Epigenetics and chromosome biology

A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of Crassostrea angulata/gigas

The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ab...

Authors: Ismael Cross, Silvia Portela-Bens, Aglaya García-Angulo, Manuel A. Merlo, María E. Rodríguez, Thomas Liehr and Laureana Rebordinos

Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations

Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlanti...

Authors: Katarina M Jørgensen, Vidar Wennevik, Anne Grete Eide Sørvik, Laila Unneland, Sergey Prusov, Fernando Ayllon and Kevin A Glover

Karyotype diversity and 2C DNA content in species of the Caesalpinia group

The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within thi...

Authors: Polliana Silva Rodrigues, Margarete Magalhães Souza, Cláusio Antônio Ferreira Melo, Telma Nair Santana Pereira and Ronan Xavier Corrêa

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat

Puberty is a pivotal stage in female animal development, and marks the onset of reproductive capability. However, little is known about the function of lncRNAs (long noncoding RNAs) in puberty. Therefore, RNA-...

Authors: Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang and Zubing Cao

Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus

Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on ...

Authors: Ujjwal Maulik, Sagnik Sen, Saurav Mallik and Sanghamitra Bandyopadhyay

Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)

Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes ...

Authors: Yongqin Zhang, Jinhui Liu, Wen Fu, Wenting Xu, Huiqin Zhang, Shujuan Chen, Wenbin Liu, Liangyue Peng and Yamei Xiao

The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata

Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concert...

Authors: Diogo Milani, Érica Ramos, Vilma Loreto, Dardo Andrea Martí, Adauto Lima Cardoso, Karen Cristiane Martinez de Moraes, Cesar Martins and Diogo Cavalcanti Cabral-de-Mello

Prenatal caloric restriction alters lipid metabolism but not hepatic Fasn gene expression and methylation profiles in rats

Undernutrition is an increasingly common problem. Insufficient calorie intake and nutrient deficiencies during pregnancy may have an impact not only on the mother, but may also alter metabolism in the infant. ...

Authors: Joanna Nowacka-Woszuk, Zofia E. Madeja and Agata Chmurzynska

Karyotype differentiation in tellin shells (Bivalvia: Tellinidae)

Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and t...

Authors: Daniel García-Souto, Gonzalo Ríos and Juan J. Pasantes

The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study

The levels of circulating cytokines fluctuate with age, acute illness, and chronic disease, and are predictive of mortality; this is also true for patterns of DNA (CpG) methylation. Given that immune cells are...

Authors: Chris P. Verschoor, Lisa M. McEwen, Vikas Kohli, Christina Wolfson, Dawn ME. Bowdish, Parminder Raina, Michael S. Kobor and Cynthia Balion

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

MicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation ...

Authors: Jinxing Hou, Xiaopeng An, Yuxuan Song, Binyun Cao, Heping Yang, Zhou Zhang, Wenzheng Shen and Yunpu Li

Karyotype diversity and chromosomal organization of repetitive DNA in Tityus obscurus (Scorpiones, Buthidae)

Holocentric chromosomes occur in approximately 750 species of eukaryotes. Among them, the genus Tityus (Scorpiones, Buthidae) has a labile karyotype that shows complex multivalent associations during male meiosis...

Authors: Bruno Rafael Ribeiro de Almeida, Susana Suely Rodrigues Milhomem-Paixão, Renata Coelho Rodrigues Noronha, Cleusa Yoshiko Nagamachi, Marlyson Jeremias Rodrigues da Costa, Pedro Pereira de Oliveira Pardal, Johne Souza Coelho and Julio Cesar Pieczarka

Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set

The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid...

Authors: A. C. Harvey, P. G. Fjelldal, M. F. Solberg, T. Hansen and K. A. Glover

A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo

Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could ...

Authors: Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto and Mikita Suyama

Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

Acipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, hig...

Authors: Radka Symonová, Miloš Havelka, Chris T. Amemiya, William Mike Howell, Tereza Kořínková, Martin Flajšhans, David Gela and Petr Ráb

Formation of diploid and triploid hybrid groupers (hybridization of Epinephelus coioides ♀ × Epinephelus lanceolatus ♂) and their 5S gene analysis

Interspecies hybridization is widely used to achieve heterosis or hybrid vigor, which has been observed and harnessed by breeders for centuries. Natural allopolyploid hybrids generally exhibit more superior he...

Authors: Wen Huang, Qinbo Qin, Huirong Yang, Shuisheng Li, Chaoqun Hu, Yude Wang, Yong Zhang, Shaojun Liu and Haoran Lin

Development of chromosomal markers based on next-generation sequencing: the B chromosome of the cichlid fish Astatotilapia latifasciata as a model

B chromosomes (Bs) are additional chromosomal elements found in a wide range of eukaryotes including fungi, plants and animals. B chromosomes are still enigmatic despite being the subject of hundreds, even tho...

Authors: Bruno E. A. Fantinatti and Cesar Martins

Is premeiotic genome elimination an exclusive mechanism for hemiclonal reproduction in hybrid males of the genus Pelophylax?

The ability to eliminate a parental genome from a eukaryotic germ cell is a phenomenon observed mostly in hybrid organisms displaying an alternative propagation to sexual reproduction. For most taxa, the under...

Authors: Marie Doležálková, Alexandr Sember, František Marec, Petr Ráb, Jörg Plötner and Lukáš Choleva

Addition of Manas barley chromosome arms to the hexaploid wheat genome

Cultivated barley belongs to the tertiary genepool of hexaploid wheat. Genes of interest can be transferred from barley into wheat through wide hybridization. The application of wheat-barley introgression line...

Authors: Edina Türkösi, András Cseh, Éva Darkó and Márta Molnár-Láng

Repetitive element hypermethylation in multiple sclerosis patients

Multiple sclerosis (MS) is a complex disorder of the central nervous system whose cause is currently unknown. Evidence is increasing that DNA methylation alterations could be involved in inflammatory and neuro...

Authors: K. Y. Neven, M. Piola, L. Angelici, F. Cortini, C. Fenoglio, D. Galimberti, A. C. Pesatori, E. Scarpini and V. Bollati

DNA methylation in peripheral tissue of schizophrenia and bipolar disorder: a systematic review

Increasing evidence suggests the involvement of epigenetic processes in the development of schizophrenia and bipolar disorder, and recent reviews have focused on findings in post-mortem brain tissue. A systema...

Authors: Nina Teroganova, Leah Girshkin, Catherine M. Suter and Melissa J. Green

Influence of grand-mother diet on offspring performances through the male line in Muscovy duck

In mammals, multigenerational environmental effects have been documented by either epidemiological studies in human or animal experiments in rodents. Whether such phenomena also occur in birds for more than on...

Authors: Jean-Michel Brun, Marie-Dominique Bernadet, Alexis Cornuez, Sophie Leroux, Loys Bodin, Benjamin Basso, Stéphane Davail, Mathilde Jaglin, Michel Lessire, Xavier Martin, Nadine Sellier, Mireille Morisson and Frédérique Pitel

MicroRNA profiles reveal female allotetraploid hybrid fertility

The bisexual fertile tetraploid fish is important in biological evolution. Tetraploid fish fertility is the key factor for stable inheritance. Therefore, elucidating tetraploid fish fertility at the molecular ...

Authors: Rong Zhou, Yanhong Wu, Min Tao, Chun Zhang and Shaojun Liu

Analysis of an independent tumor suppressor locus telomeric to Tp53 suggested Inpp5k and Myo1c as novel tumor suppressor gene candidates in this region

Several reports indicate a commonly deleted chromosomal region independent from, and distal to the TP53 locus in a variety of human tumors. In a previous study, we reported a similar finding in a rat tumor model ...

Authors: Carola Hedberg Oldfors, Diego Garcia Dios, Anna Linder, Kittichate Visuttijai, Emma Samuelson, Sandra Karlsson, Staffan Nilsson and Afrouz Behboudi

High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa

Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-b...

Authors: Ilya V. Kirov, Katrijn Van Laere and Ludmila I. Khrustaleva

Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding

X-chromosome inactivation silences one X chromosome in females to achieve dosage compensation with the single X chromosome in males. While most genes are silenced on the inactive X chromosome, the gene for the...

Authors: Andrew G Chapman, Allison M Cotton, Angela D Kelsey and Carolyn J Brown

Alteration in methylation level at 11β-hydroxysteroid dehydrogenase type 2 gene promoter in infants born to preeclamptic women

Preeclampsia reduces placental expression and activity of 11β-hydroxysteroid dehydrogenase type 2 (HSD11B2), leading to an increase in fetal glucocordicoids. The latter has been proposed to be associated with ...

Authors: Wensheng Hu, Xiaoling Weng, Minyue Dong, Yun Liu, Wenjuan Li and Hefeng Huang

Abnormal chromosome behavior during meiosis in the allotetraploid of Carassius auratus red var. (♀) × Megalobrama amblycephala(♂)

Allopolyploids generally undergo bivalent pairing at meiosis because only homologous chromosomes pair up. On the other hand, several studies have documented abnormal chromosome behavior during mitosis and meio...

Authors: Qinbo Qin, Yude Wang, Juan Wang, Jing Dai, Yun Liu and Shaojun Liu

Karyotypic diversification in Mytilus mussels (Bivalvia: Mytilidae) inferred from chromosomal mapping of rRNA and histone gene clusters

Mussels of the genus Mytilus present morphologically similar karyotypes that are presumably conserved. The absence of chromosome painting probes in bivalves makes difficult verifying this hypothesis. In this cont...

Authors: Concepción Pérez-García, Paloma Morán and Juan J Pasantes

Aberrant PTPRO methylation in tumor tissues as a potential biomarker that predicts clinical outcomes in breast cancer patients

Aberrant hypermethylation of gene promoter regions is a primary mechanism by which tumor suppressor genes become inactivated in breast cancer. Epigenetic inactivation of the protein tyrosine phosphatase recept...

Authors: Shao-ying Li, Rong Li, Yu-li Chen, Li-kuang Xiong, Hui-lin Wang, Lei Rong and Rong-cheng Luo

Karyotypic diversity in seven Amazonian anurans in the genus Hypsiboas (family Hylidae)

Hypsiboas species have been divided into seven groups using morphological and genetic characters, but for most of the species, there is no cytogenetic information available. A cytogenetic analysis using conventio...

Authors: Thais Lemos de Mattos, Ana Carolina Coelho, Carlos Henrique Schneider, David Otávio Carmo Telles, Marcelo Menin and Maria Claudia Gross

Fertility of a spontaneous hexaploid male Siberian sturgeon, Acipenser baerii

Evolution of sturgeons and paddlefishes (order Acipenseriformes) is inherently connected with polyploidization events which resulted in differentiation of ploidy levels and chromosome numbers of present acipen...

Authors: Miloš Havelka, Martin Hulák, Petr Ráb, Marie Rábová, Dietmar Lieckfeldt, Arne Ludwig, Marek Rodina, David Gela, Martin Pšenička, Dmytro Bytyutskyy and Martin Flajšhans

Two new cytotypes reinforce that Micronycteris hirsuta Peters, 1869 does not represent a monotypic taxon

The genus Micronycteris is a diverse group of phyllostomid bats currently comprising 11 species, with diploid number (2n) ranging from 26 to 40 chromosomes. The karyotypic relationships within Micronycteris and b...

Authors: Talita FA Ribas, Luis RR Rodrigues, Cleusa Y Nagamachi, Anderson JB Gomes, Thayse CM Benathar, Patricia CM O’Brien, Fengtang Yang, Malcolm A Ferguson-Smith and Julio C Pieczarka

The formation of diploid and triploid hybrids of female grass carp × male blunt snout bream and their 5S rDNA analysis

Hybridization is a useful strategy to alter the genotypes and phenotypes of the offspring. It could transfer the genome of one species to another through combing the different genome of parents in the hybrid o...

Authors: Weiguo He, Lihua Xie, Tangluo Li, Shaojun Liu, Jun Xiao, Jie Hu, Jing Wang, Qinbo Qin and Yun Liu

Cytogenetic analysis of Phyllomedusa distincta Lutz, 1950 (2n = 2x = 26), P. tetraploidea Pombal and Haddad, 1992 (2n = 4x = 52), and their natural triploid hybrids (2n = 3x = 39) (Anura, Hylidae, Phyllomedusinae)

Natural polyploidy has played an important role during the speciation and evolution of vertebrates, including anurans, with more than 55 described cases. The species of the Phyllomedusa burmeisteri group are most...

Authors: Simone Lilian Gruber, Ana Paula Zampieri Silva, Célio Fernando Baptista Haddad and Sanae Kasahara

Evaluation of the taxonomic status of populations assigned to Phyllomedusa hypochondrialis (Anura, Hylidae, Phyllomedusinae) based on molecular, chromosomal, and morphological approach

The taxonomic and phylogenetic relationships of the genus Phyllomedusa have been amply discussed. The marked morphological similarities among some species hamper the reliable identification of specimens and may o...

Authors: Daniel Pacheco Bruschi, Carmen Sílvia Busin, Luís Felipe Toledo, Gilda Andrade Vasconcellos, Christine Strussmann, Luiz Norberto Weber, Albertina Pimentel Lima, Jucivaldo Dias Lima and Shirlei Maria Recco-Pimentel

Comparative analysis of sex chromosomes in Leporinusspecies (Teleostei, Characiformes) using chromosome painting

The Leporinus genus, belonging to the Anostomidae family, is an interesting model for studies of sex chromosome evolution in fish, particularly because of the presence of heteromorphic sex chromosomes only in som...

Authors: Patrícia Pasquali Parise-Maltempi, Edson Lourenço da Silva, Willem Rens, Frances Dearden, Patricia CM O’Brien, Vladimir Trifonov and Malcolm A Ferguson-Smith

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

As a well-known epigenomic modification, DNA methylation is found to be common in plants and plays an important role in many biological processes. Relying on the unique feature of methylation-dependent digesti...

Authors: Xiaojun Huang, Hanlin Lu, Jun-Wen Wang, Liqin Xu, Siyang Liu, Jihua Sun and Fei Gao

Stability of genomic imprinting in human induced pluripotent stem cells

hiPSCs are generated through epigenetic reprogramming of somatic tissue. Genomic imprinting is an epigenetic phenomenon through which monoallelic gene expression is regulated in a parent-of-origin-specific man...

Authors: Hitoshi Hiura, Masashi Toyoda, Hiroaki Okae, Masahiro Sakurai, Naoko Miyauchi, Akiko Sato, Nobutaka Kiyokawa, Hajime Okita, Yoshitaka Miyagawa, Hidenori Akutsu, Koichiro Nishino, Akihiro Umezawa and Takahiro Arima

Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentuscomplex) from the Eastern Ukraine

Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esc...

Authors: Dmitry Dedukh, Glib Mazepa, Dmitry Shabanov, Juriy Rosanov, Spartak Litvinchuk, Leo Borkin, Alsu Saifitdinova and Alla Krasikova

Erratum to: Comparative chromosome mapping of repetitive sequences. Implications for genomic evolution in the fish, Hoplias malabaricus

Authors: Marcelo B Cioffi, Cesar Martins and Luiz AC Bertollo

Proechimys (Rodentia, Echimyidae): characterization and taxonomic considerations of a form with a very low diploid number and a multiple sex chromosome system

Proechimys is the most diverse genus in family Echimyidae, comprising 25 species (two of which are polytypic) and 39 taxa. Despite the numerous forms of this rodent and their abundance in nature, there are many t...

Authors: Paulo JS Amaral, Cleusa Y Nagamachi, Renata CR Noronha, Marlyson JR Costa, Adenilson L Pereira, Rogerio V Rossi, Ana C Mendes-Oliveira and Julio C Pieczarka

Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

Sex chromosomes are subject to evolutionary pressures distinct from the remainder of the genome, shaping their structure and sequence content. We are interested in the sex chromosomes of domestic pigs (Sus scrofa

Authors: Benjamin M Skinner, Kim Lachani, Carole A Sargent and Nabeel A Affara

Cytogenetic analyses of eight species in the genus Leptodactylus Fitzinger, 1843 (Amphibia, Anura, Leptodactylidae), including a new diploid number and a karyotype with multiple translocations

The karyotypes of Leptodactylus species usually consist of 22 bi-armed chromosomes, but morphological variations in some chromosomes and even differences in the 2n have been reported. To better understand the mec...

Authors: Thiago Gazoni, Simone L Gruber, Ana PZ Silva, Olivia GS Araújo, Hideki Narimatsu, Christine Strüssmann, Célio FB Haddad and Sanae Kasahara

B chromosome in the beetle Coprophanaeus cyanescens (Scarabaeidae): emphasis in the organization of repetitive DNA sequences

To contribute to the knowledge of coleopteran cytogenetics, especially with respect to the genomic content of B chromosomes, we analyzed the composition and organization of repetitive DNA sequences in the Coproph...

Authors: Sarah Gomes de Oliveira, Rita Cassia de Moura and Cesar Martins

Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides

Squalius alburnoides is an Iberian cyprinid fish resulting from an interspecific hybridisation between Squalius pyrenaicus females (P genome) and males of an unknown Anaecypris hispanica- like species (A genome)....

Authors: Isa Matos, Élio Sucena, Miguel P Machado, Rui Gardner, Ângela Inácio, Manfred Schartl and Maria M Coelho

Microsatellite distribution on sex chromosomes at different stages of heteromorphism and heterochromatinization in two lizard species (Squamata: Eublepharidae: Coleonyx elegans and Lacertidae: Eremias velox)

The accumulation of repetitive sequences such as microsatellites during the differentiation of sex chromosomes has not been studied in most squamate reptiles (lizards, amphisbaenians and snakes), a group which...

Authors: Martina Pokorná, Lukáš Kratochvíl and Eduard Kejnovský

Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin

Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this gr...

Authors: Diogo C Cabral-de-Mello, Sárah G Oliveira, Rita C de Moura and Cesar Martins

Methylation changes associated with early maturation stages in the Atlantic salmon

Early maturation in the Atlantic salmon is an interesting subject for numerous research lines. Prior to sea migration, parr can reach sexual maturation and successfully fertilize adult female eggs during the r...

Authors: Paloma Morán and Andrés Pérez-Figueroa

Functional characterization of the Saccharomyces cerevisiae protein Chl1 reveals the role of sister chromatid cohesion in the maintenance of spindle length during S-phase arrest

Metaphase cells have short spindles for efficient bi-orientation of chromosomes. The cohesin proteins hold sister chromatids together, creating Sister Chromatid Cohesion (SCC) that helps in the maintenance of ...

Authors: Suparna Laha, Shankar P Das, Sujata Hajra, Kaustuv Sanyal and Pratima Sinha