1
|
Zhang T, Chien RC, Budachetri K, Lin M, Boyaka P, Huang W, Rikihisa Y. Ehrlichia effector TRP120 manipulates bacteremia to facilitate tick acquisition. mBio 2024; 15:e0047624. [PMID: 38501870 PMCID: PMC11005420 DOI: 10.1128/mbio.00476-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
Ehrlichia species are obligatory intracellular bacteria that cause a potentially fatal disease, human ehrlichiosis. The biomolecular mechanisms of tick acquisition of Ehrlichia and transmission between ticks and mammals are poorly understood. Ehrlichia japonica infection of mice recapitulates the full spectrum of human ehrlichiosis. We compared the pathogenicity and host acquisition of wild-type E. japonica with an isogenic transposon mutant of E. japonica that lacks tandem repeat protein 120 (TRP120) (ΔTRP120). Both wild-type and ΔTRP120 E. japonica proliferated similarly in cultures of mammalian and tick cells. Upon inoculation into mice, both wild-type and ΔTRP120 E. japonica multiplied to high levels in various tissues, with similar clinical chemistry and hematologic changes, proinflammatory cytokine induction, and fatal disease. However, the blood levels of ΔTRP120 E. japonica were almost undetectable within 24 h, whereas the levels of the wild type increased exponentially. Greater than 90% of TRP120 was released from infected cells into the culture medium. Mouse blood monocytes exposed to native TRP120 from culture supernatants showed significantly reduced cell surface expression of the transmigration-related markers Ly6C and CD11b. Larval ticks attached to mice infected with either wild-type or ΔTRP120 E. japonica imbibed similar amounts of blood and subsequently molted to nymphs at similar rates. However, unlike wild-type E. japonica, the ΔTRP120 mutant was minimally acquired by larval ticks and subsequent molted nymphs and, thus, failed to transmit to naïve mice. Thus, TRP120 is required for bacteremia but not disease. These findings suggest a novel mechanism whereby an obligatory intracellular bacterium manipulates infected blood monocytes to sustain the tick-mammal transmission cycle. IMPORTANCE Effective prevention of tick-borne diseases such as human ehrlichiosis requires an understanding of how disease-causing organisms are acquired. Ehrlichia species are intracellular bacteria that require infection of both mammals and ticks, involving cycles of transmission between them. Mouse models of ehrlichiosis and tick-mouse transmission can advance our fundamental understanding of the pathogenesis and prevention of ehrlichiosis. Herein, a mutant of Ehrlichia japonica was used to investigate the role of a single Ehrlichia factor, named tandem repeat protein 120 (TRP120), in infection of mammalian and tick cells in culture, infection and disease progression in mice, and tick acquisition of E. japonica from infected mice. Our results suggest that TRP120 is necessary only for Ehrlichia proliferation in circulating mouse blood and ongoing bacteremia to permit Ehrlichia acquisition by ticks. This study provides new insights into the importance of bacterial factors in regulating bacteremia, which may facilitate tick acquisition of pathogens.
Collapse
Affiliation(s)
- Tsian Zhang
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Rory C. Chien
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Khemraj Budachetri
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Mingqun Lin
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Prosper Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Weiyan Huang
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Yasuko Rikihisa
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
2
|
Naish M, Henderson IR. The structure, function, and evolution of plant centromeres. Genome Res 2024; 34:161-178. [PMID: 38485193 PMCID: PMC10984392 DOI: 10.1101/gr.278409.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.
Collapse
Affiliation(s)
- Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| |
Collapse
|
3
|
Fornaini NR, Černohorská H, do Vale Martins L, Knytl M. Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution. Genome Biol Evol 2024; 16:evae028. [PMID: 38340334 DOI: 10.1093/gbe/evae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.
Collapse
Affiliation(s)
- Nicola R Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Halina Černohorská
- Genetics and Reproductive Biotechnologies, CEITEC-Veterinary Research Institute, Brno 62100, Czech Republic
| | | | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
- Department of Biology, McMaster University, Hamilton, Ontario L8S4K1, Canada
| |
Collapse
|
4
|
Holt JM, Saunders CT, Rowell WJ, Kronenberg Z, Wenger AM, Eberle M. HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics 2024; 40:btae042. [PMID: 38269623 PMCID: PMC10868326 DOI: 10.1093/bioinformatics/btae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
MOTIVATION In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased. RESULTS We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. AVAILABILITY AND IMPLEMENTATION HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.
Collapse
Affiliation(s)
- James M Holt
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | | | - William J Rowell
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Zev Kronenberg
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Aaron M Wenger
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Michael Eberle
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| |
Collapse
|
5
|
Fazal S, Danzi MC, Xu I, Kobren SN, Sunyaev S, Reuter C, Marwaha S, Wheeler M, Dolzhenko E, Lucas F, Wuchty S, Tekin M, Züchner S, Aguiar-Pulido V. RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci. Genome Biol 2024; 25:39. [PMID: 38297326 PMCID: PMC10832122 DOI: 10.1186/s13059-024-03171-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.
Collapse
Affiliation(s)
- Sarah Fazal
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Isaac Xu
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | | | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02155, USA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Francesca Lucas
- Department of Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA
- Deptartment of Biology, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building (BRB), Miami, FL, 33136, USA.
| | | |
Collapse
|
6
|
Yigit S, Nursal AF, Keskin A, Kaya S, Kuruca N, Sezer O. Association of MIF-173G/C, IL-4 VNTR, and IL-1RA VNTR variants with FMF-related amyloidosis in a Turkish cohort. J Investig Med 2024; 72:17-25. [PMID: 37803493 DOI: 10.1177/10815589231207789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
The most important complication of familial Mediterranean fever (FMF) is secondary amyloidosis. The aim of this study is to investigate the risk of developing FMF-related amyloidosis with macrophage migration inhibitory factor (MIF), interleukin 4 (IL-4), and IL-1 receptor antagonist (IL-1RA) variants. This study included 62 FMF patients with amyloidosis, 110 FMF patients without amyloidosis, and 120 controls. The clinical information of the patient groups was compared. MIF-173G/C, IL-4 variant number tandem repeat (VNTR), and IL-1RA VNTR variants were analyzed for all participants. The use of colchicine, pleurisy, and appendectomy was more common in FMF patients with amyloidosis than in FMF patients without amyloidosis. MIF-173G/C C/C genotype and C allele were higher in both patient groups compared to controls. IL-1RA VNTR A1/A2 and A1/A4 genotypes and A1-A4 alleles were more common in both patient groups than controls. The IL-4 VNTR P1 allele was more common in FMF patients with amyloidosis compared to controls. The MIF-173G/C allele and the IL-1RA VNTR A1-A4 allele are associated with FMF in the Turkish population but not with amyloidosis risk in FMF patients. The IL-4 VNTR P1 allele is more common in FMF patients with amyloidosis than in healthy individuals.
Collapse
Affiliation(s)
- Serbulent Yigit
- Department of Genetics, Faculty of Veterinary, Ondokuz Mayis University, Samsun, Turkey
| | - Ayse Feyda Nursal
- Department of Medical Genetics, Faculty of Medicine, Hitit University, Corum, Turkey
| | - Adem Keskin
- Department of Biochemistry (Medicine), Institute of Health Sciences, Aydın Adnan Menderes University, Aydin, Turkey
| | - Suheyla Kaya
- Department of Internal Medicine, Faculty of Medicine, Gaziosmanpasa University, Tokat, Turkey
| | - Nilufer Kuruca
- Department of Pathology, Faculty of Veterinary, Ondokuz Mayıs University, Samsun, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Faculty of Medicine, Samsun University, Turkey
| |
Collapse
|
7
|
Read JL, Davies KC, Thompson GC, Delatycki MB, Lockhart PJ. Challenges facing repeat expansion identification, characterisation, and the pathway to discovery. Emerg Top Life Sci 2023; 7:339-348. [PMID: 37888797 PMCID: PMC10754332 DOI: 10.1042/etls20230019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Tandem repeat DNA sequences constitute a significant proportion of the human genome. While previously considered to be functionally inert, these sequences are now broadly accepted as important contributors to genetic diversity. However, the polymorphic nature of these sequences can lead to expansion beyond a gene-specific threshold, causing disease. More than 50 pathogenic repeat expansions have been identified to date, many of which have been discovered in the last decade as a result of advances in sequencing technologies and associated bioinformatic tools. Commonly utilised diagnostic platforms including Sanger sequencing, capillary array electrophoresis, and Southern blot are generally low throughput and are often unable to accurately determine repeat size, composition, and epigenetic signature, which are important when characterising repeat expansions. The rapid advances in bioinformatic tools designed specifically to interrogate short-read sequencing and the development of long-read single molecule sequencing is enabling a new generation of high throughput testing for repeat expansion disorders. In this review, we discuss some of the challenges surrounding the identification and characterisation of disease-causing repeat expansions and the technological advances that are poised to translate the promise of genomic medicine to individuals and families affected by these disorders.
Collapse
Affiliation(s)
- Justin L Read
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Genevieve C Thompson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| |
Collapse
|
8
|
Gao J, Sun W, Li J, Ban H, Zhang T, Liao J, Kim N, Lee SH, Dong Q, Madramootoo R, Chen Y, Li F. Rex1BD and the 14-3-3 protein control heterochromatin organization at tandem repeats by linking RNAi and HDAC. Proc Natl Acad Sci U S A 2023; 120:e2309359120. [PMID: 38048463 PMCID: PMC10723143 DOI: 10.1073/pnas.2309359120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
Tandem DNA repeats are often organized into heterochromatin that is crucial for genome organization and stability. Recent studies revealed that individual repeats within tandem DNA repeats can behave very differently. How DNA repeats are assembled into distinct heterochromatin structures remains poorly understood. Here, we developed a genome-wide genetic screen using a reporter gene at different units in a repeat array. This screen led to identification of a conserved protein Rex1BD required for heterochromatin silencing. Our structural analysis revealed that Rex1BD forms a four-helix bundle structure with a distinct charged electrostatic surface. Mechanistically, Rex1BD facilitates the recruitment of Clr6 histone deacetylase (HDAC) by interacting with histones. Interestingly, Rex1BD also interacts with the 14-3-3 protein Rad25, which is responsible for recruiting the RITS (RNA-induced transcriptional silencing) complex to DNA repeats. Our results suggest that coordinated action of Rex1BD and Rad25 mediates formation of distinct heterochromatin structure at DNA repeats via linking RNAi and HDAC pathways.
Collapse
Affiliation(s)
- Jinxin Gao
- Department of Biology, New York University, New York, NY10003
| | - Wenqi Sun
- Key Laboratory of Epigenetic Regulation and Intervention, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Jie Li
- National Facility for Protein Science Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai201210, China
| | - Hyoju Ban
- Department of Biology, New York University, New York, NY10003
| | - Tuokai Zhang
- Department of Biology, New York University, New York, NY10003
| | - Junwei Liao
- Department of Biology, New York University, New York, NY10003
| | - Namho Kim
- Department of Biology, New York University, New York, NY10003
| | - Soon Hoo Lee
- Department of Biology, New York University, New York, NY10003
| | - Qianhua Dong
- Department of Biology, New York University, New York, NY10003
| | | | - Yong Chen
- Key Laboratory of Epigenetic Regulation and Intervention, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Fei Li
- Department of Biology, New York University, New York, NY10003
| |
Collapse
|
9
|
Zhao ZH, Zhang CX, Li J, Zhang AZ, Zhao FF, Yu GP, Jiang N. Effect of tandem repeats of antimicrobial peptide CC34 on production of target proteins and activity of Pichia pastoris. Protein Expr Purif 2023; 212:106342. [PMID: 37536580 DOI: 10.1016/j.pep.2023.106342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Antimicrobial peptides (AMPs) are attracting attention in the fields of medicine, food, and agriculture because of their broad-spectrum antibacterial properties, low resistance, and low-residue in the body. However, the low yield and instability of the prepared AMP drugs limit their application. In this study, we designed a tetramer of the AMP CC34, constructed and transfected two recombinant expression vectors with pGAPZαA containing a haploid CC34 and tetraploid CC34 (CC34-4js) into Pichia pastoris to explore the effect of biosynthesized peptides. The results showed that CC34 and CC34-4js expression levels were 648.2 and 1105.3 mg/L, respectively, in the fermentation supernatant of P. pastoris. The CC34-4js tetramer showed no antibacterial activity, could be cleaved to the monomer using formic acid, and the hemolytic rate of the polyploid was slightly lower than that of monomeric CC34. The average daily gain, average daily feed intake, feed conversion ratio and immune organ index of rats fed CC34 and CC34-4js showed no differences. In conclusion, CC34-4js exhibited a higher yield and lower hemolysis in P. pastoris than those of CC34. Finally, CC34 and CC34-4js enterokinase lysates showed similar antibacterial activity and both expressed peptides potentially improved the growth performance and organ indices of rats.
Collapse
Affiliation(s)
- Zi-Han Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China
| | - Chen-Xue Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China
| | - Jun Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China
| | - Ai-Zhong Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China
| | - Fang-Fang Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China
| | - Guo-Ping Yu
- Food Science College of Northeast Agricultural University, Harbin, 150030, China.
| | - Ning Jiang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Key Laboratory of Feed Resource Efficient Utilization and Nutrition Manipulation in Cold Region of Heilongjiang Province, Daqing, 163319, China.
| |
Collapse
|
10
|
Buni D, Kovács ÁB, Földi D, Bányai K, Bali K, Domán M, Wehmann E, Bradbury J, Bottinelli M, Catania S, Stefani E, Lysnyansky I, Kovács L, Grózner D, Gyuranecz M, Kreizinger Z. Development of molecular assays for the analysis of genetic relationships of Mycoplasma iowae. Vet Microbiol 2023; 287:109909. [PMID: 37925876 DOI: 10.1016/j.vetmic.2023.109909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Mycoplasma iowae is a worldwide spread and economically important avian pathogen that mostly infects turkeys. Currently, multi-locus sequence typing (MLST) serves as the gold standard method for strain identification in M. iowae. However, additional robust genotyping methods are required to effectively monitor M. iowae infections and conduct epidemiological investigations. The first aim of this study was to develop genotyping assays with high resolution, that specifically target M. iowae, namely a multiple-locus variable number of tandem-repeats analysis (MLVA) and a core genome multi-locus sequence typing (cgMLST) schema. The second aim was the determination of relationships among a diverse selection of M. iowae strains and clinical isolates with a previous and the newly developed assays. The MLVA was designed based on the analyses of tandem-repeat (TR) regions in the six serotype reference strains (I, J, K, N, Q and R). The cgMLST schema was developed based on the coding sequences (CDSs) common in 95% of the examined 99 isolates. The samples were submitted for a previously published MLST assay for comparison with the developed methods. Out of 94 TR regions identified, 17 alleles were selected for further evaluation by PCR. Finally, seven alleles were chosen to establish the MLVA assay. Additionally, whole genome sequence analyses identified a total of 676 CDSs shared by 95% of the isolates, all of which were included into the developed cgMLST schema. The MLVA discriminated 19 distinct genotypes (GT), while with the cgMLST assay 79 sequence types (ST) could be determined with Simpson's diversity indices of 0.810 (MLVA) and 0.989 (cgMLST). The applied assays consistently identified the same main clusters among the diverse selection of isolates, thereby demonstrating their suitability for various genetic analyses and their ability to yield congruent results.
Collapse
Affiliation(s)
- Dominika Buni
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary
| | - Áron Botond Kovács
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Dorottya Földi
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary; University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Marianna Domán
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Enikő Wehmann
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Janet Bradbury
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, Wirral CH64 7TE, United Kingdom
| | - Marco Bottinelli
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Salvatore Catania
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Elisabetta Stefani
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Inna Lysnyansky
- Department of Avian Diseases, Kimron Veterinary Institute, Beit Dagan, Israel
| | - László Kovács
- University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary; Poultry-Care Kft., Lehel út 21., Újszász 5052, Hungary
| | - Dénes Grózner
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary
| | - Miklós Gyuranecz
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary; University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary; MolliScience Kft., Március 15. utca 1, Biatorbágy 2051, Hungary
| | - Zsuzsa Kreizinger
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; MolliScience Kft., Március 15. utca 1, Biatorbágy 2051, Hungary.
| |
Collapse
|
11
|
Bapat AR, Moran Lauter AN, Hufford MB, Boerman NA, Scott MP. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events. G3 (Bethesda) 2023; 13:jkad196. [PMID: 37652030 PMCID: PMC10627281 DOI: 10.1093/g3journal/jkad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1-S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat sequences related to ZmPme3 and ZmGa1P. This haplotype can cross-pollinate freely and is widely present in field corn. The primary objective of this study is to characterize the repeat sequences from a diverse collection of maize and teosinte lines and use this information to understand the evolution of the Ga1 locus. First, we characterized the complexity of the Ga1 genome region in high-quality maize genome assemblies that led to their categorization into 5 groups based on the number and type of PME-like sequences found at this region. Second, we studied duplication events that led to the ga1 and Ga1-S repeats using maximum likelihood phylogenetic reconstruction. Divergence estimates of the ga1 haplotype suggest that the duplication events occurred more than 600 KYA whereas those in Ga1-S occurred at 3 time points, i.e. >600, ∼260, and ∼100 KYA. These estimates suggest that the ga1 and Ga1-S tandem duplication events occurred independently. Finally, analysis of ZmPme3 and ZmGa1P homologs in Zea and Tripsacum genomes suggests that ga1 and Ga1-S repeats originated from an ancestral pair of PME genes that duplicated and diverged through 2 evolutionary branches prior to the domestication of maize.
Collapse
Affiliation(s)
- Amruta R Bapat
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | | | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - M Paul Scott
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| |
Collapse
|
12
|
Ziaei Jam H, Li Y, DeVito R, Mousavi N, Ma N, Lujumba I, Adam Y, Maksimov M, Huang B, Dolzhenko E, Qiu Y, Kakembo FE, Joseph H, Onyido B, Adeyemi J, Bakhtiari M, Park J, Javadzadeh S, Jjingo D, Adebiyi E, Bafna V, Gymrek M. A deep population reference panel of tandem repeat variation. Nat Commun 2023; 14:6711. [PMID: 37872149 PMCID: PMC10593948 DOI: 10.1038/s41467-023-42278-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.
Collapse
Affiliation(s)
- Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Yang Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ross DeVito
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Nima Mousavi
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Nichole Ma
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ibra Lujumba
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Mikhail Maksimov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Bonnie Huang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Yunjiang Qiu
- Illumina Incorporated, San Diego, CA, 92122, USA
| | - Fredrick Elishama Kakembo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Habi Joseph
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Blessing Onyido
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Jumoke Adeyemi
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Mehrdad Bakhtiari
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sara Javadzadeh
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daudi Jjingo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Computer Science, Makerere University, Kampala, Uganda
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
Ichikawa K, Kawahara R, Asano T, Morishita S. A landscape of complex tandem repeats within individual human genomes. Nat Commun 2023; 14:5530. [PMID: 37709751 PMCID: PMC10502081 DOI: 10.1038/s41467-023-41262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Markedly expanded tandem repeats (TRs) have been correlated with ~60 diseases. TR diversity has been considered a clue toward understanding missing heritability. However, haplotype-resolved long TRs remain mostly hidden or blacked out because their complex structures (TRs composed of various units and minisatellites containing >10-bp units) make them difficult to determine accurately with existing methods. Here, using a high-precision algorithm to determine complex TR structures from long, accurate reads of PacBio HiFi, an investigation of 270 Japanese control samples yields several genome-wide findings. Approximately 322,000 TRs are difficult to impute from the surrounding single-nucleotide variants. Greater genetic divergence of TR loci is significantly correlated with more events of younger replication slippage. Complex TRs are more abundant than single-unit TRs, and a tendency for complex TRs to consist of <10-bp units and single-unit TRs to be minisatellites is statistically significant at loci with ≥500-bp TRs. Of note, 8909 loci with extended TRs (>100b longer than the mode) contain several known disease-associated TRs and are considered candidates for association with disorders. Overall, complex TRs and minisatellites are found to be abundant and diverse, even in genetically small Japanese populations, yielding insights into the landscape of long TRs.
Collapse
Affiliation(s)
- Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 277-8561, Chiba, Japan
| | - Riki Kawahara
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 277-8561, Chiba, Japan
| | - Takeshi Asano
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 277-8561, Chiba, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 277-8561, Chiba, Japan.
| |
Collapse
|
14
|
Jang J, Jung J, Lee YH, Lee S, Baik M, Kim H. Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies. Sci Data 2023; 10:560. [PMID: 37612339 PMCID: PMC10447506 DOI: 10.1038/s41597-023-02453-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations.
Collapse
Affiliation(s)
- Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Jaehoon Jung
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Sanghyun Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Myunggi Baik
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
| |
Collapse
|
15
|
Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
Collapse
Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
| |
Collapse
|
16
|
Silva BSML, Picorelli ACR, Kuhn GCS. In Silico Identification and Characterization of Satellite DNAs in 23 Drosophila Species from the Montium Group. Genes (Basel) 2023; 14:genes14020300. [PMID: 36833227 PMCID: PMC9957191 DOI: 10.3390/genes14020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Satellite DNA (satDNA) is a class of tandemly repeated non-protein coding DNA sequences which can be found in abundance in eukaryotic genomes. They can be functional, impact the genomic architecture in many ways, and their rapid evolution has consequences for species diversification. We took advantage of the recent availability of sequenced genomes from 23 Drosophila species from the montium group to study their satDNA landscape. For this purpose, we used publicly available whole-genome sequencing Illumina reads and the TAREAN (tandem repeat analyzer) pipeline. We provide the characterization of 101 non-homologous satDNA families in this group, 93 of which are described here for the first time. Their repeat units vary in size from 4 bp to 1897 bp, but most satDNAs show repeat units < 100 bp long and, among them, repeats ≤ 10 bp are the most frequent ones. The genomic contribution of the satDNAs ranges from ~1.4% to 21.6%. There is no significant correlation between satDNA content and genome sizes in the 23 species. We also found that at least one satDNA originated from an expansion of the central tandem repeats (CTRs) present inside a Helitron transposon. Finally, some satDNAs may be useful as taxonomic markers for the identification of species or subgroups within the group.
Collapse
|
17
|
Abstract
Haplotyping individual full-length transcripts can be important in diagnosis and treatment of certain genetic diseases. One set of diseases, repeat expansions of simple tandem repeat sequences are the cause of over 40 neurological disorders. In many of these conditions, expanding a polymorphic repeat beyond a given threshold has been strongly associated with disease onset and severity. Given that most repeat expansions are inherited in an autosomal dominant pattern, repeat expansion disorders are typically characterized by a heterozygous expansion locus associated with a single haplotype. Precision genetic medicines can be used to selectively target expansion-containing sequences in a haplotype-specific manner.However, repeat expansion lengths often exceed the capacity of next-generation sequencing (NGS) reads. Therefore, the accurate length and haplotype determination of repeat expansions requires special considerations and requires the development of custom methods. Here we highlight a method for targeted haplotype phasing of the HTT gene, which can be adopted for use with other full-length transcripts and in other repeat expansion disorders.
Collapse
Affiliation(s)
- Nenad Svrzikapa
- Wave Life Sciences, Cambridge, MA, USA.
- Department of Paediatrics, University of Oxford, Oxford, UK.
| | | |
Collapse
|
18
|
Wendt FR, Pathak GA, Polimanti R. Phenome-wide association study of loci harboring de novo tandem repeat mutations in UK Biobank exomes. Nat Commun 2022; 13:7682. [PMID: 36509785 PMCID: PMC9744822 DOI: 10.1038/s41467-022-35423-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
When present in coding regions, tandem repeats (TRs) may have large effects on protein structure and function contributing to health and disease. We use a family-based design to identify de novo TRs and assess their impact at the population level in 148,607 European ancestry participants from the UK Biobank. The 427 loci with de novo TR mutations are enriched for targets of microRNA-184 (21.1-fold, P = 4.30 × 10-5, FDR = 9.50 × 10-3). There are 123 TR-phenotype associations with posterior probabilities > 0.95. These relate to body structure, cognition, and cardiovascular, metabolic, psychiatric, and respiratory outcomes. We report several loci with large likely causal effects on tissue microstructure, including the FAN1-[TG]N and carotid intima-media thickness (mean thickness: beta = 5.22, P = 1.22 × 10-6, FDR = 0.004; maximum thickness: beta = 6.44, P = 1.12 × 10-6, FDR = 0.004). Two exonic repeats FNBP4-[GGT]N and BTN2A1-[CCT]N alter protein structure. In this work, we contribute clear and testable hypotheses of dose-dependent TR implications linking genetic variation and protein structure with health and disease outcomes.
Collapse
Affiliation(s)
- Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada.
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada.
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- VA CT Healthcare System, West Haven, CT, USA.
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA CT Healthcare System, West Haven, CT, USA
| |
Collapse
|
19
|
Isiktas AU, Eshov A, Yang S, Guo JU. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. Cell Rep Methods 2022; 2:100334. [PMID: 36452875 PMCID: PMC9701603 DOI: 10.1016/j.crmeth.2022.100334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
A common pathological feature of RNAs containing expanded repeat sequences is their propensity to aggregate in cells. While some repeat RNA aggregates have been shown to cause toxicity by sequestering RNA-binding proteins, the molecular mechanism of aggregation remains unclear. Here, we devised an efficient method to generate long tandem repeat DNAs de novo and applied it to systematically determine the sequence features underlying RNA aggregation. Live-cell imaging of repeat RNAs indicated that aggregation was promoted by multivalent RNA-RNA interactions via either canonical or noncanonical base pairs. While multiple runs of two consecutive base pairs were sufficient, longer runs of base pairs such as those formed by GGGGCC hexanucleotide repeats further enhanced aggregation. In summary, our study provides a unifying model for the molecular basis of repeat RNA aggregation and a generalizable approach for identifying the sequence and structural determinants underlying the distinct properties of repeat DNAs and RNAs.
Collapse
Affiliation(s)
- Atagun U. Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
20
|
Barriga FM, Tsanov KM, Ho YJ, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G, Alonso-Curbelo D, Simon J, Chaves-Perez A, Bar-Sagi D, Iacobuzio-Donahue CA, Notta F, Chaligne R, Sharma R, Pe'er D, Lowe SW. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nat Cancer 2022; 3:1367-1385. [PMID: 36344707 PMCID: PMC9701143 DOI: 10.1038/s43018-022-00443-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.
Collapse
Affiliation(s)
- Francisco M Barriga
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noor Sohail
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timour Baslan
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isabella Del Priore
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Brigita Meškauskaitė
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almudena Chaves-Perez
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ronan Chaligne
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
21
|
Malagrinò F, Fusco G, Pennacchietti V, Toto A, Nardella C, Pagano L, de Simone A, Gianni S. Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat. Protein Sci 2022; 31:e4396. [PMID: 36040267 PMCID: PMC9375522 DOI: 10.1002/pro.4396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 12/17/2022]
Abstract
PDZ domains are the most diffused protein-protein interaction modules of the human proteome and are often present in tandem repeats. An example is PDZD2, a protein characterized by the presence of six PDZ domains that undergoes a proteolytic cleavage producing sPDZD2, comprising a tandem of two PDZ domains, namely PDZ5 and PDZ6. Albeit the physiopathological importance of sPDZD2 is well-established, the interaction with endogenous ligands has been poorly characterized. To understand the determinants of the stability and function of sPDZD2, we investigated its folding pathway. Our data highlights the presence of a complex scenario involving a transiently populated folding intermediate that may be accumulated from the concurrent denaturation of both PDZ5 and PDZ6 domains. Importantly, double jump kinetic experiments allowed us to pinpoint the ability of this transient intermediate to bind the physiological ligand of sPDZD2 with increased affinity compared to the native state. In summary, our results provide an interesting example of a functionally competent misfolded intermediate, which may exert a cryptic function that is not captured from the analysis of the native state only.
Collapse
Affiliation(s)
- Francesca Malagrinò
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Giuliana Fusco
- Centre for Misfolding Diseases, Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Valeria Pennacchietti
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Angelo Toto
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Caterina Nardella
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Livia Pagano
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Alfonso de Simone
- Dipartimento di FarmaciaUniversità degli Studi di Napoli Federico IINaplesItaly
| | - Stefano Gianni
- Dipartimento di FarmaciaUniversità degli Studi di Napoli Federico IINaplesItaly
| |
Collapse
|
22
|
Jain C, Rhie A, Hansen NF, Koren S, Phillippy AM. Long-read mapping to repetitive reference sequences using Winnowmap2. Nat Methods 2022; 19:705-710. [PMID: 35365778 PMCID: PMC10510034 DOI: 10.1038/s41592-022-01457-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 03/17/2022] [Indexed: 01/10/2023]
Abstract
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
Collapse
Affiliation(s)
- Chirag Jain
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India.
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| |
Collapse
|
23
|
Belakehal F, Barth SA, Menge C, Mossadak HT, Malek N, Moser I. Evaluation of the discriminatory power of spoligotyping and 19-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat analysis (MIRU-VNTR) of Mycobacterium bovis strains isolated from cattle in Algeria. PLoS One 2022; 17:e0262390. [PMID: 35015775 PMCID: PMC8751994 DOI: 10.1371/journal.pone.0262390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/23/2021] [Indexed: 11/19/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium (M.) bovis and M. caprae is a transmissible disease of livestock, notifiable to the World Organization for Animal Health (OIE). BTB particularly affects cattle and small ruminants and can be transmitted to humans thereby posing a significant threat to veterinary and public health worldwide. M. bovis is the principal cause of bTB in Algeria. In order to better understand the route of spreading and elaborate an eradication program, isolation and characterization of mycobacteria from Algerian cattle was performed. Sixty strains belonging to the M. tuberculosis complex were analyzed by spoligotyping, thereof 42 by 19-locus-MIRU-VNTR-typing. Spoligotyping revealed 16 distinguishable patterns (Hunter-Gaston discriminatory index [HGDI] of 0.8294), with types SB0120 (n = 20) and SB0121 (n = 13) being the most frequent patterns, representing 55% of the strains. Analyses based on 19-locus-MIRU-VNTR yielded 32 different profiles, five clusters and one orphan pattern, showing higher discriminatory power (HGDI = 0.9779) than spoligotyping. Seven VNTR-loci [VNTR 577 (alias ETR C), 2163b (QU11b), 2165 (ETR A), 2461 (ETR B), 3007 (MIRU 27), 2163a (QUB11a) and 3232 (QUB 3232)] were the most discriminative loci (HGDI ˃ 0.50). In conclusion, 19-locus-MIRU-VNTR yielded more information than spoligotyping concerning molecular differentiation of strains and better supports the elucidation of transmission routes of M. bovis between Algerian cattle herds.
Collapse
Affiliation(s)
- Faïza Belakehal
- High National Veterinary School, Laboratory of Food Hygiene and Quality Insurance System, El-Alia, Oued Smar, Algeria
- * E-mail: (FB); (SAB)
| | - Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- National Reference Laboratory for Bovine Tuberculosis, at Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- * E-mail: (FB); (SAB)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
| | - Hamdi T. Mossadak
- High National Veterinary School, Laboratory of Food Hygiene and Quality Insurance System, El-Alia, Oued Smar, Algeria
| | - Naïm Malek
- Central Military Hospital, Department of Microbiology, Kouba, Algeria
| | - Irmgard Moser
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- National Reference Laboratory for Bovine Tuberculosis, at Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
| |
Collapse
|
24
|
Sepúlveda-Yáñez JH, Alvarez Saravia D, Pilzecker B, van Schouwenburg PA, van den Burg M, Veelken H, Navarrete MA, Jacobs H, Koning MT. Tandem Substitutions in Somatic Hypermutation. Front Immunol 2022; 12:807015. [PMID: 35069591 PMCID: PMC8781386 DOI: 10.3389/fimmu.2021.807015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. We investigated incidence and sequence context of tandem substitutions by massive parallel sequencing of V(D)J repertoires in healthy human donors. Mutation patterns were congruent with SHM-derived single nucleotide mutations, delineating initiation of the tandem substitution by AID. Tandem substitutions comprised 5,7% of AID-induced mutations. The majority of tandem substitutions represents single nucleotide juxtalocations of directly adjacent sequences. These observations were confirmed in an independent cohort of healthy donors. We propose a model where tandem substitutions are predominantly generated by translesion synthesis across an apyramidinic site that is typically created by UNG. During replication, apyrimidinic sites transiently adapt an extruded configuration, causing skipping of the extruded base. Consequent strand decontraction leads to the juxtalocation, after which exonucleases repair the apyramidinic site and any directly adjacent mismatched base pairs. The mismatch repair pathway appears to account for the remainder of tandem substitutions. Tandem substitutions may enhance affinity maturation and expedite the adaptive immune response by overcoming amino acid codon degeneracies or mutating two adjacent amino acid residues simultaneously.
Collapse
Affiliation(s)
- Julieta H Sepúlveda-Yáñez
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
- School of Medicine, University of Magallanes, Punta Arenas, Chile
| | | | - Bas Pilzecker
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Mirjam van den Burg
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marvyn T Koning
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
25
|
Dhatterwal P, Mehrotra S, Mehrotra R. Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana. Methods Mol Biol 2022; 2392:115-123. [PMID: 34773619 DOI: 10.1007/978-1-0716-1799-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.
Collapse
Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India.
| |
Collapse
|
26
|
Abstract
Pas2r12 is comprised of a repeat of the penetration-accelerating sequence (Pas) (Pas2: FFLIG-FFLIG) and D-form dodeca-arginine (r12), a cell-penetrating peptide. Pas2r12 significantly enhances cytosolic delivery of cargo proteins, including enhanced green fluorescent protein and immunoglobulin G. Simply incubating Pas2r12 with cargo leads to their cytosolic tranlsocation. Cytosolic delivery of cargo by Pas2r12 involves caveolae-mediated endocytosis. In this chapter, we describe methods of cytosolic delivery of cargo using Pas2r12 and provide methods for investigating the cellular uptake pathway of cargo by Pas2r12.
Collapse
Affiliation(s)
- Akiko Okuda
- Department of Medical Technology, Graduate School of Health Sciences, Niigata University, Niigata, Niigata, Japan.
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| |
Collapse
|
27
|
Rücker FG, Du L, Luck TJ, Benner A, Krzykalla J, Gathmann I, Voso MT, Amadori S, Prior TW, Brandwein JM, Appelbaum FR, Medeiros BC, Tallman MS, Savoie L, Sierra J, Pallaud C, Sanz MA, Jansen JH, Niederwieser D, Fischer T, Ehninger G, Heuser M, Ganser A, Bullinger L, Larson RA, Bloomfield CD, Stone RM, Döhner H, Thiede C, Döhner K. Molecular landscape and prognostic impact of FLT3-ITD insertion site in acute myeloid leukemia: RATIFY study results. Leukemia 2022; 36:90-99. [PMID: 34316017 PMCID: PMC8727286 DOI: 10.1038/s41375-021-01323-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022]
Abstract
In acute myeloid leukemia (AML) internal tandem duplications of the FLT3 gene (FLT3-ITD) are associated with poor prognosis. Retrospectively, we investigated the prognostic and predictive impact of FLT3-ITD insertion site (IS) in 452 patients randomized within the RATIFY trial, which evaluated midostaurin additionally to intensive chemotherapy. Next-generation sequencing identified 908 ITDs, with 643 IS in the juxtamembrane domain (JMD) and 265 IS in the tyrosine kinase domain-1 (TKD1). According to IS, patients were categorized as JMDsole (n = 251, 55%), JMD and TKD1 (JMD/TKD1; n = 117, 26%), and TKD1sole (n = 84, 19%). While clinical variables did not differ among the 3 groups, NPM1 mutation was correlated with JMDsole (P = 0.028). Overall survival (OS) differed significantly, with estimated 4-year OS probabilities of 0.44, 0.50, and 0.30 for JMDsole, JMD/TKD1, and TKD1sole, respectively (P = 0.032). Multivariate (cause-specific) Cox models for OS and cumulative incidence of relapse using allogeneic hematopoietic cell transplantation (HCT) in first complete remission as a time-dependent variable identified TKD1sole as unfavorable and HCT as favorable factors. In addition, Midostaurin exerted a significant benefit only for JMDsole. Our results confirm the distinct molecular heterogeneity of FLT3-ITD and the negative prognostic impact of TKD1 IS in AML that was not overcome by midostaurin.
Collapse
Affiliation(s)
- Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Ling Du
- Novartis Pharmaceuticals, Cambridge, MA, USA
| | - Tamara J Luck
- Department of Hematology, Oncology and Tumor Immunology, Charité University, Berlin, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | | | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Università di Roma "Tor Vergata", Rome, Italy
| | - Sergio Amadori
- Department of Biomedicine and Prevention, Università di Roma "Tor Vergata", Rome, Italy
| | - Thomas W Prior
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruno C Medeiros
- Division of Hematology, Stanford Comprehensive Cancer Center, Stanford University, Stanford, CA, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | | | - Jorge Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau and Jose Carreras Leukemia Research Institute, Autonomus University of Barcelona, Barcelona, Spain
| | | | - Miguel A Sanz
- Hospital Universitario la Fe, Hematology Department, Department of Medicine, University of Valencia, Valencia, Spain
| | - Joop H Jansen
- Radboud Institute Molecular Studies, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Thomas Fischer
- Department of Hematology and Oncology, Center of Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Gerhard Ehninger
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University, Berlin, Germany
| | - Richard A Larson
- Department of Medicine and Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Clara D Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber/Partners CancerCare, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.
| |
Collapse
|
28
|
Lemos MP, Nandi V, Dragavon J, Fleming I, Krishnan K, Musuruana M, Kramer M, Glantz H, Andrasik M, Coombs RW, McElrath MJ, Tieu HV. HIV-1 Nucleic Acids Identify Rectal HIV Exposures in Self-Collected Rectal Swabs, Whereas Y-Chromosome Single Tandem Repeat Mixtures Are Not Reliable Biomarkers of Condomless Receptive Anal Intercourse. J Acquir Immune Defic Syndr 2021; 88:138-148. [PMID: 34506358 PMCID: PMC8439546 DOI: 10.1097/qai.0000000000002748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND To focus interventions, biomarkers of HIV-1 exposure could help in identifying subpopulations at highest risk of acquisition. We assessed whether Y-chromosome single tandem repeat (YSTR) mixtures obtained from rectal swabs could serve as a biomarker of condomless receptive anal intercourse (CRAI) among men who have sex with men and transgender women and evaluated the feasibility of detecting HIV-1 virions to assess exposures. METHODS Twenty-nine sexually active HIV-seronegative men who have sex with men and one transgender woman from New York City answered on-site and mobile app sexual behavior questionnaires. They were randomized to collecting self-administered rectal swabs every morning or after receptive anal intercourse (RAI). YSTR profiles were assessed from blood sample and swabs; HIV-1 exposure was measured by conducting quantitative polymerase chain reaction in swabs. RESULTS After 2 months, the daily mobile survey had 135%-201% more instances of anal sex acts and 170%-193% more RAI than on-site surveys. Daily mobile reporting had 11%-35% less CRAI events than those reported on-site (Pdaily = 0.001; Pper-sex = 0.047). The daily swabbing arm reported less RAI (P < 0.001) and CRAI (P < 0.038) and had 2.95 lower odds of detecting YSTR mixtures (P = 0.021) than the per-sex-event arm. Surprisingly, YSTR detection was not significantly modified by report of bowel movements and lubricant, enema, or condom use. No participant became HIV-1 infected, yet HIV-1 total nucleic acids were detected in 6 independent episodes of CRAI in 2 participants taking pre-exposure prophylaxis. CONCLUSIONS YSTR mixtures demonstrated 80% specificity but only 30% sensitivity as a biomarker of CRAI in self-collected rectal swabs. However, detection of HIV-1 exposures in self-collected swabs may help in identifying those needing further HIV risk reduction strategies.
Collapse
Affiliation(s)
- Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vijay Nandi
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Joan Dragavon
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ira Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keertana Krishnan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Musuruana
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Madeline Kramer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hayley Glantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michele Andrasik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hong-Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| |
Collapse
|
29
|
Yang S, Li Y, Dai L, Wang J, He P, Li C, Fang X, Wang C, Zhao X, Huang E, Wu C, Zhong Z, Wang F, Duan X, Tian S, Wu L, Liu Y, Luo Y, Chen Z, Li F, Li J, Yu X, Ren H, Liu L, Meng S, Yan J, Hu Z, Gao L, Gao GF. Safety and immunogenicity of a recombinant tandem-repeat dimeric RBD-based protein subunit vaccine (ZF2001) against COVID-19 in adults: two randomised, double-blind, placebo-controlled, phase 1 and 2 trials. Lancet Infect Dis 2021; 21:1107-1119. [PMID: 33773111 DOI: 10.1101/2020.12.20.20248602] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Although several COVID-19 vaccines have been developed so far, they will not be sufficient to meet the global demand. Development of a wider range of vaccines, with different mechanisms of action, could help control the spread of SARS-CoV-2 globally. We developed a protein subunit vaccine against COVID-19 using a dimeric form of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein as the antigen. We aimed to assess the safety and immunogenicity of this vaccine, ZF2001, and determine the appropriate dose and schedule for an efficacy study. METHODS We did two randomised, double-blind, placebo-controlled, phase 1 and phase 2 trials. Phase 1 was done at two university hospitals in Chongqing and Beijing, China, and phase 2 was done at the Hunan Provincial Center for Disease Control and Prevention in Xiangtan, China. Healthy adults aged 18-59 years, without a history of SARS-CoV or SARS-CoV-2 infection, an RT-PCR-positive test result for SARS-CoV-2, a history of contact with confirmed or suspected COVID-19 cases, and severe allergies to any component of the vaccine were eligible for enrolment. In phase 1, participants were randomly assigned (2:2:1) to receive three doses of the vaccine (25 μg or 50 μg) or placebo intramuscularly, 30 days apart. In phase 2, participants were randomly assigned (1:1:1:1:1:1) to receive the vaccine (25 μg or 50 μg) or placebo intramuscularly, 30 days apart, in either a two-dose schedule or a three-dose schedule. Investigators, participants, and the laboratory team were masked to group allocation. For phase 1, the primary outcome was safety, measured by the occurrence of adverse events and serious adverse events. For phase 2, the primary outcome was safety and immunogenicity (the seroconversion rate and the magnitude, in geometric mean titres [GMTs], of SARS-CoV-2-neutralising antibodies). Analyses were done on an intention-to-treat and per-protocol basis. These trials are registered with ClinicalTrials.gov (NCT04445194 and NCT04466085) and participant follow-up is ongoing. FINDINGS Between June 22 and July 3, 2020, 50 participants were enrolled into the phase 1 trial and randomly assigned to receive three doses of placebo (n=10), the 25 μg vaccine (n=20), or the 50 μg vaccine (n=20). The mean age of participants was 32·6 (SD 9·4) years. Between July 12 and July 17, 2020, 900 participants were enrolled into the phase 2 trial and randomly assigned to receive two doses of placebo (n=150), 25 μg vaccine (n=150), or 50 μg vaccine (n=150), or three doses of placebo (n=150), 25 μg vaccine (n=150), or 50 μg vaccine (n=150). The mean age of participants was 43·5 (SD 9·2) years. In both phase 1 and phase 2, adverse events reported within 30 days after vaccination were mild or moderate (grade 1 or 2) in most cases (phase 1: six [60%] of ten participants in the placebo group, 14 [70%] of 20 in the 25 μg group, and 18 [90%] of 20 in the 50 μg group; phase 2: 37 [25%] of 150 in the two-dose placebo group, 43 [29%] of 150 in the two-dose 25 μg group, 50 [33%] of 150 in the two-dose 50 μg group, 47 [31%] of 150 in the three-dose placebo group, 72 [48%] of 150 in the three-dose 25 μg group, and 65 [43%] of 150 in the three-dose 50 μg group). In phase 1, two (10%) grade 3 or worse adverse events were reported in the 50 μg group. In phase 2, grade 3 or worse adverse events were reported by 18 participants (four [3%] in the two-dose 25 μg vaccine group, two [1%] in the two-dose 50 μg vaccine group, two [1%] in the three-dose placebo group, four [3%] in the three-dose 25 μg vaccine group, and six [4%] in the three-dose 50 μg vaccine group), and 11 were considered vaccine related (two [1%] in the two-dose 25 μg vaccine group, one [1%] in the two-dose 50 μg vaccine group, one [1%] in the three-dose placebo group, two [1%] in the three-dose 25 μg vaccine group, and five [3%] in the three-dose 50 μg vaccine group); seven participants reported serious adverse events (one [1%] in the two-dose 25 μg vaccine group, one [1%] in the two-dose 50 μg vaccine group, two [1%] in the three-dose placebo group, one [1%] in the three-dose 25 μg vaccine group, and two [1%] in the three-dose 50 μg vaccine group), but none was considered vaccine related. In phase 2, on the two-dose schedule, seroconversion rates of neutralising antibodies 14 days after the second dose were 76% (114 of 150 participants) in the 25 μg group and 72% (108 of 150) in the 50 μg group; on the three-dose schedule, seroconversion rates of neutralising antibodies 14 days after the third dose were 97% (143 of 148 participants) in the 25 μg group and 93% (138 of 148) in the 50 μg group. In the two-dose groups in phase 2, the SARS-CoV-2-neutralising GMTs 14 days after the second dose were 17·7 (95% CI 13·6-23·1) in the 25 μg group and 14·1 (10·8-18·3) in the 50 μg group. In the three-dose groups in phase 2, the SARS-CoV-2-neutralising GMTs 14 days after the third dose were 102·5 (95% CI 81·8-128·5) in the 25 μg group and 69·1 (53·0-90·0) in the 50 μg group. INTERPRETATION The protein subunit vaccine ZF2001 appears to be well tolerated and immunogenic. The safety and immunogenicity data from the phase 1 and 2 trials support the use of the 25 μg dose in a three-dose schedule in an ongoing phase 3 trial for large-scale evaluation of ZF2001's safety and efficacy. FUNDING National Program on Key Research Project of China, National Science and Technology Major Projects of Drug Discovery, Strategic Priority Research Program of the Chinese Academy of Sciences, and Anhui Zhifei Longcom Biopharmaceutical. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
Collapse
Affiliation(s)
- Shilong Yang
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Yan Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianfeng Wang
- National Institute for Food and Drug Control, Beijing, China
| | - Peng He
- National Institute for Food and Drug Control, Beijing, China
| | - Changgui Li
- National Institute for Food and Drug Control, Beijing, China
| | - Xin Fang
- National Institute for Food and Drug Control, Beijing, China
| | - Chenfei Wang
- National Institute for Food and Drug Control, Beijing, China
| | - Xiang Zhao
- National Institute for Food and Drug Control, Beijing, China
| | - Enqi Huang
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Changwei Wu
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Zaixin Zhong
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Fengze Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Duan
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Siyu Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lili Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- Chongqing Medleader Bio-Pharm, Chongqing, China
| | - Yi Luo
- Beijing Keytech Statistical Technology, Beijing, China
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangjun Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Junhua Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Xian Yu
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lihong Liu
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Shufang Meng
- National Institute for Food and Drug Control, Beijing, China
| | - Jinghua Yan
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhongyu Hu
- National Institute for Food and Drug Control, Beijing, China
| | - Lidong Gao
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
30
|
Nguyen LXT, Zhang B, Hoang DH, Zhao D, Wang H, Wu H, Su YL, Dong H, Rodriguez-Rodriguez S, Armstrong B, Ghoda LY, Perrotti D, Pichiorri F, Chen J, Li L, Kortylewski M, Rockne RC, Kuo YH, Khaled S, Carlesso N, Marcucci G. Cytoplasmic DROSHA and non-canonical mechanisms of MiR-155 biogenesis in FLT3-ITD acute myeloid leukemia. Leukemia 2021; 35:2285-2298. [PMID: 33589748 PMCID: PMC8973317 DOI: 10.1038/s41375-021-01166-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 01/29/2023]
Abstract
We report here on a novel pro-leukemogenic role of FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) that interferes with microRNAs (miRNAs) biogenesis in acute myeloid leukemia (AML) blasts. We showed that FLT3-ITD interferes with the canonical biogenesis of intron-hosted miRNAs such as miR-126, by phosphorylating SPRED1 protein and inhibiting the "gatekeeper" Exportin 5 (XPO5)/RAN-GTP complex that regulates the nucleus-to-cytoplasm transport of pre-miRNAs for completion of maturation into mature miRNAs. Of note, despite the blockage of "canonical" miRNA biogenesis, miR-155 remains upregulated in FLT3-ITD+ AML blasts, suggesting activation of alternative mechanisms of miRNA biogenesis that circumvent the XPO5/RAN-GTP blockage. MiR-155, a BIC-155 long noncoding (lnc) RNA-hosted oncogenic miRNA, has previously been implicated in FLT3-ITD+ AML blast hyperproliferation. We showed that FLT3-ITD upregulates miR-155 by inhibiting DDX3X, a protein implicated in the splicing of lncRNAs, via p-AKT. Inhibition of DDX3X increases unspliced BIC-155 that is then shuttled by NXF1 from the nucleus to the cytoplasm, where it is processed into mature miR-155 by cytoplasmic DROSHA, thereby bypassing the XPO5/RAN-GTP blockage via "non-canonical" mechanisms of miRNA biogenesis.
Collapse
Affiliation(s)
- Le Xuan Truong Nguyen
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
| | - Bin Zhang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dandan Zhao
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Huafeng Wang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Herman Wu
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yu-Lin Su
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Haojie Dong
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Sonia Rodriguez-Rodriguez
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Brian Armstrong
- Light Microscopy Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lucy Y Ghoda
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Danilo Perrotti
- Department of Medicine, Biochemistry and Molecular Biology and the Marlene and Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Flavia Pichiorri
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of System Biology, City of Hope Medical Center, Duarte, CA, USA
| | - Ling Li
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Russell C Rockne
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Samer Khaled
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Nadia Carlesso
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
| |
Collapse
|
31
|
Chaux-Jukic F, O'Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 2021. [PMID: 34165564 DOI: 10.1101/2021.01.29.428817)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.
Collapse
Affiliation(s)
- Frédéric Chaux-Jukic
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Samuel O'Donnell
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Olivier Vallon
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| |
Collapse
|
32
|
Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, Purugganan MD. Natural variation in plant telomere length is associated with flowering time. Plant Cell 2021; 33:1118-1134. [PMID: 33580702 PMCID: PMC8599780 DOI: 10.1093/plcell/koab022] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/14/2021] [Indexed: 05/05/2023]
Abstract
Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.
Collapse
Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Jun Yin
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Inna B Chastukhina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Alabama 35806, USA
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
- Department of Biological Sciences, College of Science, Marshall University, West Virginia 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, West Virginia 25755, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| |
Collapse
|
33
|
Baev V, Ivanova Z, Yahubyan G, Toneva V, Apostolova E, Minkov G, Minkov I. Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis. Acta Biochim Pol 2021; 68:277-286. [PMID: 33979512 DOI: 10.18388/abp.2020_5555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022]
Abstract
Haberlea rhodopensis is a paleolithic tertiary relict species that belongs to the unique group of resurrection plants sharing remarkable tolerance to desiccation. When exposed to severe drought stress, this species shows an ability to maintain structural integrity of its deactivated photosynthetic apparatus, which easily reactivates upon rehydration. In addition to its homoiochlorophyllous nature, the resurrection capability of H. rhodopensis is of particular importance to the global climate change mitigation. In this study, we sequenced, assembled, and analyzed the mitochondrial (mt) genome of H. rhodopensis for the first time. The master circle has a typical circular structure of 484 138 bp in length with a 44.1% GC content in total. The mt genome of H. rhodopensis contains 59 genes in total, including 35 protein-coding, 21 tRNAs, and 3 rRNAs genes. 7 tandem repeats and 85 simple sequence repeats (SSRs) are distributed throughout the mt genome. The alignment of 20 plant mt genomes confirms the phylogenetic position of H. rhodopensis in the Lamiales order. Our comprehensive analysis of the complete mt genome of H. rhodopensis is a significant addition to the limited database of organelle genomes of resurrection species. Comparative and phylogenetic analysis provides valuable information for a better understanding of mitochondrial molecular evolution in plants.
Collapse
Affiliation(s)
- Vesselin Baev
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria.
| | - Zdravka Ivanova
- Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria
| | - Galina Yahubyan
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Valentina Toneva
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Elena Apostolova
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Georgi Minkov
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Ivan Minkov
- 1Institute of Molecular Biology and Biotechnology, Plovdiv, Bulgaria; 2Centre of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| |
Collapse
|
34
|
Mousavi N, Margoliash J, Pusarla N, Saini S, Yanicky R, Gymrek M. TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics 2021; 37:731-733. [PMID: 32805020 PMCID: PMC8097685 DOI: 10.1093/bioinformatics/btaa736] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
SUMMARY A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers. AVAILABILITY AND IMPLEMENTATION TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Nima Mousavi
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Jonathan Margoliash
- Department of Medicine, University of California San Diego, La Jolla, 92093, USA
| | - Neha Pusarla
- Department of Bioengineering, University of California San Diego, La Jolla, 92093, USA
| | - Shubham Saini
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Richard Yanicky
- Department of Medicine, University of California San Diego, La Jolla, 92093, USA
| | - Melissa Gymrek
- Department of Medicine, University of California San Diego, La Jolla, 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, 92093, USA
| |
Collapse
|
35
|
Despot-Slade E, Mravinac B, Širca S, Castagnone-Sereno P, Plohl M, Meštrović N. The Centromere Histone Is Conserved and Associated with Tandem Repeats Sharing a Conserved 19-bp Box in the Holocentromere of Meloidogyne Nematodes. Mol Biol Evol 2021; 38:1943-1965. [PMID: 33399875 PMCID: PMC8097292 DOI: 10.1093/molbev/msaa336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although centromeres have conserved function, centromere-specific histone H3 (CenH3) and centromeric DNA evolve rapidly. The centromere drive model explains this phenomenon as a consequence of the conflict between fast-evolving DNA and CenH3, suggesting asymmetry in female meiosis as a crucial factor. We characterized evolution of the CenH3 protein in three closely related, polyploid mitotic parthenogenetic species of the Meloidogyne incognita group, and in the distantly related meiotic parthenogen Meloidogyne hapla. We identified duplication of the CenH3 gene in a putative sexual ancestral Meloidogyne. We found that one CenH3 (αCenH3) remained conserved in all extant species, including in distant Meloidogyne hapla, whereas the other evolved rapidly and under positive selection into four different CenH3 variants. This pattern of CenH3 evolution in Meloidogyne species suggests the subspecialization of CenH3s in ancestral sexual species. Immunofluorescence performed on mitotic Meloidogyne incognita revealed a dominant role of αCenH3 on its centromere, whereas the other CenH3s have lost their function in mitosis. The observed αCenH3 chromosome distribution disclosed cluster-like centromeric organization. The ChIP-Seq analysis revealed that in M. incognita αCenH3-associated DNA dominantly comprises tandem repeats, composed of divergent monomers which share a completely conserved 19-bp long box. Conserved αCenH3-associated DNA is also confirmed in the related mitotic Meloidogyne incognita group species suggesting preservation of both centromere protein and DNA constituents. We hypothesize that the absence of centromere drive in mitosis might allow for CenH3 and its associated DNA to achieve an equilibrium in which they can persist for long periods of time.
Collapse
Affiliation(s)
| | | | - Saša Širca
- Agricultural Institute Slovenia, Ljubljana, Slovenia
| | | | | | | |
Collapse
|
36
|
Yu M, Zhou S, Ding Y, Guo H, Li Y, Huang Q, Zheng X, Xiu Y. Molecular characterization and functional study of a tandem-repeat Galectin-9 from Japanese flounder (Paralichthys olivaceus). Fish Shellfish Immunol 2021; 112:23-30. [PMID: 33617959 DOI: 10.1016/j.fsi.2021.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Galectin-9 is a β-galactoside-binding lectin which could modulate a variety of biological functions including recognition, aggregation and clearance of pathogen. In this study, one Galectin-9 (named PoGalectin-9) was identified from Japanese flounder Paralichthys olivaceus. PoGalectin-9 belongs to the tandem-repeat type, containing one 127-amino acids CRD domain within N terminal and one 122-amino acids CRD domain within C-terminal. The open reading frame of PoGalectin-9 cDNA was 921 bp encoding 306 amino acids. Sequence similarity comparison confirmed that PoGalectin-9 shared high homology with other Galectin-9. The tissue distribution and expression profiles after bacterial infection were also investigated. PoGalectin-9 was widely distributed in all of the examined tissues of Japanese flounder but was predominantly expressed in the spleen, kidney and intestine. After Edwardsiella tarda challenge, the expression of PoGalectin-9 was up-regulated in spleen and down regulated in kidney. ELISA experiment showed that recombinant PoGalectin-9 (rPoGalectin-9) exhibit binding capacity to lipopolysaccharide (LPS) and peptidoglycan (PGN), which is significantly correlated with the concentration of rPoGalectin-9. Meanwhile, the rPoGalectin-9 protein showed strong agglutinating activities against both Gram-negative bacteria and Gram-positive bacteria. Bacterial binding experiments showed that rPoGalectin-9 could bind all examined bacteria. In conclusion, the present study indicate that PoGalectin-9 might play important roles during the immune responses of Japanese flounder against bacterial pathogens.
Collapse
Affiliation(s)
- Mingming Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shun Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuanyuan Ding
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huimin Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ying Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xujia Zheng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yunji Xiu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
37
|
Domínguez A. Interrogating the 5'UTR tandem repeats of retrotransposon roo of Drosophila about horizontal transfer. Genetica 2021; 149:171-177. [PMID: 33900494 DOI: 10.1007/s10709-021-00120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/13/2021] [Indexed: 11/26/2022]
Abstract
Horizontal transfer in Drosophila has been inferred for several families of transposable elements. Specifically, the retroelement roo has been suggested to have been horizontally transferred between the species D. melanogaster, D. simulans, D. sechellia and D. yakuba. The inferences were based on the observation that divergence between transposable elements in different species was lower than the divergence found in typical nuclear genes and in the incongruence of phylogenies of the species and their TEs. Here, we address the question of the possible horizontal transfer of roo between species of the Drosophila genus by studying the presence absence of a duplication of 99 bp in the 5'UTR of the transposon, as well as comparing the sequences of the paralogous and orthologous duplicated repeats within and between species. First, the repeats were only found in five species of the melanogaster subgroup. Second, the date of occurrence of the duplication event originating the repeats was posterior to the split of the subgroup. The duplication date suggests an origin previous to the split of D. simulans and D. sechellia and close to the divergence of D. melanogaster from the D. simulans complex. These data point to horizontal transfer to the afrotropical species D. yakuba and D. erecta from one of the cosmopolitan species D. melanogaster or D. simulans. We propose that the parasitoid wasp Leptopilina could have been the vector of horizontal transfer after the observation that a sequence of 845 bp with high homology to a fragment of roo was isolated from this wasp.
Collapse
Affiliation(s)
- Ana Domínguez
- Departamento de Biología Funcional, Área de Genética, Universidad de Oviedo, 33071, Oviedo, Spain.
| |
Collapse
|
38
|
Kähl S, Volke D, Fornefett J, Fingas F, Klose K, Benga L, Grunwald T, Ulrich R, Hoffmann R, Baums CG. Identification of a large repetitive RTX immunogen in a highly virulent Rodentibacter heylii strain. Microbes Infect 2021; 23:104771. [PMID: 33164813 DOI: 10.1016/j.micinf.2020.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/15/2020] [Accepted: 10/17/2020] [Indexed: 11/30/2022]
Abstract
Rodentibacter (R.) heylii is frequently detected in laboratory rodents. Repeats in toxin (RTX) toxins are considered important virulence factors of this major murine pathogen. We evaluated the virulence of a R.heylii strain negative for all known RTX toxin genes and Muribacter (M.) muris, a commensal in mice, in experimental infections of C57BL/6 and BALB/c mice. Experimental intranasal infection with 108 CFU of the pnxI-, pnxII- and pnxIII- R. heylii strain resulted in 75% and 100% mortality in C57BL/6 and BALB/c mice, respectively. In early losses, multiple internal organs were infected and purulent bronchopneumonia was the main pathology. Intranasal application of M. muris did not result in mortality or severe weight loss. Immunoproteomics led to the identification of a surface-associated and specific immunogen, which was designated as R. heylii immunogen A (RhiA) and which was exclusively recognised by sera obtained from mice infected with this R. heylii pathotype. RhiA is a 262.6 kDa large protein containing long imperfect tandem repeats and C-terminal RTX consensus sequences. Immunohistochemical analysis confirmed that this R.heylii pathotype expresses RhiA in the lower respiratory tract. In summary, this study describes a specific immunogen in a virulent R. heylii, strain which is an excellent antigen for pathotype-specific serological screenings and which might carry out RTX-related functions.
Collapse
Affiliation(s)
- Sophie Kähl
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Centre for Biotechnology and Biomedicine, University Leipzig, 04103, Leipzig, Germany
| | - Juliane Fornefett
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | | | - Kristin Klose
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | - Laurentiu Benga
- Central Unit for Animal Research and Animal Welfare Affairs, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | - Thomas Grunwald
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Centre for Biotechnology and Biomedicine, University Leipzig, 04103, Leipzig, Germany
| | - Christoph Georg Baums
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany.
| |
Collapse
|
39
|
Woolbright WC, Wong V, Severson E, Kuo DJ. The Application of Next-generation Sequencing Tumor Molecular Profiling in the Diagnosis and Management of a Case of Acute Myelogenous Leukemia With MLL-PTD in a Pediatric Heart Transplant Recipient. J Pediatr Hematol Oncol 2021; 43:e246-e249. [PMID: 32134843 DOI: 10.1097/mph.0000000000001772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/10/2020] [Indexed: 01/18/2023]
Abstract
A 6-year-old girl with a history of heart transplantation was diagnosed with myelodysplastic syndrome, which progressed to acute myelogenous leukemia. Comprehensive genomic profiling of her tumor discovered an MLL-PTD (partial tandem duplication) and she received chemotherapy and a hematopoietic stem cell transplant (HSCT). She subsequently relapsed and tumor molecular profiling was repeated, revealing 2 new potentially targetable mutations (FLT3 and IDH2). A novel treatment regimen targeting these mutations with sorafenib and azacitidine without using cytotoxic chemotherapy produced remission and she subsequently pursued a second HSCT. She remains disease-free 17 months after HSCT. This case report demonstrates how repeated tumor molecular profiling provided novel actionable information for the diagnosis and management at 2 timepoints.
Collapse
Affiliation(s)
- William C Woolbright
- Division of Pediatric Hematology-Oncology, St. Joseph's Children's Hospital, Paterson, NJ
| | - Victor Wong
- Division of Pediatric Hematology-Oncology, University of California, San Diego/Rady Children's Hospital San Diego, San Diego, CA
| | | | - Dennis J Kuo
- Division of Pediatric Hematology-Oncology, University of California, San Diego/Rady Children's Hospital San Diego, San Diego, CA
| |
Collapse
|
40
|
Sarwar S, Hasnain S. Association of variable number of tandem repeats (VNTR) and T941G polymorphism of monoamine oxidase (MAO-A) gene with aggression in Pakistani subjects. Afr Health Sci 2021; 21:180-188. [PMID: 34394296 PMCID: PMC8356572 DOI: 10.4314/ahs.v21i1.24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Human behavioral traits are known to be significantly heritable. Certain individuals have a greater tendency of negative behavioral aspects including aggression. The quest to identify tunderlying genetic causes has led to identification of a number of genetic markers, one of them is the monoamine oxidase-A (MAO-A) gene. Objective We aimed to genotype a variable number of tandem repeats (VNTRs) in the promoter region and a functional SNP within this gene (T941G, dbSNP ID: rs6323) in the recruited cohort of 482 subjects. Methods After DNA isolation, genotyping was done by PCR-RFLP and the results were confirmed by sequencing. Results For VNTRs, the results showed, highest frequency of 3.5 repeats in males and 4 repeats in females in the promoter region. The genotype frequencies for the SNP in cases were GG=16.3%, TG=20.6% and TT=63.1%, while in controls, the frequencies were GG=12.7%, TG=6.3%, and TT=81.0%. The allele frequencies were significantly different between cases and controls (p=0.015; OR=1.51; CI=1.085–2.102). Conclusion The selected VNTR and SNP appeared to be significantly associated with aggression. These VNTRs and SNP have not been studied previously in the Pakistani population, hence they represent a unique ethnic group. These results, however, would have to be replicated in larger cohorts.
Collapse
Affiliation(s)
- Sumbal Sarwar
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan, 54590
| | - Shahida Hasnain
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan, 54590
| |
Collapse
|
41
|
Xu Y, Wang P, Li M, Wu Z, Li X, Shen J, Xu R. Natural small molecule triptonide inhibits lethal acute myeloid leukemia with FLT3-ITD mutation by targeting Hedgehog/FLT3 signaling. Biomed Pharmacother 2021; 133:111054. [PMID: 33254022 DOI: 10.1016/j.biopha.2020.111054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/29/2022] Open
Abstract
Acute myeloid leukemia harboring internal tandem duplication of FMS-like tyrosine kinase 3 (FLT3-ITD AML) is a subset of highly aggressive malignancies with poor clinical outcome. Despite some advances in the development of FLT3 tyrosine kinase inhibitors (FLT3 inhibitors), most of FLT3-ITD AML patients suffer from lethal disease relapse, suggesting the requirement of novel targets and agents. Here we describe a natural small molecule, triptonide that can efficiently inhibit FLT3-ITD-driven AML in vitro and in vivo. Mechanistically, triptonide targeted Hedgehog/FLT3 signaling by inhibiting its critical effectors, which are GLI2, c-Myc and FLT3 and induced apoptosis of FLT3-ITD-driven leukemia cells. In addition, we also observed that triptonide activated tumor suppressor p53. In vivo, triptonide treatment markedly suppressed lethal FLT3-ITD-driven AML with good tolerance and prolonged survival time in orthotopic mouse model. Our studies identify Hedgehog/FLT3 axis as a novel target for treating FLT3-ITD-driven leukemia and demonstrate that triptonide is an active lead compound that can kill FLT3-ITD-driven leukemia cells.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Cell Cycle Checkpoints
- Cell Line, Tumor
- Female
- Gene Expression Regulation, Neoplastic
- Hedgehog Proteins/genetics
- Hedgehog Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Signal Transduction
- Tandem Repeat Sequences
- Triterpenes/pharmacology
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
- Zinc Finger Protein Gli2/genetics
- Zinc Finger Protein Gli2/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
Collapse
Affiliation(s)
- Ying Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Ping Wang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Mengyuan Li
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Zhaoxing Wu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Xian Li
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Jianping Shen
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310009, China.
| | - Rongzhen Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, 310009, China.
| |
Collapse
|
42
|
Otsuka F. [Transcription Factor MTF-1 Involved in the Cellular Response to Zinc]. YAKUGAKU ZASSHI 2021; 141:857-867. [PMID: 34078794 DOI: 10.1248/yakushi.20-00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heavy metals, both toxic and essential, have long been an important research focus in life science. To investigate the intracellular actions of heavy metals at the molecular level, I have been exploring protein factors involved in induction of metallothionein (MT) genes by heavy metals that specifically bind to a metal responsive element (MRE) in the region upstream of the human MT-IIA gene. Purification of a zinc-dependent MRE-binding factor, and cloning of its cDNA identified a sequence identical to that of metal-responsive transcription factor-1 (MTF-1). MTF-1, which is characterized by six tandem repeats of the C2H2 type zinc finger motif, is indispensable for induction of MT gene expression by multiple types of heavy metal, but zinc is the only metal that can directly activate MTF-1 binding to the MRE, indicating that other heavy metal signals act through zinc as a second messenger. Functional analysis of various MTF-1 point mutants revealed several cysteine (Cys) residues critical for DNA binding and/or transactivation activity. Interestingly, six finger motifs seem to mediate several MTF-1 functions other than DNA binding. Immunohistochemical analyses of various mouse tissues revealed selective expression of MTF-1 in spermatocytes among the testicular cells, suggesting roles relevant to spermatogenesis. The zinc regulon, under the control of MTF-1, will likely provide good clues to aid in unraveling novel functions of intracellular zinc ions.
Collapse
Affiliation(s)
- Fuminori Otsuka
- Laboratory of Molecular Environmental Health, Faculty of Pharma-Sciences, Teikyo University
| |
Collapse
|
43
|
Matoulek D, Borůvková V, Ocalewicz K, Symonová R. GC and Repeats Profiling along Chromosomes-The Future of Fish Compositional Cytogenomics. Genes (Basel) 2020; 12:50. [PMID: 33396302 PMCID: PMC7823971 DOI: 10.3390/genes12010050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.
Collapse
Affiliation(s)
- Dominik Matoulek
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Veronika Borůvková
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, 80-309 Gdansk, Poland;
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 80333 Freising, Germany
| |
Collapse
|
44
|
Ahmad SF, Singchat W, Jehangir M, Suntronpong A, Panthum T, Malaivijitnond S, Srikulnath K. Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. Cells 2020; 9:E2714. [PMID: 33352976 PMCID: PMC7767330 DOI: 10.3390/cells9122714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.
Collapse
Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| |
Collapse
|
45
|
Ge C, Moolhuijzen P, Hickey L, Wentzel E, Deng W, Dinglasan EG, Ellwood SR. Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number. Int J Mol Sci 2020; 21:E8769. [PMID: 33233522 PMCID: PMC7699567 DOI: 10.3390/ijms21228769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/31/2022] Open
Abstract
Wild barley accessions have evolved broad-spectrum defence against barley powdery mildew through recessive mlo mutations. However, the mlo defence response is associated with deleterious phenotypes with a cost to yield and fertility, with implications for natural fitness and agricultural productivity. This research elucidates the mechanism behind a novel mlo allele, designated mlo-11(cnv2), which has a milder phenotype compared to standard mlo-11. Bisulphite sequencing and histone ChIP-seq analyses using near-isogenic lines showed pronounced repression of the Mlo promoter in standard mlo-11 compared to mlo-11(cnv2), with repression governed by 24 nt heterochromatic small interfering RNAs. The mlo-11(cnv2) allele appears to largely reduce the physiological effects of mlo while still endorsing a high level of powdery mildew resistance. RNA sequencing showed that this is achieved through only partly restricted expression of Mlo, allowing adequate temporal induction of defence genes during infection and expression close to wild-type Mlo levels in the absence of infection. The two mlo-11 alleles showed copy number proportionate oxidase and peroxidase expression levels during infection, but lower amino acid and aromatic compound biosynthesis compared to the null allele mlo-5. Examination of highly expressed genes revealed a common WRKY W-box binding motif (consensus ACCCGGGACTAAAGG) and a transcription factor more highly expressed in mlo-11 resistance. In conclusion, mlo-11(cnv2) appears to significantly mitigate the trade-off between mlo defence and normal gene expression.
Collapse
Affiliation(s)
- Cynthia Ge
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; (C.G.); (P.M.); (E.W.); (W.D.)
| | - Paula Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; (C.G.); (P.M.); (E.W.); (W.D.)
| | - Lee Hickey
- Centre Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4069, Australia; (L.H.); (E.G.D.)
| | - Elzette Wentzel
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; (C.G.); (P.M.); (E.W.); (W.D.)
| | - Weiwei Deng
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; (C.G.); (P.M.); (E.W.); (W.D.)
| | - Eric G. Dinglasan
- Centre Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4069, Australia; (L.H.); (E.G.D.)
| | - Simon R. Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia; (C.G.); (P.M.); (E.W.); (W.D.)
| |
Collapse
|
46
|
Magee M, Sletten TL, Murray JM, Gordon CJ, Lovato N, Bartlett DJ, Kennaway DJ, Lockley SW, Lack LC, Grunstein RR, Archer SN, Rajaratnam SMW. A PERIOD3 variable number tandem repeat polymorphism modulates melatonin treatment response in delayed sleep-wake phase disorder. J Pineal Res 2020; 69:e12684. [PMID: 32682347 DOI: 10.1111/jpi.12684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022]
Abstract
We examined whether a polymorphism of the PERIOD3 gene (PER3; rs57875989) modulated the sleep-promoting effects of melatonin in Delayed Sleep-Wake Phase Disorder (DSWPD). One hundred and four individuals (53 males; 29.4 ±10.0 years) with DSWPD and a delayed dim light melatonin onset (DLMO) collected buccal swabs for genotyping (PER34/4 n = 43; PER3 5 allele [heterozygous and homozygous] n = 60). Participants were randomised to placebo or 0.5 mg melatonin taken 1 hour before desired bedtime (or ~1.45 hours before DLMO), with sleep attempted at desired bedtime (4 weeks; 5-7 nights/week). We assessed sleep (diary and actigraphy), Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), Patient-Reported Outcomes Measurement Information System (PROMIS: Sleep Disturbance, Sleep-Related Impairment), Sheehan Disability Scale (SDS) and Patient- and Clinician-Global Improvement (PGI-C, CGI-C). Melatonin treatment response on actigraphic sleep onset time did not differ between genotypes. For PER34/4 carriers, self-reported sleep onset time was advanced by a larger amount and sleep onset latency (SOL) was shorter in melatonin-treated patients compared to those receiving placebo (P = .008), while actigraphic sleep efficiency in the first third of the sleep episode (SE T1) did not differ. For PER3 5 carriers, actigraphic SOL and SE T1 showed a larger improvement with melatonin (P < .001). Melatonin improved ISI (P = .005), PROMIS sleep disturbance (P < .001) and sleep-related impairment (P = .017), SDS (P = .019), PGI-C (P = .028) and CGI-C (P = .016) in PER34/4 individuals only. Melatonin did not advance circadian phase. Overall, PER34/4 DSWPD patients have a greater response to melatonin treatment. PER3 genotyping may therefore improve DSWPD patient outcomes.
Collapse
Affiliation(s)
- Michelle Magee
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Centre for Neuroscience of Speech, Department of Audiology and Speech Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Tracey L Sletten
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
| | - Jade M Murray
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
| | - Christopher J Gordon
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
- Sydney Nursing School, The University of Sydney, Sydney, NSW, Australia
| | - Nicole Lovato
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Adelaide Institute for Sleep Health: A Flinders Centre of Research Excellence, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Delwyn J Bartlett
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - David J Kennaway
- Robinson Research Institute, Adelaide School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Steven W Lockley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Leon C Lack
- Adelaide Institute for Sleep Health: A Flinders Centre of Research Excellence, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Ronald R Grunstein
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Simon N Archer
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Shantha M W Rajaratnam
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Cooperative Research Centre for Alertness, Safety and Productivity, Clayton, Victoria, Australia
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
47
|
Safonova Y, Pevzner PA. V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res 2020; 30:1547-1558. [PMID: 32948615 PMCID: PMC7605257 DOI: 10.1101/gr.259598.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that these nonamers explain the vast majority of tandem fusions in human repertoires. We further reveal large clonal lineages formed by tandem fusions in antigen-stimulated immunosequencing data sets, suggesting that such data sets contain many more tandem fusions than previously thought and that about a quarter of large clonal lineages with unusually long CDR3s are generated through tandem fusions. Finally, we developed the SEARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently completed Vertebrate Genomes Project assemblies, nearly doubling the number of mammalian species with known D genes. Our analysis revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J recombination is not a "bug" but an important feature preserved throughout mammalian evolution.
Collapse
Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
48
|
Abstract
The proper segregation of basic elements such as the compartmentalization of the genome and the shuttling of macromolecules between the nucleus and the cytoplasm is a crucial mechanism for homeostasis maintenance in eukaryotic cells. XPO1 (Exportin 1) is the major nuclear export receptor and is required for the export of proteins and RNAs out of the nucleus. STK38 (also known as NDR1) is a Hippo pathway serine/threonine kinase with multifarious functions in normal and cancer cells. In this review, we summarize the history of the discovery of the nucleo/cytoplasmic shuttling of proteins and focus on the major actor of nuclear export: XPO1. After describing the molecular events required for XPO1-mediated nuclear export of proteins, we introduce the Hippo pathway STK38 kinase, synthetize its regulation mechanisms as well as its biological functions in both normal and cancer cells, and finally its intersection with XPO1 biology. We discuss the recently identified mechanism of XPO1 activation by phosphorylation of XPO1_S1055 by STK38 and contextualize this finding according to the biological functions previously reported for both XPO1 and STK38, including the second identity of STK38 as an autophagy regulator. Finally, we phrase this newly identified activation mechanism into the general nuclear export machinery and examine the possible outcomes of nuclear export inhibition in cancer treatment.
Collapse
Affiliation(s)
- Alexandre PJ Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Jacques H Camonis
- Inserm U830, Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris, France
| |
Collapse
|
49
|
Bolognini D, Magi A, Benes V, Korbel JO, Rausch T. TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data. Gigascience 2020; 9:giaa101. [PMID: 33034633 PMCID: PMC7539535 DOI: 10.1093/gigascience/giaa101] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/07/2020] [Accepted: 09/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Tandem repeat sequences are widespread in the human genome, and their expansions cause multiple repeat-mediated disorders. Genome-wide discovery approaches are needed to fully elucidate their roles in health and disease, but resolving tandem repeat variation accurately remains a challenging task. While traditional mapping-based approaches using short-read data have severe limitations in the size and type of tandem repeats they can resolve, recent third-generation sequencing technologies exhibit substantially higher sequencing error rates, which complicates repeat resolution. RESULTS We developed TRiCoLOR, a freely available tool for tandem repeat profiling using error-prone long reads from third-generation sequencing technologies. The method can identify repetitive regions in sequencing data without a prior knowledge of their motifs or locations and resolve repeat multiplicity and period size in a haplotype-specific manner. The tool includes methods to interactively visualize the identified repeats and to trace their Mendelian consistency in pedigrees. CONCLUSIONS TRiCoLOR demonstrates excellent performance and improved sensitivity and specificity compared with alternative tools on synthetic data. For real human whole-genome sequencing data, TRiCoLOR achieves high validation rates, suggesting its suitability to identify tandem repeat variation in personal genomes.
Collapse
Affiliation(s)
- Davide Bolognini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Pieraccini 6, Florence 50134, Italy
- European Molecular Biology Laboratory (EMBL), GeneCore, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Alberto Magi
- Department of Information Engineering, University of Florence, Via di S. Marta 3, Florence 50134, Italy
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), GeneCore, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), GeneCore, Meyerhofstraße 1, Heidelberg 69117, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg 69117, Germany
| |
Collapse
|
50
|
Wang X, Yang X. A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small 2020; 16:e2003671. [PMID: 33006262 DOI: 10.1002/smll.202003671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/26/2020] [Indexed: 06/11/2023]
Abstract
DNA tandem repeats are frequently found in eukaryotic genomes. High-copy DNA repeats can serve as building blocks of complex DNA structures, but the in vitro synthesis of DNA repeats has been challenging due to complicated procedures and the high cost. Here, a new, simple method is developed using the strategy of blocking polymerase chain reaction for highly efficient DNA repeat expansion (BPRE). With BPRE, dsDNA fragments composed of more than 40 copies of the repeat sequence can be quickly produced, while the cost is reduced by at least 90%. As a typical application, reannealing of the dsDNA repeats generates elastic hydrogels, which shows a high capacity for doxycycline absorption and prolonged release.
Collapse
Affiliation(s)
- Xin Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| |
Collapse
|