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The fate of a suppressed X-linked meiotic driver: experimental evolution in Drosophila simulans 被抑制的X连锁减数分裂驱动因子的命运:模拟果蝇的实验进化
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-05-30 DOI: 10.1007/s10577-022-09698-1
Héloïse Bastide, D. Ogereau, C. Montchamp-Moreau, P. R. Gérard
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引用次数: 1
Mendelian nightmares: the germline-restricted chromosome of songbirds 孟德尔梦魇:鸣禽种系限制性染色体
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-04-13 DOI: 10.1007/s10577-022-09688-3
P. Borodin, Augustin Chen, W. Forstmeier, Simone Fouché, L. Malinovskaya, Yifan Pei, Radka Reifová, Francisco J. Ruiz-Ruano, Stephen A. Schlebusch, Manuelita Sotelo-Muñoz, A. Torgasheva, Niki Vontzou, Alexander Suh
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引用次数: 8
The non-Mendelian behavior of plant B chromosomes 植物B染色体的非孟德尔行为
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-04-12 DOI: 10.1007/s10577-022-09687-4
Jianyong Chen, J. Birchler, A. Houben
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引用次数: 8
CTCF supports preferentially short lamina-associated domains. CTCF优先支持短层相关结构域。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-03 DOI: 10.1007/s10577-022-09686-5
Lukasz Stanislaw Kaczmarczyk,Nehora Levi,Tamar Segal,Mali Salmon-Divon,Gabi Gerlitz
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.
超过三分之一的哺乳动物基因组与核层密切相关,因此这些基因组区域被称为层相关结构域(lamina-associated domains, LADs)。这种关联是染色质生物学许多方面的基础,包括转录、复制和DNA损伤修复。LADs与核膜的关联被认为依赖于两种主要机制:第一种机制是核膜蛋白(如LBR)与富含LADs染色质的异染色质修饰之间的相互作用。第二种机制是基于结合LADs边界并支持LADs与核膜结合的蛋白质。两个因子被认为支持第二种机制:ccctc结合因子(CTCF)和YY1,基于它们与LADs边界的丰富结合。然而,这种机制尚未在全基因组水平上得到证实。在这里,为了测试CTCF是否支持LADs景观,我们通过CRISPR-Cas9系统生成了CTCF部分功能丧失(pLoF)的黑色素瘤细胞,并通过lamin B ChIP-seq分析确定了LADs景观。我们发现,在正常生长条件下,CTCF pLoF导致LADs景观的适度变化,包括2%的LADs信号增加和8%的LADs信号减少。然而,在染色质胁迫诱导下,CTCF对LADs景观的重要性要高得多。我们通过抑制RNA聚合酶II来诱导染色质应激,这是一种已知的改变染色质压实和超卷曲的干预。值得注意的是,只有在CTCF pLoF细胞中,染色质应激导致7%的LADs从层中分离。CTCF依赖性lad的中位长度几乎比未受影响的lad短三倍,其边界富含CTCF结合,并且其兼性状态(细胞类型特异性)更高。因此,CTCF似乎是在染色质胁迫下促进短兼性LADs与核层关联的关键因素。
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引用次数: 0
CTCF supports preferentially short lamina-associated domains CTCF优先支持短层相关结构域
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-03 DOI: 10.1007/s10577-022-09686-5
Lukasz Stanislaw Kaczmarczyk, Nehora Levi, Tamar Segal, Mali Salmon-Divon, Gabi Gerlitz

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.

超过三分之一的哺乳动物基因组与核层密切相关,因此这些基因组区域被称为层相关结构域(lamina-associated domains, LADs)。这种关联是染色质生物学许多方面的基础,包括转录、复制和DNA损伤修复。LADs与核膜的关联被认为依赖于两种主要机制:第一种机制是核膜蛋白(如LBR)与富含LADs染色质的异染色质修饰之间的相互作用。第二种机制是基于结合LADs边界并支持LADs与核膜结合的蛋白质。两个因子被认为支持第二种机制:ccctc结合因子(CTCF)和YY1,基于它们与LADs边界的丰富结合。然而,这种机制尚未在全基因组水平上得到证实。在这里,为了测试CTCF是否支持LADs景观,我们通过CRISPR-Cas9系统生成了CTCF部分功能丧失(pLoF)的黑色素瘤细胞,并通过lamin B ChIP-seq分析确定了LADs景观。我们发现,在正常生长条件下,CTCF pLoF导致LADs景观的适度变化,包括2%的LADs信号增加和8%的LADs信号减少。然而,在染色质胁迫诱导下,CTCF对LADs景观的重要性要高得多。我们通过抑制RNA聚合酶II来诱导染色质应激,这是一种已知的改变染色质压实和超卷曲的干预。值得注意的是,只有在CTCF pLoF细胞中,染色质应激导致7%的LADs从层中分离。CTCF依赖性lad的中位长度几乎比未受影响的lad短三倍,其边界富含CTCF结合,并且其兼性状态(细胞类型特异性)更高。因此,CTCF似乎是在染色质胁迫下促进短兼性LADs与核层关联的关键因素。
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引用次数: 5
Mobility of kinetochore proteins measured by FRAP analysis in living cells. FRAP法测定活细胞中着丝点蛋白的迁移率。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-01 Epub Date: 2022-01-08 DOI: 10.1007/s10577-021-09678-x
Reito Watanabe, Yasuhiro Hirano, Masatoshi Hara, Yasushi Hiraoka, Tatsuo Fukagawa

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.

在有丝分裂过程中,着丝粒对染色体的忠实分离至关重要,并通过涉及许多着丝粒蛋白的动态过程进行组装。不同的实验策略被用来理解着丝点组装过程。光漂白后荧光恢复(FRAP)分析也是揭示着丝点组装动力学的有用策略。在这项研究中,我们将荧光蛋白标记的着丝点蛋白cdna引入每个内源性位点,并对鸡DT40细胞进行了FRAP分析。着丝粒蛋白(CENP)-C在间期高度移动,但在有丝分裂期间不移动。缺乏cenp - a结合结构域的CENP-C突变体在有丝分裂期间变得可移动。与CENP-C相比,CENP-T和CENP-H在间期和有丝分裂期间都是不动的。Dsn1是Mis12复合体的一个组成部分,直接与CENP-C结合,其迁移依赖于有丝分裂过程中CENP-C的迁移。因此,我们的FRAP分析提供了着丝点如何组装的动态方面。
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引用次数: 9
The Arabidopsis HOP2 gene has a role in preventing illegitimate connections between nonhomologous chromosome regions. 拟南芥HOP2基因在防止非同源染色体区域之间的非法连接中起作用。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-01 Epub Date: 2022-01-22 DOI: 10.1007/s10577-021-09681-2
Yisell Farahani-Tafreshi, Chun Wei, Peilu Gan, Jenya Daradur, C Daniel Riggs, Clare A Hasenkampf

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.

减数分裂同源染色体突触并进行交叉(CO)。在许多真核生物中,突触和交叉都需要诱导双链断裂(DSBs)并随后通过同源重组进行修复。在这些生物体中,两个关键蛋白是重组酶RAD51和DMC1。重组酶调节剂HOP2和MND1协助RAD51和DMC1,并且也是突触和CO所必需的。我们研究了拟南芥在减数分裂和有丝分裂分离阶段的HOP2 -1表型。尽管在I前期普遍缺乏突触,但我们观察到二倍体hop2-1核在第一次和第二次减数分裂中非同源染色体之间广泛而稳定的相互连接。利用γ - h2ax作为未修复dsb的标记,我们检测到γ - h2ax在瘦素期到粗素期早期都有灶,但在粗素期中期以后没有灶。我们得出结论,从中期I开始看到的桥是由于dsb修复不当,而不是未修复的。通过对单倍体的检测,我们发现野生型单倍体只产生单价体,而hop2-1单倍体和hop2-1二倍体一样,在分离过程中具有足够稳定的非法连接,可以产生桥接染色体。我们的研究结果表明,HOP2在减数分裂期间防止使用非同源染色体的修复中具有重要的积极作用。我们还发现证据表明,HOP2在防止辐射诱导的快速分裂花瓣细胞dsb的不正当修复中起作用。我们得出结论,HOP2在拟南芥中既可以促进突触,又可以防止DSB通过非同源染色体进行修复。意义声明:减数分裂过程中同源重组(HR)的保真度对于产生活配子和维持营养细胞基因组完整性至关重要。HOP2是确定植物减数分裂HR的重要蛋白。我们已经发现了HOP2 -1突变体在减数分裂期间和辐照花瓣细胞中非同源染色体之间高水平的非法修复的证据,这表明HOP2的作用超出了其在突触和杂交中的既定作用。
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引用次数: 3
2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions. 拟南芥细胞核的二维形态分析揭示了不同细胞类型和接入的特征。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-01 Epub Date: 2021-10-19 DOI: 10.1007/s10577-021-09673-2
Penka Pavlova, Martijn van Zanten, Basten L Snoek, Hans de Jong, Paul Fransz

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.

细胞在发育开关和环境提示下的功能变化通常反映在核表型上,显示出与转录变化相对应的独特的染色质状态。这种特征的核形状已经在显微镜下监测,并可以在常染色质和异染色质结构域的差异染色后定量。在这里,我们使用标准的二维荧光显微镜检查了与基因和转座子元件(TEs)的空间分布有关的几个核参数(大小、DNA含量、DNA密度、染色质压实度、相对异染色质分数(RHF)和色中心数量)。我们提供了不同细胞类型和不同加入量的拟南芥的核谱。除了保护细胞外,在所有细胞类型的色中心外都发现了一个可变但重要的te部分。后一种细胞类型的细胞核具有最高水平的染色质压实,而它们的色中心似乎包含基因丰富的区域。其中,Cvi的相关系数最高,而Ler的相关系数较低。这可能表明在不同的品种间表型稳健性存在差异。w和Cvi的NOR色中心的显著高相关性与它们的低RHF水平相对应。
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引用次数: 6
Correction to: 2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions. 校正:拟南芥细胞核的二维形态分析揭示了不同细胞类型和加入的特征概况。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-01 DOI: 10.1007/s10577-021-09677-y
Penka Pavlova, Martijn van Zanten, Basten L Snoek, Hans de Jong, Paul Fransz
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引用次数: 0
Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. 厚柱头菟丝子亚属核型不对称反映了其重复DNA组成。
IF 2.6 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-03-01 Epub Date: 2022-01-28 DOI: 10.1007/s10577-021-09683-0
Amalia Ibiapino, Mariana Báez, Miguel A García, Mihai Costea, Saša Stefanović, Andrea Pedrosa-Harand

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.

菟丝子是一个细胞遗传学多样化的属,其核型在染色体数目上变化18倍,在基因组大小上变化127倍。其四个亚属中的每一个亚属也表现出特定的染色体特征,例如厚柱头的双峰核型。为了了解双峰核型的起源,我们对粗柱头亚属(Cuscuta nitida)的基因组进行了低覆盖率测序,并对三个亚属代表进行了染色体显带和分子细胞遗传学分析。nitida、C. africana (2n = 28)和C. angulata (2n = 30)在最大的染色体对上均显示异色带。在黑螺旋藻基因组中鉴定出18个卫星dna,其中2个与移动元件相似。最丰富的存在于最大的对,以及高度丰富的核糖体dna。最丰富的Ty1/Copia和Ty3/Gypsy元素也高度富集在最大的对上,除了Ty3/Gypsy CRM,它也标记了最小染色体的中心点周围区域。这种大对重复DNA的积累表明,这些序列在很大程度上负责在肿柱头亚属的双峰核型的形成。重复DNA片段与库斯库塔的核型进化直接相关。
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引用次数: 5
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Chromosome Research
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