions, or NORs. The primary function of ribosomal DNA (rDNA) is to produce RNA components of ribosomes
-
The chromatin landscape of the ribosomal RNA genes in mouse and human. Chromosome Res. (IF 3.413) Pub Date : 2019-01-09 Tom Moss,Jean-Clement Mars,Michel G Tremblay,Marianne Sabourin-Felix
The rRNA genes of mouse and human encode the three major RNAs of the ribosome and as such are essential for growth and development. These genes are present in high copy numbers and arranged as direct repeats at the Nucleolar Organizer Regions on multiple chromosomes. Not all the rRNA genes are transcriptionally active, but the molecular mechanisms that determine activity are complex and still poorly
-
UVA irradiation strengthened an interaction between UBF1/2 proteins and H4K20 di-/tri-methylation. Chromosome Res. (IF 3.413) Pub Date : 2019-01-06 Lenka Stixová,Denisa Komůrková,Alena Svobodová Kovaříková,Eva Bártová
Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). We
-
Cytogenetic instability of chromosomal nucleolar organizer regions (NORs) in cloned mouse L929 fibroblasts. Chromosome Res. (IF 3.413) Pub Date : 2019-01-04 Olga V Zatsepina
Ribosomal DNA (rDNA) gene codes for 18S, 5.8S, and 28S rRNA form tandem repetitive clusters, which occupy distinct chromosomal loci called nucleolar organizer regions (NORs). The number and position of NORs on chromosomes are genetic characteristics of the species although within a cell, the NOR sizes can significantly vary due to loss or multiplication of rDNA copies. In the current study, we used
-
Ribosomal DNA instability and genome adaptability. Chromosome Res. (IF 3.413) Pub Date : 2019-01-04 Devika Salim,Jennifer L Gerton
Ribosomes are large, multi-subunit ribonucleoprotein complexes, essential for protein synthesis. To meet the high cellular demand for ribosomes, all eukaryotes have numerous copies of ribosomal DNA (rDNA) genes that encode ribosomal RNA (rRNA), usually far in excess of the requirement for ribosome biogenesis. In all eukaryotes studied, rDNA genes are arranged in one or more clusters of tandem repeats
-
Heterochromatic regions in Japanese quail chromosomes: comprehensive molecular-cytogenetic characterization and 3D mapping in interphase nucleus. Chromosome Res. (IF 3.413) Pub Date : 2018-12-20 Anna Zlotina,Antonina Maslova,Nadezda Kosyakova,Ahmed B Hamid Al-Rikabi,Thomas Liehr,Alla Krasikova
Chromosomes of Japanese quail (Coturnix coturnix japonica, 2n=78), a galliform domestic species closely related to chicken, possess multiple heterochromatic segments. Due to the difficulties in careful analysis of such heterochromatic regions, there is a lack of data on their DNA composition, epigenetic status, as well as spatial distribution in interphase nucleus. In the present study, we applied
-
Keeping ribosomal DNA intact: a repeating challenge. Chromosome Res. (IF 3.413) Pub Date : 2018-12-18 Daniël O Warmerdam,Rob M F Wolthuis
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia
-
The nucleolar transcriptome regulates Piwi shuttling between the nucleolus and the nucleoplasm. Chromosome Res. (IF 3.413) Pub Date : 2018-12-13 Elena A Mikhaleva,Toomas A Leinsoo,Hirotsugu Ishizu,Vladimir A Gvozdev,Mikhail S Klenov
The nucleolus contains a lot of proteins unrelated to ribosome biogenesis. Some of these proteins shuttle between the nucleolus and the nucleoplasm regulating the cell cycle and stress response. The piRNA binding protein Piwi is involved in silencing of transposable elements (TEs) in the Drosophila gonads. Here we used cultured ovarian somatic cells (OSC) to characterize Piwi as a visitor to the nucleolus
-
The methylation and telomere landscape in two families of marsupials with different rates of chromosome evolution. Chromosome Res. (IF 3.413) Pub Date : 2018-12-13 Emory D Ingles,Janine E Deakin
Two marsupial families exemplify divergent rates of karyotypic change. The Dasyurid family has an extremely conserved karyotype. In contrast, there is significant chromosomal variation within the Macropodidae family, best exemplified by members of the genus Petrogale (rock-wallabies). Both families are also distinguished by their telomere landscape (length and epigenetics), with the dasyurids having
-
The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. Chromosome Res. (IF 3.413) Pub Date : 2018-12-04 Farah Bughio,Keith A Maggert
Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations
-
Distribution of CR1-like transposable element in woodpeckers (Aves Piciformes): Z sex chromosomes can act as a refuge for transposable elements. Chromosome Res. (IF 3.413) Pub Date : 2018-12-01 Natasha Avila Bertocchi,Thays Duarte de Oliveira,Analía Del Valle Garnero,Rafael Luiz Buogo Coan,Ricardo José Gunski,Cesar Martins,Fabiano Pimentel Torres
Birds have relatively few repetitive sequences compared to other groups of vertebrates; however, the members of order Piciformes (woodpeckers) have more of these sequences, composed mainly of transposable elements (TE). The TE most often found in birds is a retrotransposon chicken repeat 1 (CR1). Piciformes lineages were subjected to an expansion of the CR1 elements, carrying a larger fraction of transposable
-
A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin. Chromosome Res. (IF 3.413) Pub Date : 2018-11-18 Natalya A Lemskaya,Anastasia I Kulemzina,Violetta R Beklemisheva,Larisa S Biltueva,Anastasia A Proskuryakova,John M Hallenbeck,Polina L Perelman,Alexander S Graphodatsky
Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals. The difficulty in identification of individual chromosomes represents an unresolved problem of this method as the
-
Nucleoli in embryos: a central structural platform for embryonic chromatin remodeling? Chromosome Res. (IF 3.413) Pub Date : 2018-11-09 Helena Fulka,Alena Langerova
Nucleoli are the site of ribosomal RNA production and subunit assembly. In contrast to active nucleoli in somatic cells, where three basic sub-compartments can be observed, mammalian oocytes and early embryos contain atypical nucleoli termed "nucleolus-like bodies" or "nucleolus precursor bodies", respectively. Unlike their somatic counterparts, these structures are composed of dense homogenous fibrillar
-
Genes involved in miRNA biogenesis affect meiosis and fertility. Chromosome Res. (IF 3.413) Pub Date : 2018-10-22 Mónica Pradillo,Juan L Santos
MicroRNAs (miRNAs) are a class of small (containing about 22 nucleotides) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level in plants and animals, being absent from unicellular organisms. They act on diverse key physiological and cellular processes, such as development and tissue differentiation, cell identity, cell cycle progression, and programmed cell
-
Dosage effects of human ribosomal genes (rDNA) in health and disease. Chromosome Res. (IF 3.413) Pub Date : 2018-10-22 L N Porokhovnik,N A Lyapunova
Human ribosomal RNA genes encoding a pre-transcript of the three major ribosomal RNA (18S, 5.8S, and 28S rRNA) are tandemly repeated in human genome. Their total copy number varies from 250 to 670 per diploid genome with a mean of approximately 420 copies, but only a fraction of them is transcriptionally active. The functional consequences of human ribosomal RNA gene dosage are not widely known and
-
Contents have been reproduced by permission of the publishers.