{"title":"Prediction of transcription factors associated with DNA demethylation during human cellular development.","authors":"Yurina Miyajima, Shuhei Noguchi, Yuki Tanaka, Jing-Ru Li, Hajime Nishimura, Mami Kishima, Joanne Lim, Erina Furuhata, Takahiro Suzuki, Takeya Kasukawa, Harukazu Suzuki","doi":"10.1007/s10577-022-09685-6","DOIUrl":"https://doi.org/10.1007/s10577-022-09685-6","url":null,"abstract":"<p><p>DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8942926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39906233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2022-03-01Epub Date: 2022-01-19DOI: 10.1007/s10577-022-09684-7
Dongying Gao, Eliza F M B Nascimento, Soraya C M Leal-Bertioli, Brian Abernathy, Scott A Jackson, Ana C G Araujo, David J Bertioli
{"title":"TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.).","authors":"Dongying Gao, Eliza F M B Nascimento, Soraya C M Leal-Bertioli, Brian Abernathy, Scott A Jackson, Ana C G Araujo, David J Bertioli","doi":"10.1007/s10577-022-09684-7","DOIUrl":"https://doi.org/10.1007/s10577-022-09684-7","url":null,"abstract":"<p><p>Telomeres are the physical ends of eukaryotic linear chromosomes that play critical roles in cell division, chromosome maintenance, and genome stability. In many plants, telomeres are comprised of TTTAGGG tandem repeat that is widely found in plants. We refer to this repeat as canonical plant telomeric repeat (CPTR). Peanut (Arachis hypogaea L.) is a spontaneously formed allotetraploid and an important food and oil crop worldwide. In this study, we analyzed the peanut genome sequences and identified a new type of tandem repeat with 10-bp basic motif TTTT(C/T)TAGGG named TAndem Repeat (TAR) 30. TAR30 showed significant sequence identity to TTTAGGG repeat in 112 plant genomes suggesting that TAR30 is a homolog of CPTR. It also is nearly identical to the telomeric tandem repeat in Cestrum elegans. Fluorescence in situ hybridization (FISH) analysis revealed interstitial locations of TAR30 in peanut chromosomes but we did not detect visible signals in the terminal ends of chromosomes as expected for telomeric repeats. Interestingly, different TAR30 hybridization patterns were found between the newly induced allotetraploid ValSten and its diploid wild progenitors. The canonical telomeric repeat TTTAGGG is also present in the peanut genomes and some of these repeats are closely adjacent to TAR30 from both cultivated peanut and its wild relatives. Overall, our work identifies a new homolog of CPTR and reveals the unique distributions of TAR30 in cultivated peanuts and wild species. Our results provide new insights into the evolution of tandem repeats during peanut polyploidization and domestication.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39920936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2022-03-01Epub Date: 2022-01-06DOI: 10.1007/s10577-021-09680-3
Kai Wang, Hon Cheng, Jinlei Han, Ayman Esh, Jiayong Liu, Yuebin Zhang, Baohua Wang
{"title":"A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars.","authors":"Kai Wang, Hon Cheng, Jinlei Han, Ayman Esh, Jiayong Liu, Yuebin Zhang, Baohua Wang","doi":"10.1007/s10577-021-09680-3","DOIUrl":"https://doi.org/10.1007/s10577-021-09680-3","url":null,"abstract":"<p><p>Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40-128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Ten cultivars were analyzed by fluorescence in situ hybridization adopting chromosome painting and S. spontaneum-specific probes. The results showed six types of chromosomes in the studied cultivars, including S. spontaneum or S. officinarum chromosomes, interspecific recombinations from homoeologous or nonhomoeologous chromosomes, and translocations of S. spontaneum or S. officinarum chromosomes. The results showed unexpectedly high proportions of interspecific recombinations in these cultivars (11.9-40.9%), which renew our knowledge that less than 13% of chromosomes result from interspecific exchanges. Also, the results showed a high frequency of translocations (an average of 2.15 translocations per chromosome) between S. officinarum chromosomes. The diverse types of chromosomes in cultivars imply that hybrid gametes of S. spontaneum and S. officinarum may form unusual chromosome pairs, including homoeologous or nonhomoeologous chromosomes either between or within S. spontaneum and S. officinarum. Moreover, we consistently observed 11 or 12 copies for the four studied chromosomes, i.e., chromosomes 1, 2, 7, and 8, suggesting steady transmission during the breeding program. By comparison, we found a relatively fewer copies of S. spontaneum chromosome 1 than those of S. spontaneum chromosomes 2, 7, and 8. These results provide deep insights into the structure of cultivars and may facilitate chromosome-assisted selection in sugarcane breeding.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39901397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Agundez, A. Alfirevic, S. Aliño, L. Becquemont, S. Bell, L. Benhaim, W. Berrettini, M. Białecka, E. Bleecker, L. Cavallari, A. Cederbaum, D. Chasman, L. Chen, B. Chowbay, M. Coenen, J. Corvol, W. Sadee, Y. Saito, R. Sargis, A. Schatzberg, S. Scherer, C. Schindler, M. Schirmer, K. Schmiegelow, W. Schroth, B. Tomlinson, J. Trontelj, T. Tsunoda, A. Turkistani, M. Tzvetkov, R. Uher, J. Upham, T. V. Gelder, L. H. J. Huis, R. V. Schaik
{"title":"Thanks to Referees","authors":"J. Agundez, A. Alfirevic, S. Aliño, L. Becquemont, S. Bell, L. Benhaim, W. Berrettini, M. Białecka, E. Bleecker, L. Cavallari, A. Cederbaum, D. Chasman, L. Chen, B. Chowbay, M. Coenen, J. Corvol, W. Sadee, Y. Saito, R. Sargis, A. Schatzberg, S. Scherer, C. Schindler, M. Schirmer, K. Schmiegelow, W. Schroth, B. Tomlinson, J. Trontelj, T. Tsunoda, A. Turkistani, M. Tzvetkov, R. Uher, J. Upham, T. V. Gelder, L. H. J. Huis, R. V. Schaik","doi":"10.1007/s10577-005-1902-8","DOIUrl":"https://doi.org/10.1007/s10577-005-1902-8","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-005-1902-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41788936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2021-12-01Epub Date: 2021-06-04DOI: 10.1007/s10577-021-09663-4
Anahí Mara Yañez-Santos, Rosalía Cristina Paz, Paula Beatriz Paz-Sepúlveda, Juan Domingo Urdampilleta
{"title":"Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.","authors":"Anahí Mara Yañez-Santos, Rosalía Cristina Paz, Paula Beatriz Paz-Sepúlveda, Juan Domingo Urdampilleta","doi":"10.1007/s10577-021-09663-4","DOIUrl":"https://doi.org/10.1007/s10577-021-09663-4","url":null,"abstract":"<p><p>Capsicum annuum is a species that has undergone an expansion of the size of its genome caused mainly by the amplification of repetitive DNA sequences, including mobile genetic elements. Based on information obtained from sequencing the genome of pepper, the estimated fraction of retroelements is approximately 81%, and previous results revealed an important contribution of lineages derived from Gypsy superfamily. However, the dynamics of the retroelements in the C. annuum genome is poorly understood. In this way, the present work seeks to investigate the phylogenetic diversity and genomic abundance of the families of autonomous (complete and intact) LTR retroelements from C. annuum and inspect their distribution along its chromosomes. In total, we identified 1151 structurally full-length retroelements (340 Copia; 811 Gypsy) grouped in 124 phylogenetic families in the base of their retrotranscriptase. All the evolutive lineages of LTR retroelements identified in plants were present in pepper; however, three of them comprise 83% of the entire LTR retroelements population, the lineages Athila, Del/Tekay, and Ale/Retrofit. From them, only three families represent 70.8% of the total number of the identified retroelements. A massive family-specific wave of amplification of two of them occurred in the last 0.5 Mya (GypsyCa_16; CopiaCa_01), whereas the third is more ancient and occurred 3.0 Mya (GypsyCa_13). Fluorescent in situ hybridization performed with family and lineage-specific probes revealed contrasting patterns of chromosomal affinity. Our results provide a database of the populations LTR retroelements specific to C. annuum genome. The most abundant families were analyzed according to chromosome insertional preferences, suppling useful tools to the design of retroelement-based markers specific to the species.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09663-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39060939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2021-12-01Epub Date: 2021-10-16DOI: 10.1007/s10577-021-09675-0
Noorhariza Mohd Zaki, Trude Schwarzacher, Rajinder Singh, Maria Madon, Corey Wischmeyer, Nordiana Hanim Mohd Nor, Muhammad Azwan Zulkifli, J S Pat Heslop-Harrison
{"title":"Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.","authors":"Noorhariza Mohd Zaki, Trude Schwarzacher, Rajinder Singh, Maria Madon, Corey Wischmeyer, Nordiana Hanim Mohd Nor, Muhammad Azwan Zulkifli, J S Pat Heslop-Harrison","doi":"10.1007/s10577-021-09675-0","DOIUrl":"https://doi.org/10.1007/s10577-021-09675-0","url":null,"abstract":"<p><p>Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39524277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2021-12-01Epub Date: 2021-08-18DOI: 10.1007/s10577-021-09670-5
Ryan N Douglas, Hua Yang, Bing Zhang, Chen Chen, Fangpu Han, Jianlin Cheng, James A Birchler
{"title":"De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays).","authors":"Ryan N Douglas, Hua Yang, Bing Zhang, Chen Chen, Fangpu Han, Jianlin Cheng, James A Birchler","doi":"10.1007/s10577-021-09670-5","DOIUrl":"https://doi.org/10.1007/s10577-021-09670-5","url":null,"abstract":"<p><p>The B chromosome of maize undergoes nondisjunction at the second pollen mitosis as part of its accumulation mechanism. Previous work identified 9-Bic-1 (9-B inactivated centromere-1), which comprises an epigenetically silenced B chromosome centromere that was translocated to the short arm of chromosome 9(9S). This chromosome is stable in isolation, but when normal B chromosomes are added to the genotype, it will attempt to undergo nondisjunction during the second pollen mitosis and usually fractures the chromosome in 9S. These broken chromosomes allow a test of whether the inactive centromere is reactivated or whether a de novo centromere is formed elsewhere on the chromosome to allow recovery of fragments. Breakpoint determination on the B chromosome and chromosome 9 showed that mini chromosome B1104 has the same breakpoint as 9-Bic-1 in the B centromere region and includes a portion of 9S. CENH3 binding was found on the B centromere region and on 9S, suggesting both centromere reactivation and de novo centromere formation. Another mini chromosome, B496, showed evidence of rearrangement, but it also only showed evidence for a de novo centromere. Other mini chromosome fragments recovered were directly derived from the B chromosome with breakpoints concentrated near the centromeric knob region, which suggests that the B chromosome is broken at a low frequency due to the failure of the sister chromatids to separate at the second pollen mitosis. Our results indicate that both reactivation and de novo centromere formation could occur on fragments derived from the progenitor possessing an inactive centromere.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09670-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39322521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosome ResearchPub Date : 2021-12-01Epub Date: 2021-08-24DOI: 10.1007/s10577-021-09669-y
Maxim A Krivov, Fazoil I Ataullakhanov, Pavel S Ivanov
{"title":"Computer simulation of merotelic kinetochore-microtubule attachments: corona size is more important than other cell parameters.","authors":"Maxim A Krivov, Fazoil I Ataullakhanov, Pavel S Ivanov","doi":"10.1007/s10577-021-09669-y","DOIUrl":"https://doi.org/10.1007/s10577-021-09669-y","url":null,"abstract":"<p><p>The even chromosome segregation between daughter cells during mitosis is crucial for genome integrity and is mostly regulated by proper attachments of spindle microtubules to kinetochores. Abnormalities in this process can lead to chromosome mis-segregation and potentially result in severe developmental disorders such as aneuploidy and cancer. Merotelic attachments when tubulin microtubules captured by the kinetochore of one chromatid originate from both spindle poles are considered as one of the key molecular processes that cause such abnormalities. In this paper, we use computer modeling and the Monte Carlo approach to reveal the reasons for retaining merotelic attachments at the end of metaphase. To this end, we varied, in small increments, the basic cell parameters within ensembles of 100, 500, and 1000 virtual cells. The analysis of configurations that ensure the preservation of the largest fraction of merotelic attachments enabled us to conclude that only a change in the size of the kinetochore corona can significantly increase the number of merotelic attachments and the angle between the centromere axis and the spindle axis. The effect of the other changes in model parameters, if any, was steadily suppressed by the end of metaphase. In addition, our computer model was validated by successfully reproducing the results of third-party theoretical studies as well as some experimental observations. We also found that the orientation of chromosomes and the number of merotelic attachments do not have an explicit correlation with each other and within some limits can change independently.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09669-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39341610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Communal living: the role of polyploidy and syncytia in tissue biology.","authors":"Nora G Peterson, Donald T Fox","doi":"10.1007/s10577-021-09664-3","DOIUrl":"https://doi.org/10.1007/s10577-021-09664-3","url":null,"abstract":"<p><p>Multicellular organisms are composed of tissues with diverse cell sizes. Whether a tissue primarily consists of numerous, small cells as opposed to fewer, large cells can impact tissue development and function. The addition of nuclear genome copies within a common cytoplasm is a recurring strategy to manipulate cellular size within a tissue. Cells with more than two genomes can exist transiently, such as in developing germlines or embryos, or can be part of mature somatic tissues. Such nuclear collectives span multiple levels of organization, from mononuclear or binuclear polyploid cells to highly multinucleate structures known as syncytia. Here, we review the diversity of polyploid and syncytial tissues found throughout nature. We summarize current literature concerning tissue construction through syncytia and/or polyploidy and speculate why one or both strategies are advantageous.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09664-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9291922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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