Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells.
Abstract 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 DNA binding proteins, such zinc finger proteins (ZFP), transcription activator-like effectors (TALE), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein ...
Source: Chromosome Research - December 3, 2019 Category: Genetics & Stem Cells Authors: Khosravi S, Ishii T, Dreissig S, Houben A Tags: Chromosome Res Source Type: research

Genomic methods in profiling DNA accessibility and factor localization.
Abstract 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 occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene re...
Source: Chromosome Research - November 27, 2019 Category: Genetics & Stem Cells Authors: Klein DC, Hainer SJ Tags: Chromosome Res Source Type: research

Characterization of chromatin at structurally abnormal inactive X chromosomes reveals potential evidence of a rare hybrid active and inactive isodicentric X chromosome.
Abstract 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 Xq isochromosome, and two isodicentric chromosomes were examined. Consistent with previous differential staining methods, at interphase, the X isochromosome and isodicentric X chromosomes frequently formed bipar...
Source: Chromosome Research - November 27, 2019 Category: Genetics & Stem Cells Authors: Chadwick BP Tags: Chromosome Res Source Type: research

Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi.
Abstract 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 elements in some species of these genera. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrot...
Source: Chromosome Research - November 16, 2019 Category: Genetics & Stem Cells Authors: Ribeiro T, Vasconcelos E, Dos Santos KGB, Vaio M, Brasileiro-Vidal AC, Pedrosa-Harand A Tags: Chromosome Res Source Type: research

The maize B chromosome is capable of expressing microRNAs and altering the expression of microRNAs derived from A chromosomes.
Abstract 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 of genes on A chromosomes. To better understand the regulatory mechanisms underlying the maize B, we constructed two small RNA libraries from maize B73 inbred lines with and without Bs. The sequencing re...
Source: Chromosome Research - November 11, 2019 Category: Genetics & Stem Cells Authors: Huang YH, Peng SF, Lin YP, Cheng YM Tags: Chromosome Res Source Type: research

DNA double-strand breaks: a potential therapeutic target for neurodegenerative diseases.
Abstract 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. Recent studies highlight the role of DNA damage, particularly, DNA double-strand breaks (DSBs), in the progression of neuronal loss in a broad spectrum of human neurodegenerative diseases. This is not unexpecte...
Source: Chromosome Research - November 9, 2019 Category: Genetics & Stem Cells Authors: Thadathil N, Hori R, Xiao J, Khan MM Tags: Chromosome Res Source Type: research

Comparative meiosis and cytogenomic analysis in euploid and aneuploid hybrids of Urochloa P. Beauv.
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 x U. brizantha. Later, the chromosomes and respective genomes involved in pairing configurations and abnormalities were identified through GISH, with an emphasis on tracking the behavior of the additional chromosomes in the aneuploid hybrid U. ruziziensis x U. decumbens (B1B2B2B2 genomes). The aneuploid U. ruziziensis x U. decumbens shows a higher frequency of univalents, reduction of biv...
Source: Chromosome Research - September 4, 2019 Category: Genetics & Stem Cells Authors: da Rocha MJ, Chiavegatto RB, Damasceno AG, Rocha LC, Souza Sobrinho F, Techio VH Tags: Chromosome Res Source Type: research

Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini.
Abstract 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 conducted an extensive study to define the features in the subtelomeric heterochromatic regions of chimpanzee chromosomes undergoing mitotic metaphase and meiotic cell division. Molecular cytogenetic analyse...
Source: Chromosome Research - August 15, 2019 Category: Genetics & Stem Cells Authors: Hirai H, Hirai Y, Udono T, Matsubayashi K, Tosi AJ, Koga A Tags: Chromosome Res Source Type: research

A database of amphibian karyotypes.
Abstract 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 of accessible karyotype data that can be linked to phylogenies has limited the application of comparative approaches that could help us understand the evolution of genome structure. Furthermore, for taxonomi...
Source: Chromosome Research - July 23, 2019 Category: Genetics & Stem Cells Authors: Perkins RD, Gamboa JR, Jonika MM, Lo J, Shum A, Adams RH, Blackmon H Tags: Chromosome Res Source Type: research

Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH.
and A Abstract 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, the aim of this study was to establish chromosome-specific markers for the yellow passion fruit using single-copy and repetitive sequences as probes in fluorescent in situ hybridizations (FI...
Source: Chromosome Research - July 18, 2019 Category: Genetics & Stem Cells Authors: Sader MA, Dias Y, Costa ZP, Munhoz C, Penha H, Bergès H, Vieira MLC, Pedrosa-Harand A Tags: Chromosome Res Source Type: research

Global epigenetic changes of histone modification under environmental stresses in rice root.
In this study, we investigated how quantitative changes in epigenetic markers in this region influence rice morphology and physiology. Both iron and salinity treatments changed the epigenetic landscape from euchromatic to heterochromatic according to heterochromatin (H3K9me2) and euchromatin (H3K4me) markers, especially in the proximal meristem region. Moreover, supplementation with external abscisic acid (ABA) was able to mimic the effect of environmental stresses on global epigenetic changes. In contrast, the addition of external auxin (IAA) to rice under saline conditions affected heterochromatin formation without influ...
Source: Chromosome Research - July 6, 2019 Category: Genetics & Stem Cells Authors: Polosoro A, Enggarini W, Ohmido N Tags: Chromosome Res Source Type: research

Hybrids between Brassica napus and B. nigra show frequent pairing between the B and A/C genomes and resistance to blackleg.
Abstract 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 doubling of the triploids. These hybrids demonstrated r...
Source: Chromosome Research - July 6, 2019 Category: Genetics & Stem Cells Authors: Gaebelein R, Alnajar D, Koopmann B, Mason AS Tags: Chromosome Res Source Type: research

Correction to: Implications of sequence variation on the evolution of rRNA.
Abstract 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). PMID: 31254145 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - June 28, 2019 Category: Genetics & Stem Cells Authors: Parks MM, Kurylo CM, Batchelder JE, Theresa Vincent C, Blanchard SC Tags: Chromosome Res Source Type: research

The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies.
Abstract 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 the D. incompta mobilome and generate a curated dataset. A total of 277 elements were identified, corresponding to approximately 14% of the genome, and 164 of these elements are new, of which 32.62% are pu...
Source: Chromosome Research - May 22, 2019 Category: Genetics & Stem Cells Authors: Fonseca PM, Moura RD, Wallau GL, Loreto ELS Tags: Chromosome Res Source Type: research

MiR-153 regulates cardiomyocyte apoptosis by targeting Nrf2/HO-1 signaling.
In this study, we aimed to explore the role of miR-153 in the regulation of I/R-induced cardiomyocyte apoptosis and to investigate the miR-153-mediated molecular signaling pathway responsible for its effect on cardiomyocytes using an oxygen-glucose deprivation and reoxygenation (OGD/R) cellular model. We found that OGD/R treatment induced significant upregulation of miR-153 in cardiomyocytes causing reactive oxygen species (ROS) production and cell apoptosis signaling activation and subsequently leading to cardiomyocyte apoptosis. Suppression of miR-153 protected cardiomyocytes against OGD/R treatment. We further identifie...
Source: Chromosome Research - April 29, 2019 Category: Genetics & Stem Cells Authors: Zhu X, Zhao Y, Hou W, Guo L Tags: Chromosome Res Source Type: research

Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex.
This study aims to improve the understanding of underlying disease mechanisms using genome-wide DNA copy number and gene expression analysis of spontaneous HM across several dog breeds. Extensive DNA copy number disruption was evident, with losses of segments of chromosomes 16 and 31 detected in 93% and 72% of tumors, respectively. Droplet digital PCR (ddPCR) evaluation of these regions in numerous cancer specimens effectively discriminated HM from other common round cell tumors, including lymphoma and hemangiosarcoma, resulting in a novel, rapid diagnostic aid for veterinary medicine. Transcriptional analysis demonstrated...
Source: Chromosome Research - April 23, 2019 Category: Genetics & Stem Cells Authors: Kennedy K, Thomas R, Durrant J, Jiang T, Motsinger-Reif A, Breen M Tags: Chromosome Res Source Type: research

Fluorescence in situ hybridization in plants: recent developments and future applications.
Abstract 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 intends to summarize and discuss key technical development and applications of FISH in plants since 2006. The most significant recent advance of FISH is the development and application of probes based on sy...
Source: Chromosome Research - March 9, 2019 Category: Genetics & Stem Cells Authors: Jiang J Tags: Chromosome Res Source Type: research

A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive.
Abstract 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, are hotspots for chromosome rearrangements that may drive speciation events by contributing to reproductive isolation. However, the relationship between the evolution of heterochromatic sequences and th...
Source: Chromosome Research - February 15, 2019 Category: Genetics & Stem Cells Authors: Smalec BM, Heider TN, Flynn BL, O'Neill RJ Tags: Chromosome Res Source Type: research

Implications of sequence variation on the evolution of rRNA.
Abstract 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 can affect gene expression and physiology and that intra-individual rRNA alleles exhibit both context- and tissue-specific expression. PMID: 30719681 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - February 5, 2019 Category: Genetics & Stem Cells Authors: Parks MM, Kurylo CM, Batchelder JE, Theresa Vincent C, Blanchard SC Tags: Chromosome Res Source Type: research

Ribosomal DNA-connecting ribosome biogenesis and chromosome biology.
Abstract 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 also genome organization, stability and integrity, providing a link between translation and chromosome biology. PMID: 30663012 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - January 21, 2019 Category: Genetics & Stem Cells Authors: Porokhovnik L, Gerton JL Tags: Chromosome Res Source Type: research

The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis.
Abstract 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 of differentiation of mesenchymal stem cells derived from bone marrow and adipose tissue into adipocytes. The differentiation process was carried out for 7 days, and the cells were examined using the 3D...
Source: Chromosome Research - January 17, 2019 Category: Genetics & Stem Cells Authors: Stachecka J, Nowacka-Woszuk J, Kolodziejski PA, Szczerbal I Tags: Chromosome Res Source Type: research

Ribosomal DNA and the nucleolus in the context of genome organization.
Abstract 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. Yet, ribosomal DNA also plays a pivotal role in nuclear organization by assembling the nucleolus. This review is focused on the rDNA and associated proteins in the context of genome organization. Recent adva...
Source: Chromosome Research - January 17, 2019 Category: Genetics & Stem Cells Authors: Potapova TA, Gerton JL Tags: Chromosome Res Source Type: research

The chromatin landscape of the ribosomal RNA genes in mouse and human.
Abstract 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 understood. Recent studies applying a novel Deconvolution Chromatin Immunoprecipitation (DChIP-Seq) technique in conjunction with conditional gene inactivation provide new insights into the structure of the ac...
Source: Chromosome Research - January 8, 2019 Category: Genetics & Stem Cells Authors: Moss T, Mars JC, Tremblay MG, Sabourin-Felix M Tags: Chromosome Res Source Type: research

UVA irradiation strengthened an interaction between UBF1/2 proteins and H4K20 di-/tri-methylation.
te;ková A, Bártová E Abstract 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 found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3. Ribosomal genes, regulated via UBF1/2 proteins, were char...
Source: Chromosome Research - January 4, 2019 Category: Genetics & Stem Cells Authors: Stixová L, Komůrková D, Svobodová Kovaříková A, Bártová E Tags: Chromosome Res Source Type: research

Ribosomal DNA instability and genome adaptability.
Abstract 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 localized to nucleoli. The tandem arrangement of repeats, combined with the high rates of transcription at the rDNA loci, and the difficulty of replicating repetitive sequences make the rDNA inherently unstab...
Source: Chromosome Research - January 3, 2019 Category: Genetics & Stem Cells Authors: Salim D, Gerton JL Tags: Chromosome Res Source Type: research

Cytogenetic instability of chromosomal nucleolar organizer regions (NORs) in cloned mouse L929 fibroblasts.
Abstract 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 mouse L929 fibroblasts, the aneuploid cells which differ in the FISH- and Ag-NOR numbers, to examine whether the parental NOR variability is inherited in clones. By statistical analysis, we showed that the clon...
Source: Chromosome Research - January 3, 2019 Category: Genetics & Stem Cells Authors: Zatsepina OV Tags: Chromosome Res Source Type: research

Heterochromatic regions in Japanese quail chromosomes: comprehensive molecular-cytogenetic characterization and 3D mapping in interphase nucleus.
Abstract 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 giant lampbrush chromosome (LBC) microdissection for high-resolution analysis of quail centromeric regions of macrochromosomes and polymorphic short arms of submetacentric microchromosomes. FISH with the dissect...
Source: Chromosome Research - December 18, 2018 Category: Genetics & Stem Cells Authors: Zlotina A, Maslova A, Kosyakova N, Al-Rikabi ABH, Liehr T, Krasikova A Tags: Chromosome Res Source Type: research

Keeping ribosomal DNA intact: a repeating challenge.
Abstract 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 and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis rema...
Source: Chromosome Research - December 17, 2018 Category: Genetics & Stem Cells Authors: Warmerdam DO, Wolthuis RMF Tags: Chromosome Res Source Type: research

The methylation and telomere landscape in two families of marsupials with different rates of chromosome evolution.
Abstract 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 a unique telomere length dimorphism not observed in other marsupials and hypothesised to be regulated in a parent-of-origin fashion. Previous work has shown that proximal ends of chromosomes are enriched in cy...
Source: Chromosome Research - December 12, 2018 Category: Genetics & Stem Cells Authors: Ingles ED, Deakin JE Tags: Chromosome Res Source Type: research

The nucleolar transcriptome regulates Piwi shuttling between the nucleolus and the nucleoplasm.
Abstract 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. Dynamic Piwi localization was shown to vary from its uniform distribution between the nucleoplasm and the nucleolus to pronounced nucleolar immobilization. We were intrigued by this localization behavio...
Source: Chromosome Research - December 12, 2018 Category: Genetics & Stem Cells Authors: Mikhaleva EA, Leinsoo TA, Ishizu H, Gvozdev VA, Klenov MS Tags: Chromosome Res Source Type: research

The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance.
Abstract 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 are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that ...
Source: Chromosome Research - December 4, 2018 Category: Genetics & Stem Cells Authors: Bughio F, Maggert KA Tags: Chromosome Res Source Type: research

Distribution of CR1-like transposable element in woodpeckers (Aves Piciformes): Z sex chromosomes can act as a refuge for transposable elements.
This study compared patterns of chromosome distribution among five bird species, through chromosome mapping of the CR1 sequence and reconstructed their phylogenetic tree. We analyzed several members of Piciformes (Colaptes campestris, Colaptes melanochloros, Melanerpes candidus, and Veniliornis spilogaster), as well as Galliformes (Gallus gallus). Gallus gallus is the species with which most genomic and hence cytogenetic studies have been performed. The results showed that CR1 sequences are a monophyletic group and do not depend on their hosts. All species analyzed showed a hybridization signal by fluorescence in situ hybr...
Source: Chromosome Research - November 29, 2018 Category: Genetics & Stem Cells Authors: Bertocchi NA, de Oliveira TD, Del Valle Garnero A, Coan RLB, Gunski RJ, Martins C, Torres FP Tags: Chromosome Res Source Type: research

A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin.
Abstract 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 body of the chromosome is stained uniformly and does not have banding pattern beyond C-bands. Here, we present the method that we called CDAG for sequential heterochromatin staining after differential GTG-ban...
Source: Chromosome Research - November 15, 2018 Category: Genetics & Stem Cells Authors: Lemskaya NA, Kulemzina AI, Beklemisheva VR, Biltueva LS, Proskuryakova AA, Hallenbeck JM, Perelman PL, Graphodatsky AS Tags: Chromosome Res Source Type: research

Nucleoli in embryos: a central structural platform for embryonic chromatin remodeling?
Abstract 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 material and exhibit no polymerase activity. Irrespective of these unusual properties, they have been shown to be absolutely essential for embryonic development, as their microsurgical...
Source: Chromosome Research - November 8, 2018 Category: Genetics & Stem Cells Authors: Fulka H, Langerova A Tags: Chromosome Res Source Type: research

Genes involved in miRNA biogenesis affect meiosis and fertility.
Abstract 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 death. They are also likely to be involved in a broad spectrum of human diseases. Particularly, this review examines and summarizes work characterizing the function of miRNAs in gametogenesis and fertility. Al...
Source: Chromosome Research - October 20, 2018 Category: Genetics & Stem Cells Authors: Pradillo M, Santos JL Tags: Chromosome Res Source Type: research

Dosage effects of human ribosomal genes (rDNA) in health and disease.
Abstract 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 often assumed to be negligible. Here, we review the facts of rRNA gene dosage effects on normal growth and aging, stress resistance of healthy individuals, and survivability of patients with chromosomal abnorma...
Source: Chromosome Research - October 20, 2018 Category: Genetics & Stem Cells Authors: Porokhovnik LN, Lyapunova NA Tags: Chromosome Res Source Type: research

Herbert Macgregor (1933-2018).
PMID: 30276581 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - October 1, 2018 Category: Genetics & Stem Cells Authors: Gall JG Tags: Chromosome Res Source Type: research

But where did the centromeres go in the chicken genome models?
got Y Abstract The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide number of scientists. Here, we review the location and features of a very basic element, the centromeres of chromosomes in the galGal5 genome model. Centromeres are elements that are not determined by their...
Source: Chromosome Research - September 17, 2018 Category: Genetics & Stem Cells Authors: Piégu B, Arensburger P, Guillou F, Bigot Y Tags: Chromosome Res Source Type: research

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold.
Abstract During cell division, chromosomes must be folded into their compact mitotic form to ensure their segregation. This process is thought to be largely controlled by the action of condensin SMC protein complexes on chromatin fibers. However, how condensins organize metaphase chromosomes is not understood. We have combined micromanipulation of single human mitotic chromosomes, sub-nanonewton force measurement, siRNA interference of condensin subunit expression, and fluorescence microscopy, to analyze the role of condensin in large-scale chromosome organization. Condensin depletion leads to a dramatic (~&thinsp...
Source: Chromosome Research - August 24, 2018 Category: Genetics & Stem Cells Authors: Sun M, Biggs R, Hornick J, Marko JF Tags: Chromosome Res Source Type: research

Nuclear localization signal region in nuclear receptor PXR governs the receptor association with mitotic chromatin.
In this study, we have shown, for the first time, that mitotic chromatin association of this factor is mediated by the combined action of two zinc fingers present in the DNA-binding domain of PXR. Overall, the nuclear localization signal (NLS) region appears to play a major role in this interaction with mitotic chromatin. Also, we have identified a sub-region of 11 amino acid residues within NLS region of PXR (R66-76R) essential for receptor interaction with the mitotic chromatin. Interestingly, this minimal region is sequence-specific and independent of its basic charge. We have termed this minimal sub-region as 'mitotic ...
Source: Chromosome Research - July 15, 2018 Category: Genetics & Stem Cells Authors: Rana M, Dash AK, Ponnusamy K, Tyagi RK Tags: Chromosome Res Source Type: research

Alpha satellite DNA biology: finding function in the recesses of the genome.
Abstract Repetitive DNA, formerly referred to by the misnomer "junk DNA," comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assemblies at centromeres using traditional next-generation sequencing approaches, and thus, centromeres represent gaps in the current human genome assembly. Moreover, alpha satellite DNA is tran...
Source: Chromosome Research - July 5, 2018 Category: Genetics & Stem Cells Authors: McNulty SM, Sullivan BA Tags: Chromosome Res Source Type: research

Comparative chromosome painting in Columbidae (Columbiformes) reinforces divergence in Passerea and Columbea.
Abstract Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the karyotype evolution within Columbiformes remains unclear. To delineate the synteny-conserved segments and karyotypic differences among four Columbidae species, we used chromosome painting from Gallus gallus (GGA, 2n = 78) and Leucopternis albicollis (LAL, 2n = 68). Besides that, a set of painting probes for the eared dove, Zenaida auriculata (ZAU, 2n = 76), was generated from flow-sorted chromosomes. Chromosome painting with GGA and ZAU probes showed con...
Source: Chromosome Research - June 7, 2018 Category: Genetics & Stem Cells Authors: Kretschmer R, de Oliveira Furo I, Gunski RJ, Del Valle Garnero A, Pereira JC, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC, de Freitas TRO Tags: Chromosome Res Source Type: research

Clonal reproduction assured by sister chromosome pairing in dojo loach, a teleost fish.
Abstract Wild-type dojo loach (Misgurnus anguillicaudatus) commonly reproduces bisexually as a gonochoristic diploid (2n = 50), but gynogenetically reproducing clonal diploid lines (2n = 50) exist in certain districts in Japan. Clones have been considered to develop from past hybridization event(s) between two genetically diverse groups, A and B, within the species. Fluorescence in situ hybridization analyses using the repetitive sequence "ManDra" as a probe clearly distinguished 25 chromosomes derived from group B out of a total of 50 diploid chromosomes of the clone, providi...
Source: Chromosome Research - June 7, 2018 Category: Genetics & Stem Cells Authors: Kuroda M, Fujimoto T, Murakami M, Yamaha E, Arai K Tags: Chromosome Res Source Type: research

Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions.
Abstract Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of the SORE-1 family of soybean retrotransposons using genome sequencing data. Insertion time of each SORE-1 element into the genome was estimated on the basis of sequence differences between the 5' and 3' long terminal repeats (LTRs). Combining this estimation w...
Source: Chromosome Research - May 22, 2018 Category: Genetics & Stem Cells Authors: Nakashima K, Abe J, Kanazawa A Tags: Chromosome Res Source Type: research

Insight into the mechanisms and consequences of recurrent telomere capture associated with a sub-telomeric deletion.
rg C Abstract A complex mosaicism of the short arm of chromosome 1 detected by SNP microarray analysis is described in a patient presenting a 4-Mb 1p36 terminal deletion and associated phenotypic features. The array pattern of chromosome 1p displayed an intriguing increase in divergence of the SNP heterozygote frequency from the expected 50% from the centromere towards the 1p36 breakpoint. This suggests that various overlapping segments of UPD were derived by somatic recombination between the 1p homologues. The most likely explanation was the occurrence of a series of events initiated in either a gamete or an earl...
Source: Chromosome Research - May 12, 2018 Category: Genetics & Stem Cells Authors: Dos Santos A, Campagnari F, Krepischi ACV, Ribeiro Câmara ML, de Arruda Brasil RCE, Vieira L, Vianna-Morgante AM, Otto PA, Pearson PL, Rosenberg C Tags: Chromosome Res Source Type: research

Changes in the position and volume of inactive X chromosomes during the G0/G1 transition.
Abstract In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI...
Source: Chromosome Research - April 21, 2018 Category: Genetics & Stem Cells Authors: Lyu G, Tan T, Guan Y, Sun L, Liang Q, Tao W Tags: Chromosome Res Source Type: research

Insights into the karyotype evolution and speciation of the beetle Euchroma gigantea (Coleoptera: Buprestidae).
ura R Abstract Euchroma Dejean, 1833 (Buprestidae: Coleoptera) is a monotypic genus comprising the species Euchroma gigantea, with populations presenting a degree of karyotypic variation/polymorphism rarely found within a single taxonomic (specific) unit, as well as drastically incompatible meiotic configurations in populations from extremes of the species range. To better understand the complex karyotypic evolution of E. gigantea, the karyotypes of specimens from five populations in Brazil were investigated using molecular cytogenetics and phylogenetic approaches. Herein, we used FISH with histone genes as well a...
Source: Chromosome Research - March 9, 2018 Category: Genetics & Stem Cells Authors: Xavier C, Soares RVS, Amorim IC, Cabral-de-Mello DC, de Cássia de Moura R Tags: Chromosome Res Source Type: research

Correction to: Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.
Abstract The original version of this article unfortunately contained a mistake in publishing the panel C for Figures 3, 5 and 6. PMID: 29502298 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - March 3, 2018 Category: Genetics & Stem Cells Authors: Glinsky GV Tags: Chromosome Res Source Type: research

Transposable elements and the multidimensional genome.
PMID: 29492778 [PubMed - as supplied by publisher] (Source: Chromosome Research)
Source: Chromosome Research - February 28, 2018 Category: Genetics & Stem Cells Authors: Larsen PA Tags: Chromosome Res Source Type: research

Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.
Abstract Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potenti...
Source: Chromosome Research - February 19, 2018 Category: Genetics & Stem Cells Authors: Larsen PA, Hunnicutt KE, Larsen RJ, Yoder AD, Saunders AM Tags: Chromosome Res Source Type: research