Chromosome Research最新文献

{"title":"CTCF supports preferentially short lamina-associated domains.","authors":"Lukasz Stanislaw Kaczmarczyk,Nehora Levi,Tamar Segal,Mali Salmon-Divon,Gabi Gerlitz","doi":"10.1007/s10577-022-09686-5","DOIUrl":"https://doi.org/10.1007/s10577-022-09686-5","url":null,"abstract":"More than one third of the mammalian genome is in a close association with the nuclear lamina, thus these genomic regions were termed lamina-associated domains (LADs). This association is fundamental for many aspects of chromatin biology including transcription, replication, and DNA damage repair. LADs association with the nuclear envelope is thought to be dependent on two major mechanisms: The first mechanism is the interaction between nuclear membrane proteins such as LBR with heterochromatin modifications that are enriched in LADs chromatin. The second mechanism is based on proteins that bind the borders of the LADs and support the association of the LADs with the nuclear envelope. Two factors were suggested to support the second mechanism: CCCTC-binding factor (CTCF) and YY1 based on their enriched binding to LADs borders. However, this mechanism has not been proven yet at a whole genome level. Here, to test if CTCF supports the LADs landscape, we generated melanoma cells with a partial loss of function (pLoF) of CTCF by the CRISPR-Cas9 system and determined the LADs landscape by lamin B ChIP-seq analysis. We found that under regular growth conditions, CTCF pLoF led to modest changes in the LADs landscape that included an increase in the signal of 2% of the LADs and a decrease in the signal of 8% of the LADs. However, CTCF importance for the LADs landscape was much higher upon induction of a chromatin stress. We induced chromatin stress by inhibiting RNA polymerase II, an intervention that is known to alter chromatin compaction and supercoiling. Notably, only in CTCF pLoF cells, the chromatin stress led to the dissociation of 7% of the LADs from the lamina. The CTCF-dependent LADs had almost three times shorter median length than the non-affected LADs, were enriched in CTCF binding at their borders, and were higher in their facultative-status (cell-type specific). Thus, it appears that CTCF is a key factor in facilitating the association of short facultative LADs with the nuclear lamina upon chromatin stress.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"308 ","pages":"123-136"},"PeriodicalIF":2.6,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138506745","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":"CTCF supports preferentially short lamina-associated domains","authors":"Lukasz Stanislaw Kaczmarczyk, Nehora Levi, Tamar Segal, Mali Salmon-Divon, Gabi Gerlitz","doi":"10.1007/s10577-022-09686-5","DOIUrl":"https://doi.org/10.1007/s10577-022-09686-5","url":null,"abstract":"<p>More than one third of the mammalian genome is in a close association with the nuclear lamina, thus these genomic regions were termed lamina-associated domains (LADs). This association is fundamental for many aspects of chromatin biology including transcription, replication, and DNA damage repair. LADs association with the nuclear envelope is thought to be dependent on two major mechanisms: The first mechanism is the interaction between nuclear membrane proteins such as LBR with heterochromatin modifications that are enriched in LADs chromatin. The second mechanism is based on proteins that bind the borders of the LADs and support the association of the LADs with the nuclear envelope. Two factors were suggested to support the second mechanism: CCCTC-binding factor (CTCF) and YY1 based on their enriched binding to LADs borders. However, this mechanism has not been proven yet at a whole genome level. Here, to test if CTCF supports the LADs landscape, we generated melanoma cells with a partial loss of function (pLoF) of CTCF by the CRISPR-Cas9 system and determined the LADs landscape by lamin B ChIP-seq analysis. We found that under regular growth conditions, CTCF pLoF led to modest changes in the LADs landscape that included an increase in the signal of 2% of the LADs and a decrease in the signal of 8% of the LADs. However, CTCF importance for the LADs landscape was much higher upon induction of a chromatin stress. We induced chromatin stress by inhibiting RNA polymerase II, an intervention that is known to alter chromatin compaction and supercoiling. Notably, only in CTCF pLoF cells, the chromatin stress led to the dissociation of 7% of the LADs from the lamina. The CTCF-dependent LADs had almost three times shorter median length than the non-affected LADs, were enriched in CTCF binding at their borders, and were higher in their facultative-status (cell-type specific). Thus, it appears that CTCF is a key factor in facilitating the association of short facultative LADs with the nuclear lamina upon chromatin stress.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"32 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138506732","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":"Mobility of kinetochore proteins measured by FRAP analysis in living cells.","authors":"Reito Watanabe,&nbsp;Yasuhiro Hirano,&nbsp;Masatoshi Hara,&nbsp;Yasushi Hiraoka,&nbsp;Tatsuo Fukagawa","doi":"10.1007/s10577-021-09678-x","DOIUrl":"https://doi.org/10.1007/s10577-021-09678-x","url":null,"abstract":"<p><p>The kinetochore is essential for faithful chromosome segregation during mitosis and is assembled through dynamic processes involving numerous kinetochore proteins. Various experimental strategies have been used to understand kinetochore assembly processes. Fluorescence recovery after photobleaching (FRAP) analysis is also a useful strategy for revealing the dynamics of kinetochore assembly. In this study, we introduced fluorescence protein-tagged kinetochore protein cDNAs into each endogenous locus and performed FRAP analyses in chicken DT40 cells. Centromeric protein (CENP)-C was highly mobile in interphase, but immobile during mitosis. CENP-C mutants lacking the CENP-A-binding domain became mobile during mitosis. In contrast to CENP-C, CENP-T and CENP-H were immobile during both interphase and mitosis. The mobility of Dsn1, which is a component of the Mis12 complex and directly binds to CENP-C, depended on CENP-C mobility during mitosis. Thus, our FRAP assays provide dynamic aspects of how the kinetochore is assembled.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"43-57"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8942963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39795589","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}

{"title":"The Arabidopsis HOP2 gene has a role in preventing illegitimate connections between nonhomologous chromosome regions.","authors":"Yisell Farahani-Tafreshi,&nbsp;Chun Wei,&nbsp;Peilu Gan,&nbsp;Jenya Daradur,&nbsp;C Daniel Riggs,&nbsp;Clare A Hasenkampf","doi":"10.1007/s10577-021-09681-2","DOIUrl":"https://doi.org/10.1007/s10577-021-09681-2","url":null,"abstract":"<p><p>Meiotic homologous chromosomes synapse and undergo crossing over (CO). In many eukaryotes, both synapsis and crossing over require the induction of double stranded breaks (DSBs) and subsequent repair via homologous recombination. In these organisms, two key proteins are recombinases RAD51 and DMC1. Recombinase-modulators HOP2 and MND1 assist RAD51 and DMC1 and also are required for synapsis and CO. We have investigated the hop2-1 phenotype in Arabidopsis during the segregation stages of both meiosis and mitosis. Despite a general lack of synapsis during prophase I, we observed extensive, stable interconnections between nonhomologous chromosomes in diploid hop2-1 nuclei in first and second meiotic divisions. Using γH2Ax as a marker of unrepaired DSBs, we detected γH2AX foci from leptotene through early pachytene but saw no foci from mid-pachytene onward. We conclude that the bridges seen from metaphase I onward are due to mis-repaired DSBs, not unrepaired ones. Examining haploids, we found that wild type haploids produce only univalents, but hop2-1 haploids like hop2-1 diploids have illegitimate connections stable enough to produce bridged chromosomes during segregation. Our results suggest that HOP2 has a significant active role in preventing repairs that use nonhomologous chromosomes during meiosis. We also found evidence that HOP2 plays a role in preventing illegitimate repair of radiation-induced DSBs in rapidly dividing petal cells. We conclude that HOP2 in Arabidopsis plays both a positive role in promoting synapsis and a separable role in preventing DSB repair using nonhomologous chromosomes. SIGNIFICANCE STATEMENT : The fidelity of homologous recombination (HR) during meiosis is essential to the production of viable gametes and for maintaining genome integrity in vegetative cells. HOP2 is an important protein for accurate meiotic HR in plants. We have found evidence of high levels of illegitimate repairs between nonhomologous chromosomes during meiosis and in irradiated petal cells in hop2-1 mutants, suggesting a role for HOP2 beyond its established role in synapsis and crossing over.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"59-75"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39847914","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":"2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions.","authors":"Penka Pavlova,&nbsp;Martijn van Zanten,&nbsp;Basten L Snoek,&nbsp;Hans de Jong,&nbsp;Paul Fransz","doi":"10.1007/s10577-021-09673-2","DOIUrl":"https://doi.org/10.1007/s10577-021-09673-2","url":null,"abstract":"<p><p>Functional changes of cells upon developmental switches and in response to environmental cues are often reflected in nuclear phenotypes, showing distinctive chromatin states corresponding to transcriptional changes. Such characteristic nuclear shapes have been microscopically monitored and can be quantified after differential staining of euchromatin and heterochromatin domains. Here, we examined several nuclear parameters (size, DNA content, DNA density, chromatin compaction, relative heterochromatin fraction (RHF), and number of chromocenters) in relation to spatial distribution of genes and transposon elements (TEs), using standard 2D fluorescence microscopy. We provide nuclear profiles for different cell types and different accessions of Arabidopsis thaliana. A variable, yet significant, fraction of TEs was found outside chromocenters in all cell types, except for guard cells. The latter cell type features nuclei with the highest level of chromatin compaction, while their chromocenters seem to contain gene-rich regions. The highest number of parameter correlations was found in the accession Cvi, whereas Ler showed only few correlations. This may point at differences in phenotype robustness between accessions. The significantly high association of NOR chromocenters in accessions Ws and Cvi corresponds to their low RHF level.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"5-24"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8942920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39532268","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}

{"title":"Correction to: 2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions.","authors":"Penka Pavlova,&nbsp;Martijn van Zanten,&nbsp;Basten L Snoek,&nbsp;Hans de Jong,&nbsp;Paul Fransz","doi":"10.1007/s10577-021-09677-y","DOIUrl":"https://doi.org/10.1007/s10577-021-09677-y","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"25-27"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9172669/pdf/10577_2021_Article_9677.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39630844","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}

{"title":"Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition.","authors":"Amalia Ibiapino,&nbsp;Mariana Báez,&nbsp;Miguel A García,&nbsp;Mihai Costea,&nbsp;Saša Stefanović,&nbsp;Andrea Pedrosa-Harand","doi":"10.1007/s10577-021-09683-0","DOIUrl":"https://doi.org/10.1007/s10577-021-09683-0","url":null,"abstract":"<p><p>Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"91-107"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39867083","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":"Prediction of transcription factors associated with DNA demethylation during human cellular development.","authors":"Yurina Miyajima,&nbsp;Shuhei Noguchi,&nbsp;Yuki Tanaka,&nbsp;Jing-Ru Li,&nbsp;Hajime Nishimura,&nbsp;Mami Kishima,&nbsp;Joanne Lim,&nbsp;Erina Furuhata,&nbsp;Takahiro Suzuki,&nbsp;Takeya Kasukawa,&nbsp;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":"30 1","pages":"109-121"},"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}

{"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,&nbsp;Eliza F M B Nascimento,&nbsp;Soraya C M Leal-Bertioli,&nbsp;Brian Abernathy,&nbsp;Scott A Jackson,&nbsp;Ana C G Araujo,&nbsp;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":"30 1","pages":"77-90"},"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}

{"title":"Scientist Spotlight: Karen Wing Yee Yeun.","authors":"","doi":"10.1007/s10577-021-09682-1","DOIUrl":"https://doi.org/10.1007/s10577-021-09682-1","url":null,"abstract":"","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"30 1","pages":"1-3"},"PeriodicalIF":2.6,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39602984","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}