ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference inArabidopsis

During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8–cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8–cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly,asy1/+heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases inasy1/+occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal inasy1/+, it is undetectable inasy1mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.

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Interplay between Pds5 and Rec8 in regulating chromosome axis length and crossover frequency

Science Advances ◽

10.1126/sciadv.abe7920 ◽

2021 ◽

Vol 7 (11) ◽

pp. eabe7920

Author(s):

Meihui Song ◽

Binyuan Zhai ◽

Xiao Yang ◽

Taicong Tan ◽

Ying Wang ◽

...

Keyword(s):

Recombination Frequency ◽

Crossover Frequency ◽

Wild Type ◽

Protein Levels ◽

Homolog Pairing ◽

Meiotic Chromosomes ◽

Homologous Chromosome Pairing ◽

Axis Length ◽

Chromosome Axis

Meiotic chromosomes have a loop/axis architecture, with axis length determining crossover frequency. Meiosis-specific Pds5 depletion mutants have shorter chromosome axes and lower homologous chromosome pairing and recombination frequency. However, it is poorly understood how Pds5 coordinately regulates these processes. In this study, we show that only ~20% of wild-type level of Pds5 is required for homolog pairing and that higher levels of Pds5 dosage-dependently regulate axis length and crossover frequency. Moderate changes in Pds5 protein levels do not explicitly impair the basic recombination process. Further investigations show that Pds5 does not regulate chromosome axes by altering Rec8 abundance. Conversely, Rec8 regulates chromosome axis length by modulating Pds5. These findings highlight the important role of Pds5 in regulating meiosis and its relationship with Rec8 to regulate chromosome axis length and crossover frequency with implications for evolutionary adaptation.

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LOCALIZED CONVERSION IN STREPTOCOCCUS PNEUMONIAE RECOMBINATION: HETERODUPLEX PREFERENCE

Genetics ◽

10.1093/genetics/110.4.557 ◽

1985 ◽

Vol 110 (4) ◽

pp. 557-568

Author(s):

Michel Sicard ◽

Jean-Claude Lefevre ◽

Pezechpour Mostachfi ◽

Anne-Marie Gasc ◽

Claudine Sarda

Keyword(s):

Recombination Frequency ◽

Point Mutations ◽

Repair System ◽

Wild Type ◽

Base Pairs ◽

Present Evidence ◽

Conversion System ◽

Mismatch Repair System ◽

Dna Strands

ABSTRACT In pneumococcal transformation the frequency of recombinants between point mutations is generally proportional to distance. We have recently described an aberrant marker in the amiA locus that appeared to enhance recombination frequency when crossed with any other allele of this gene. The hyperrecombination that we have observed in two-point crosses could be explained by two hypotheses: the aberrant marker induces frequent crossovers in its vicinity or the mutant is converted to wild type. In this report we present evidence showing that, in suitable three-point crosses, this hyperrecombination does not modify the recombination frequency between outside markers, suggesting that a conversion occurs at the site of this mutation. To estimate the length over which this event occurs, we isolated very closely linked markers and used them in two-point crosses. It appears that the conversion system removes only a few base pairs (from three to 27) around the aberrant marker. This conversion process is quite different from the mismatch-repair system controlled by hex genes in pneumococcus, which involves several thousand base pairs. Moreover, we have constructed artificial heteroduplexes using separated DNA strands. It appears that only one of the two heteroduplexes is specifically converted. The conversion system acts upon 5′..ATTAAT..3′/3′..TAAGTA..5′. A possible role of the palindrome resulting from the mutation is discussed.

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Regulation of Msh4-Msh5 association with meiotic chromosomes in budding yeast

Genetics ◽

10.1093/genetics/iyab102 ◽

2021 ◽

Author(s):

Krishnaprasad G Nandanan ◽

Sagar Salim ◽

Ajith V Pankajam ◽

Miki Shinohara ◽

Gen Lin ◽

...

Keyword(s):

Binding Sites ◽

Holliday Junction ◽

Crossing Over ◽

Wild Type ◽

Yeast Saccharomyces Cerevisiae ◽

Meiotic Chromosomes ◽

Genome Wide ◽

Double Holliday Junction

Abstract In the baker’s yeast Saccharomyces cerevisiae, most of the meiotic crossovers are generated through a pathway involving the highly conserved mismatch repair related Msh4-Msh5 complex. To understand the role of Msh4-Msh5 in meiotic crossing over, we determined its genome wide in vivo binding sites in meiotic cells. We show that Msh5 specifically associates with DSB hotspots, chromosome axes, and centromeres on chromosomes. A basal level of Msh5 association with these chromosomal features is observed even in the absence of DSB formation (spo11Δ mutant) at the early stages of meiosis. But efficient binding to DSB hotspots and chromosome axes requires DSB formation and resection and is enhanced by double Holliday junction structures. Msh5 binding is also correlated to DSB frequency and enhanced on small chromosomes with higher DSB and crossover density. The axis protein Red1 is required for Msh5 association with the chromosome axes and DSB hotspots but not centromeres. Although binding sites of Msh5 and other pro-crossover factors like Zip3 show extensive overlap, Msh5 associates with centromeres independent of Zip3. These results on Msh5 localization in wild type and meiotic mutants have implications for how Msh4-Msh5 works with other pro-crossover factors to ensure crossover formation.

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Aberrations of Genes Regulating NF Kappa B Pathway in B-Cell Malignant Lymphoma.

Blood ◽

10.1182/blood.v114.22.971.971 ◽

2009 ◽

Vol 114 (22) ◽

pp. 971-971

Author(s):

Motohiro Kato ◽

Masashi Sanada ◽

Itaru Kato ◽

Yasuharu Sato ◽

Junko Takita ◽

...

Keyword(s):

B Cell ◽

Malignant Lymphoma ◽

Copy Number ◽

Copy Number Alterations ◽

Wild Type ◽

Genome Wide Analysis ◽

Genome Wide ◽

B Lineage ◽

Nfκb Pathway

Abstract Abstract 971 NFκB is a tightly regulated transcription factor of lymphocyte activation, proliferation and development. Controlled activity of NF κ B signaling pathway plays critical roles in coordination of immune and inflammatory response. Constitutive NFκB activation is recognized as a key pathological feature in several subsets of B-cell malignant lymphoma, and it is well known that lymphoma frequently occurred in association with chronic inflammation. Recently, our group showed frequent inactivation of A20, a negative regulator of NF κ B, in B-lineage malignant lymphomas. However, the molecular mechanism underlying the aberrant NF κ B activation in lymphomagenesis has not fully understood. In this study, to clarify the genetic basis of the aberrant NFκB activation, we performed genome-wide analysis of copy number alterations as well as allelic imbalances of primary B-lineage lymphoma specimens using Affymetrix GeneChip 250K genomic microarray with the CNAG/AsCNAR algorithm. We also searched for possible mutations in CARD11, CYLD, IKK and TRAF family genes and IκB genes, to obtain comprehensive registry of lesions in genes regulating NFκB pathway. This study included 238 primary lymphoma samples, including 64 samples of diffuse large B-cell lymphomas (DLBCL), 52 of follicular lymphomas (FL), 35 of mantle cell lymphomas (MCL), and 87 of mucosa-associated tissue (MALT) lymphomas. Five Hodgkin lymphoma-derived cell line (KM-H2, L1236, HDLM2, RPMI1666, L540) was also analyzed. Through a genome-wide analysis, we identified that each histology type had a unique genomic signature, suggesting a distinctive underlying molecular pathogenesis for different histology types. In contrast to the fact that A20 mutation was highly associated with loss of heterozygosity at 6q23.3, mutations of CARD11 (5 cases of DLBCL, 2 cases of MALT lymphoma) and IκB family genes (2 cases of DLBCL and 1 cases of MALT lymphoma) had no association with copy number abnormality at the locus of the genes. In total, mutations and copy number alterations in genes regulating NFκB pathway were found in more than 40% of B-cell lymphomas, which underpinned the importance of aberrant NFκB activation in lymphomagenesis. To also assess the role of uncontrolled signaling of NFκB pathway in lymphomagenesis, we re-expressed wild-type A20 in two lymphoma-derived cell lines without normal functional A20 alleles (KM-H2 and L1236). In both cells, re-expression of wild-type A20 resulted in suppression of cell growth and induction of apoptosis, accompanied by down-regulation of NFκB activation. The A20-deficient KM-H2 stably generated tumors in immunodeficient mice, whereas the tumorigenicity was effectively suppressed by re-expression of A20. We further investigated the role of A20 inactivation during clonal expansion of lymphoma by competitive proliferation assays using A20-deficient lymphoma-derived cell lines with or without re-expression of A20. The proportion of A20-expressing cells gradually decreased during competitive cell culture, and A20-expressing cells outgrew control cells in NOG mice, indicating the importance of A20 inactivation in clonal evolution of lymphoma. We demonstrated that uncontrolled NFκB signaling caused by alterations of multiple genes is a common feature of B-lineage lymphomas. Considering the physiological function of NFκB activation induced upon a variety of upstream stimuli, our observations provide an intriguing insight into and the pathogenesis of lymphoma. Our study also indicated that NFκB inhibition may have a role in lymphoma therapeutics. Disclosures: No relevant conflicts of interest to declare.

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Clinical Genetics Can Solve the Pitfalls of Genome-Wide Investigations: Lesson from Mismapping a Loss-of-Function Variant in KANSL1

Genes ◽

10.3390/genes11101177 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1177

Author(s):

Stefania Bigoni ◽

Giuseppe Marangi ◽

Silvia Frangella ◽

Arianna Panfili ◽

Davide Ognibene ◽

...

Keyword(s):

Clinical Genetics ◽

Incomplete Penetrance ◽

Loss Of Function ◽

Cdna Sequencing ◽

Wild Type ◽

Exon 2 ◽

Healthy Mother ◽

Genome Wide ◽

De Vries

Massive parallel sequencing of 70 genes in a girl with a suspicion of chromatinopathy detected the (NM_015443.4:)c.985_986delTT variant in exon 2 of KANSL1, which led to a diagnostic consideration of Koolen De Vries syndrome. The same variant was present in the healthy mother, consistent with either incomplete penetrance or variant mismapping. A network of second opinion was implemented among clinical geneticists first, and a diagnosis of Koolen De Vries syndrome was considered unlikely. By MLPA, a duplication spanning exons 1-3 of KANSL1 was detected in both the mother and the daughter. On cDNA sequencing, biallelic wild type mRNA was observed. We concluded that the variant affects the noncoding duplicated gene region in our family, and we finally classified it as benign. Parallel wide genomic sequencing is increasingly the first genetic investigation in individuals with intellectual disability. The c.985_986delTT variant in KANSL1 was described both in individuals with typical KdVS and in a limited number of healthy subjects. This report highlights the role of clinical genetics to correctly classify variants and to define proper clinical and diagnostic correlations.

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TNK2/ACK1 Strengthen Influenza A Virus Infection by Blocking Viral Matrix 2 Protein(M2) into Lysosome to Degradation

10.21203/rs.3.rs-153964/v1 ◽

2021 ◽

Author(s):

Ao Zhou ◽

Xia Dong ◽

Bin Tang

Keyword(s):

Influenza Virus ◽

Virus Infection ◽

Influenza A Virus ◽

Protein Trafficking ◽

Influenza A ◽

Influenza Virus Infection ◽

Wild Type ◽

Genome Wide ◽

Mutant Cells

Abstract BackgroundTNK2/ACK1, a non-receptor tyrosine kinase, plays critical roles in signalling transduces and trafficking. Our previous genome-wide CRISPR/CAS9 knockout screen revealed that mutant of TNK2 produced more restrict to influenza virus infection. In this study, we aim to illustrate the role of TNK2 for influenza A virus (IAV) replication in human cells.ResultsCRISPR/Cas9-mediated mutant of TNK2 resulted in a significant reduction in viral proteins expression and viral titres for multiple influenza strains, and furthermore, a decrease of nuclear import of IAV in the infected TNK2 mutant cells was observed in 3h post-infection. Interestingly, TNK2 mutation enhanced the colocalization of LC3 with autophagic receptor p62 and led to the attenuation of influenza virus-caused accumulation of autophagosomes in TNK2 mutant cells. Further, confocal microscopy visualization result showed that influenza viral matrix 2 (M2) was colocalized with Lamp1 in the infected TNK2 mutant cells in early infection, while almost no colocalization between M2 and Lamp1 was observed in IAV-infected wild-type cells. Moreover, TNK2 depletion also affected the trafficking of early endosome and the movement of influenza viral NP and M2.ConclusionsOur results identified TNK2 as a critical host factor for influenza viral M2 protein trafficking, suggesting that TNK2 will be an attractive target for the development of antivirals therapeutics.

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Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

10.21203/rs.3.rs-29695/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Mohammad Aslam ◽

Kenji Sugita ◽

Yuan Qin ◽

Abidur Rahman

Keyword(s):

Stress Response ◽

Cold Stress ◽

Expression Analysis ◽

Stress Responses ◽

Auxin Signaling ◽

Potential Candidate ◽

Wild Type ◽

Gene Expressions ◽

Genome Wide

Abstract The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation deep sequencing revealed 180 known and 86 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26nt-31nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows differential expression of 13 miRNAs in slr1 compared with wild-type. Target gene expression analysis of one of the potential candidate miRNAs, miR169 revelaed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin

Scientific Reports ◽

10.1038/s41598-020-63209-y ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Wenbo Dong ◽

Eriko Oya ◽

Yasaman Zahedi ◽

Punit Prasad ◽

J. Peter Svensson ◽

...

Keyword(s):

Constitutive Heterochromatin ◽

Genomic Stability ◽

Wild Type ◽

Key Factors ◽

Facultative Heterochromatin ◽

Heterochromatin Formation ◽

Aaa Atpase ◽

Genome Wide ◽

Heterochromatin Silencing

AbstractHeterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.

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Structural basis of Stu2 recruitment to yeast kinetochores

eLife ◽

10.7554/elife.65389 ◽

2021 ◽

Vol 10 ◽

Author(s):

Jacob A Zahm ◽

Michael G Stewart ◽

Joseph S Carrier ◽

Stephen C Harrison ◽

Matthew P Miller

Keyword(s):

Cell Cycle Progression ◽

Terminal Segment ◽

Structural Basis ◽

Wild Type ◽

Cycle Progression ◽

Delay Cell ◽

Sister Chromatids

Chromosome segregation during cell division requires engagement of kinetochores of sister chromatids with microtubules emanating from opposite poles. As the corresponding microtubules shorten, these ‘bioriented’ sister kinetochores experience tension-dependent stabilization of microtubule attachments. The yeast XMAP215 family member and microtubule polymerase, Stu2, associates with kinetochores and contributes to tension-dependent stabilization in vitro. We show here that a C-terminal segment of Stu2 binds the four-way junction of the Ndc80 complex (Ndc80c) and that residues conserved both in yeast Stu2 orthologs and in their metazoan counterparts make specific contacts with Ndc80 and Spc24. Mutations that perturb this interaction prevent association of Stu2 with kinetochores, impair cell viability, produce biorientation defects, and delay cell cycle progression. Ectopic tethering of the mutant Stu2 species to the Ndc80c junction restores wild-type function in vivo. These findings show that the role of Stu2 in tension-sensing depends on its association with kinetochores by binding with Ndc80c.

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Differential Role of Components of the Fibrinolytic System in the Formation and Removal of Thrombus Induced by Endothelial Injury

Thrombosis and Haemostasis ◽

10.1055/s-0037-1614532 ◽

1999 ◽

Vol 81 (04) ◽

pp. 601-604 ◽

Cited By ~ 55

Author(s):

Hiroyuki Matsuno ◽

Osamu Kozawa ◽

Masayuki Niwa ◽

Shigeru Ueshima ◽

Osamu Matsuo ◽

...

Keyword(s):

Plasminogen Activator ◽

Thrombus Formation ◽

Endothelial Injury ◽

Fibrinolytic System ◽

Tissue Type ◽

Clot Lysis ◽

Wild Type ◽

Type Plasminogen Activator ◽

Pai 1

SummaryThe role of fibrinolytic system components in thrombus formation and removal in vivo was investigated in groups of six mice deficient in urokinase-type plasminogen activator (u-PA), tissue-type plasminogen activator (t-PA), or plasminogen activator inhibitor-1 (PAI-1) (u-PA-/-, t-PA-/- or PAI-1-/-, respectively) or of their wild type controls (u-PA+/+, t-PA+/+ or PAI-1+/+). Thrombus was induced in the murine carotid artery by endothelial injury using the photochemical reaction between rose bengal and green light (540 nm). Blood flow was continuously monitored for 90 min on day 0 and for 20 min on days 1, 2 and 3. The times to occlusion after the initiation of endothelial injury in u-PA+/+, t-PA+/+ or PAI-1+/+ mice were 9.4 ± 1.3, 9.8 ± 1.1 or 9.7 ± 1.6 min, respectively. u-PA-/- and t-PA-/- mice were indistinguishable from controls, whereas that of PAI-1-/- mice were significantly prolonged (18.4 ± 3.7 min). Occlusion persisted for the initial 90 min observation period in 10 of 18 wild type mice and was followed by cyclic reflow and reocclusion in the remaining 8 mice. At day 1, persistent occlusion was observed in 1 wild type mouse, 8 mice had cyclic reflow and reocclusion and 9 mice had persistent reflow. At day 2, all injured arteries had persistent reflow. Persistent occlusion for 90 min on day 0 was observed in 3 u-PA-/-, in all t-PA-/- mice at day 1 and in 2 of the t-PA-/-mice at day 2 (p <0.01 versus wild type mice). Persistent patency was observed in all PAI-1-/- mice at day 1 and in 5 of the 6 u-PA-/- mice at day 2 (both p <0.05 versus wild type mice). In conclusion, t-PA increases the rate of clot lysis after endothelial injury, PAI-1 reduces the time to occlusion and delays clot lysis, whereas u-PA has little effect on thrombus formation and spontaneous lysis.

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