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Rey-Millet M, Bystricky K. The genome in space and time comes of age. Nucleus 2024; 15:2307665. [PMID: 38302443 PMCID: PMC10841031 DOI: 10.1080/19491034.2024.2307665] [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: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
DNA sequencing is not enough to grasp the complexity of genome organization and function. The four-dimensional (three in space, one in time) configuration of the eukaryotic nucleus varies with cell types, during development and in diseased tissues, and has to be taken into account to decipher genome function. To study, discuss, and advance in such direction, the International Nucleome Consortium COST Action, funded by the European Union, held its concluding symposium 'The Genome in Space and Time' at the Ionian University in Corfu, Greece, on September 10-13, 2023.
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Affiliation(s)
- Martin Rey-Millet
- Molecular, Cellular and Developmental biology unit (MCD), Center for Integrative Biology (CBI), Université Paul Sabatier (UPS), CNRS, Toulouse, France
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental biology unit (MCD), Center for Integrative Biology (CBI), Université Paul Sabatier (UPS), CNRS, Toulouse, France
| | - the International Nucleome Consortium
- Molecular, Cellular and Developmental biology unit (MCD), Center for Integrative Biology (CBI), Université Paul Sabatier (UPS), CNRS, Toulouse, France
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2
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Khan MM, Suhail SM, Majid HA, Ahmad I, Sadique U, Khan R, Ahmad I, Ijaz A, Khan K, Ali F, Khan MS, El-Mansi AA. Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat. Anim Biotechnol 2024; 35:2290528. [PMID: 38142270 DOI: 10.1080/10495398.2023.2290528] [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: 12/25/2023]
Abstract
The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.
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Affiliation(s)
- Muhammad Munir Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Syed Muhammad Suhail
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Hafiz Abdul Majid
- Department of Livestock and Dairy Development (Research Wing), Government of Khyber Pakhtunkhwa-Peshawar, Peshawar, Pakistan
| | - Ijaz Ahmad
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Umer Sadique
- Department of Animal Health, Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Iftikhar Ahmad
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Asim Ijaz
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Khalid Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Farhad Ali
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Muhammad Saeed Khan
- Department of Animal Health, Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Ahmed A El-Mansi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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Bursakov SA, Kovaleva AV, Brigida AV, Zaripov OG. Functional analysis of the GPAT4 gene mutation predicted to affect splicing. Anim Biotechnol 2024; 35:2269210. [PMID: 37906284 DOI: 10.1080/10495398.2023.2269210] [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: 11/02/2023]
Abstract
The GPAT4 gene is considered as a potential functional candidate for single nucleotide polymorphism (SNP) studies in dairy cattle breeding due to its association with dairy performance in cattle by encoding an enzyme responsible for the presence of diacylglycerols and triacylglycerols in milk. Using the example of the GPAT4 gene, we applied the minigene splicing assay to analyze the functional consequences of its variant that was predicted to affect normal splicing. The results of functional analysis revealed the sequence variations (rs442541537), transfection experiments in a wild type and mutant cell line model system demonstrated that the investigated mutation in the second intron of the GPAT4 gene was responsible for the presence of a second exon in mature messenger RNA (mRNA). The cases of its absence in the spliced mature mRNA transcript resulted in a truncated dysfunctional protein due to the appearance of a stop codon. Thus, the discovered SNP led to alternative splicing in pre-mRNA by the 'cassette exon' ('exon skipping') mechanism. The studied mutation can potentially be a molecular genetic marker for alternative splicing for the GPAT4 gene and, therefore contributes to economic benefits in cattle breeding programs.
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Affiliation(s)
- Sergey A Bursakov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
- Federal State Budgetary Scientific Institution "All-Russia Research Institute of Agricultural Biotechnology", Moscow, Russia
| | - Anastasia V Kovaleva
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Artyom V Brigida
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Oleg G Zaripov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
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Malik M, Malik F, Fatma T, Qasim Hayat M, Jamal A, Gul A, Faraz Bhatti M. The complete mitochondrial genome of Penicillium expansum: Insights into the fungal evolution and phylogeny. Gene 2024; 910:148315. [PMID: 38417689 DOI: 10.1016/j.gene.2024.148315] [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: 12/26/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.
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Affiliation(s)
- Mahnoor Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Fatima Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Muhammad Qasim Hayat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
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Zhang X, Ferree PM. PSRs: Selfish chromosomes that manipulate reproductive development. Semin Cell Dev Biol 2024; 159-160:66-73. [PMID: 38394822 DOI: 10.1016/j.semcdb.2024.01.008] [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: 09/15/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
B chromosomes are intriguing "selfish" genetic elements, many of which exhibit higher-than-Mendelian transmission. This perspective highlights a group of B chromosomes known as Paternal Sex Ratio chromosomes (PSRs), which are found in several insects with haplo-diploid reproduction. PSRs harshly alter the organism's reproduction to facilitate their own inheritance. A manifestation of this effect is the conversion of female destined individuals into males. Key to this conversion is the mysterious ability of PSRs to cause elimination of the sperm-inherited half of the genome during zygote formation. Here we discuss how PSRs were discovered, what is known about how they alter paternal chromatin dynamics to cause sex conversion, and how PSR-induced genome elimination is different from other forms of programmed genome elimination in different insects. PSRs also stand out because their DNA sequence compositions differ in remarkable ways from their insect's essential chromosomes, a characteristic suggestive of interspecies origins. Broadly, we also highlight poorly understood aspects of PSR dynamics that need to be investigated.
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Affiliation(s)
- Xinmi Zhang
- W. M. Keck Science Department, Pitzer and Scripps Colleges, Claremont, CA 91711, USA
| | - Patrick M Ferree
- W. M. Keck Science Department, Pitzer and Scripps Colleges, Claremont, CA 91711, USA.
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Tang M, Zhu KJ, Sun W, Yuan X, Wang Z, Zhang R, Ai Z, Liu K. Ultrasimple size encoded microfluidic chip for rapid simultaneous multiplex detection of DNA sequences. Biosens Bioelectron 2024; 253:116172. [PMID: 38460210 DOI: 10.1016/j.bios.2024.116172] [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: 11/17/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/11/2024]
Abstract
Simultaneous multiplexed analysis can provide comprehensive information for disease diagnosis. However, the current multiplex methods rely on sophisticated barcode technology, which hinders its wider application. In this study, an ultrasimple size encoding method is proposed for multiplex detection using a wedge-shaped microfluidic chip. Driving by negative pressure, microparticles are naturally arranged in distinct stripes based on their sizes within the chip. This size encoding method demonstrates a high level of precision, allowing for accuracy in distinguishing 3-5 sizes of microparticles with a remarkable accuracy rate of up to 99%, even the microparticles with a size difference as small as 0.5 μm. The entire size encoding process is completed in less than 5 min, making it ultrasimple, reliable, and easy to operate. To evaluate the function of this size encoding microfluidic chip, three commonly co-infectious viruses' nucleic acid sequences (including complementary DNA sequences of HIV and HCV, and DNA sequence of HBV) are employed for multiplex detection. Results indicate that all three DNA sequences can be sensitively detected without any cross-interference. This size-encoding microfluidic chip-based multiplex detection method is simple, rapid, and high-resolution, its successful application in serum samples renders it highly promising for potential clinical promotion.
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Affiliation(s)
- Man Tang
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China; Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan, 430200, China
| | - Kuan-Jie Zhu
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Wei Sun
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Xinyue Yuan
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Zhipeng Wang
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Ruyi Zhang
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Zhao Ai
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China; Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan, 430200, China.
| | - Kan Liu
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan, 430200, China; Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan, 430200, China.
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Arakawa J, Kondoh H, Matsushita T, Ogino Y, Asai M, Tanuma SI, Uchiumi F. Induction of the human CDC45 gene promoter activity by natural compound trans‑resveratrol. Mol Med Rep 2024; 29:92. [PMID: 38577929 DOI: 10.3892/mmr.2024.13216] [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: 09/21/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
GGAA motifs in the human TP53 and HELB gene promoters play a part in responding to trans‑resveratrol (Rsv) in HeLa S3 cells. This sequence is also present in the 5'‑upstream region of the human CDC45 gene, which encodes a component of CMG DNA helicase protein complex. The cells were treated with Rsv (20 µM), then transcripts and the translated protein were analyzed by quantitative RT‑PCR and western blotting, respectively. The results showed that the CDC45 gene and protein expression levels were induced after the treatment. To examine whether they were due to the activation of transcription, a 5'‑upstream 556‑bp of the CDC45 gene was cloned and inserted into a multi‑cloning site of the Luciferase (Luc) expression vector. In the present study, various deletion/point mutation‑introduced Luc expression plasmids were constructed and they were used for the transient transfection assay. The results showed that the GGAA motif, which is included in a putative RELB protein recognizing sequence, plays a part in the promoter activity with response to Rsv in HeLa S3 cells.
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Affiliation(s)
- Jun Arakawa
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Hikaru Kondoh
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Tokiyoshi Matsushita
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Yoko Ogino
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Masashi Asai
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Sei-Ichi Tanuma
- Genomic Medicinal Science, Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278‑8510, Japan
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Shokrpoor S, Darabian Aghdas R, Ziafati Kafi Z, Abdollahi M, Ashrafi Tamai I. Lumpy jaw caused by Nocardia farcinica in a Holstein cow. Vet Med Sci 2024; 10:e1433. [PMID: 38520249 PMCID: PMC10981914 DOI: 10.1002/vms3.1433] [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: 11/21/2023] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
A 3-year-old Holstein cow was examined in an intensive system due to unilateral swelling in the mandible. A right mandibular mass was associated with painful mastication and Ptyalism. In palpation, the mass was raised, ulcerated, attached to the mandible bone and firm, approximately 17 × 12 × 10 cm3 in size. The lesion was sampled, and after routine bacteriology and histopathology procedures, the occurrence of lumpy jaw caused by Nocardia farcinica was confirmed. The bacterium was analysed using genome sequencing and new strain called Najm 114. Due to the risk of zoonosis of the isolated agent, the cow was euthanized. This is the first report of lumpy jaw caused by N. farcinica in a cow. This study showed that N. farcinica should be considered a possible etiological agent for lumpy jaw in cattle.
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Affiliation(s)
- Sara Shokrpoor
- Department of Pathology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
| | | | - Zahra Ziafati Kafi
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
| | - Mostafa Abdollahi
- Department of Clinical Sciences, Faculty of Veterinary MedicineSemnan UniversitySemnanIran
| | - Iradj Ashrafi Tamai
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
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Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Methylation-based markers for the estimation of age in African cheetah, Acinonyx jubatus. Mol Ecol Resour 2024; 24:e13940. [PMID: 38390700 DOI: 10.1111/1755-0998.13940] [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: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Age is a key demographic in conservation where age classes show differences in important population metrics such as morbidity and mortality. Several traits, including reproductive potential, also show senescence with ageing. Thus, the ability to estimate age of individuals in a population is critical in understanding the current structure as well as their future fitness. Many methods exist to determine age in wildlife, with most using morphological features that show inherent variability with age. These methods require significant expertise and become less accurate in adult age classes, often the most critical groups to model. Molecular methods have been applied to measuring key population attributes, and more recently epigenetic attributes such as methylation have been explored as biomarkers for age. There are, however, several factors such as permits, sample sovereignty, and costs that may preclude the use of extant methods in a conservation context. This study explored the utility of measuring age-related changes in methylation in candidate genes using mass array technology. Novel methods are described for using gene orthologues to identify and assay regions for differential methylation. To illustrate the potential application, African cheetah was used as a case study. Correlation analyses identified six methylation sites with an age relationship, used to develop a model with sufficient predictive power for most conservation contexts. This model was more accurate than previous attempts using PCR and performed similarly to candidate gene studies in other mammal species. Mass array presents an accurate and cost-effective method for age estimation in wildlife of conservation concern.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Desiré L Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
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Flaven-Pouchon J, Froschauer C, Moussian B. Dynamics of cuticle-associated transcript profiles during moulting of the bed bug Cimexlectularius. Insect Biochem Mol Biol 2024; 168:104112. [PMID: 38513961 DOI: 10.1016/j.ibmb.2024.104112] [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] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/23/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
The bed bug Cimex lectularius is a worldwide human pest. The sequenced genome allows molecular analyses of all aspects of bed bug biology. The present work was conducted to contribute to bed bug cuticle biology. As in other insect species, the C. lectularius cuticle consists of the three horizontal layers procuticle, epicuticle and envelope. To analyse the genes needed for the establishment of the stratified cuticle, we studied the expression pattern of 42 key cuticle-related genes at the transition of the penultimate nymphal stage to adult animals when a new cuticle is formed. Based on gene expression dynamics, in simplified model, we distinguish two key events during cuticle renewal in C. lectularius. First, upon blood feeding, modulation of ecdysone signalling culminates in the transcriptional activation of the transcription factor Clec-Ftz-F1 that possibly controls the expression of 32 of the 42 genes tested. Second, timed expression of Clec-Ftz-F1 seems to depend also on the insulin signalling pathway as RNA interference against transcripts of the insulin receptor delays Clec-Ftz-F1 expression and stage transition. An important observation of our transcript survey is that genes needed for the construction of the three cuticle layers are largely expressed simultaneously. Based on these data, we hypothesise a considerable synchronous mechanism of layer formation rather than a strictly sequential one. Together, this work provides a basis for functional analyses of cuticle formation in C. lectularius.
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Affiliation(s)
- Justin Flaven-Pouchon
- Universität Tübingen, Interfaculty Institute for Cell Biology, Genetik der Tiere, Tübingen, Germany
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Wan H, Yu L, Cui X, Guo S, Mu S, Kang X. A pattern recognition receptor interleukin-1 receptor is involved in reproductive immunity in Macrobrachium nipponense ovary. Fish & Shellfish Immunology 2024; 148:109481. [PMID: 38479568 DOI: 10.1016/j.fsi.2024.109481] [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: 01/01/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
The family of TIR domain-containing receptors includes numerous proteins involved in innate immunity. In this study, a member of this family was characterized from the ovary of the oriental river prawn Macrobrachium nipponense and identified as interleukin-1 receptor (MnIL-1R). Meanwhile, to elucidate the conservation of IL-1R, its orthologous were identified in several crustacean species as well. In addition, the expression pattern of MnIL-1R in various adult tissues and post different pathogen-associated molecular patterns (PAMPs) challenge in ovary was analyzed with qRT-PCR technology. Finally, the roles of MnIL-1R in the ovary were analyzed by RNAi technology. The main results are as follows: (1) MnIL-1R comprises a 1785 bp ORF encoding 594 amino acids and is structurally composed of five domains: a signal peptide, two immunoglobulin (IG) domains, a transmembrane region, and a TIR-2 domain; (2) the TIR domain showed a high conservation among analyzed crustacean species; (3) MnIL-1R is widely detected in all tested tissues including ovary; (4) MnIL-1R showed a positive response to challenges with LPS, PGN, and polyI:C in the ovary; (5) its IG domain showed strong binding ability to LPS and PGN, confirming its role as a pattern recognition receptor; (6) the expression patterns of several members of the Toll signaling pathway (Myd88, TRAF-6, Dorsal, and Relish) was similar to that of MnIL-1R after challenges with LPS, PGN, and polyI:C in the ovary; (7) the silencing of MnIL-1R resulted in down-regulation of theses gene' (Myd88, TRAF-6, Dorsal, and Relish) expression level in the ovary. These results suggest that MnIL-1R can activate the Toll signaling pathway in the ovary by directly recognizing LPS and PGN through its IG domain, thereby contributing to the immune response in the ovary of M. nipponense.
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Affiliation(s)
- Haifu Wan
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China; Postdoctoral Research Station of Biology, Hebei University, Baoding City, Hebei Province, 071002, China
| | - Lei Yu
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
| | - Xiaodong Cui
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
| | - Shuai Guo
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China.
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China.
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Stojak J, Rocha D, Mörke C, Kühn C, Blanquet V, Taniguchi H. Establishment of a cloning-free CRISPR/Cas9 protocol to generate large deletions in the bovine MDBK cell line. J Appl Genet 2024; 65:399-402. [PMID: 38418802 PMCID: PMC11003909 DOI: 10.1007/s13353-024-00846-3] [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: 07/24/2023] [Revised: 01/11/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
The CRISPR/Cas9 technique applied to modify the cattle genome has value in increasing animal health and welfare. Here, we established a simple, fast, and efficient cloning-free CRISPR/Cas9 protocol for large deletions of genomic loci in the frequently used model bovine MDBK cell line. The main advantages of our protocol are as follows: (i) pre-screening of the sgRNA efficiency with a fast and simple cleavage assay, (ii) reliable detection of genomic edits primarily by PCR and confirmed by DNA sequencing, and (iii) single cell sorting with FACS providing specific genetic information from modified cells of interest. Therefore, our method could be successfully applied in different studies, including functional validation of any genetic or regulatory elements.
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Affiliation(s)
- Joanna Stojak
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Caroline Mörke
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany
- Friedrich-Loeffler-Institut (FLI), 17493, Greifswald, Insel Riems, Germany
| | - Veronique Blanquet
- Faculté Des Sciences Et Techniques, University of Limoges, 123 Avenue Albert Thomas, 87060, Limoges, France
| | - Hiroaki Taniguchi
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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13
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Cooley NP, Wright ES. Many purported pseudogenes in bacterial genomes are bona fide genes. BMC Genomics 2024; 25:365. [PMID: 38622536 DOI: 10.1186/s12864-024-10137-0] [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: 10/10/2023] [Accepted: 02/17/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed to result from gene degradation during evolution but could also be technical artifacts of genome sequencing or assembly. RESULTS Using a combination of observational and experimental data, we show that many putative pseudogenes are attributable to errors that are incorporated into genomes during assembly. Within 126,564 publicly available genomes, we observed that nearly identical genomes often substantially differed in pseudogene counts. Causal inference implicated assembler, sequencing platform, and coverage as likely causative factors. Reassembly of genomes from raw reads confirmed that each variable affects the number of putative pseudogenes in an assembly. Furthermore, simulated sequencing reads corroborated our observations that the quality and quantity of raw data can significantly impact the number of pseudogenes in an assembler dependent fashion. The number of unexpected pseudogenes due to internal stops was highly correlated (R2 = 0.96) with average nucleotide identity to the ground truth genome, implying relative pseudogene counts can be used as a proxy for overall assembly correctness. Applying our method to assemblies in RefSeq resulted in rejection of 3.6% of assemblies due to significantly elevated pseudogene counts. Reassembly from real reads obtained from high coverage genomes showed considerable variability in spurious pseudogenes beyond that observed with simulated reads, reinforcing the finding that high coverage is necessary to mitigate assembly errors. CONCLUSIONS Collectively, these results demonstrate that many pseudogenes in microbial genome assemblies are actually genes. Our results suggest that high read coverage is required for correct assembly and indicate an inflated number of pseudogenes due to internal stops is indicative of poor overall assembly quality.
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Affiliation(s)
- Nicholas P Cooley
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Evolutionary Biology and Medicine, Pittsburgh, PA, USA.
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14
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Li Y, Yi H, Zhu Y. Novel insights into adaptive evolution based on the unusual AT-skew in Acheilognathus gracilis mitogenome and phylogenetic relationships of bitterling. Gene 2024; 902:148154. [PMID: 38218382 DOI: 10.1016/j.gene.2024.148154] [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: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Acheilognathus gracilis, a bitterling species, distribute in lower reaches of Yangtze River. They are identified as the top-priority bitterling species for conservation as having high evolutionary distinctiveness and are at risk of extinction. In present study, we first sequenced the complete mitogenome of A. gracilis and analyzed its phylogenetic position using 13 PCGs. The A. gracilis mitogenome is 16,774 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of A. gracilis in descending order is T 27.9 %, A 27.7 %, C 26.1 % and G 18.3 %, shows a unusual AT-skew with slightly negative. Further investigation revealed A. gracilis uses excess T over A in NADH dehydrogenase 5 (nd5), whereas the most of other bitterlings are biased toward to use A not T, implying there is likely to be unique strategy of adaptive evolution in A. gracilis. We also compared 13 PCGs of 30 bitterling mitogenomes and the results exhibit highly conservative. Phylogenetic trees constructed by 13 PCGs strongly support the monophyly of Acheilognathus and the paraphyly of Rhodeus and Tanakia. Current results will provide valuable information for follow-up research on conservation of species facing with serious population decline and can provide novel insights into the phylogenetic analysis and evolutionary biology research.
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Affiliation(s)
- Yuxuan Li
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Yi
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China.
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15
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Arakawa H, Miura H, Quadros RM, Ohtsuka M, Gurumurthy C. Cross-contamination of CRISPR guides and other unrelated nucleotide sequences among commercial oligonucleotides. Nucleic Acids Res 2024; 52:3137-3145. [PMID: 38324466 PMCID: PMC11014326 DOI: 10.1093/nar/gkae068] [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: 09/26/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Custom oligonucleotides (oligos) are widely used reagents in biomedical research. Some common applications of oligos include polymerase chain reaction (PCR), sequencing, hybridization, microarray, and library construction. The reliability of oligos in such applications depends on their purity and specificity. Here, we report that commercially available oligos are frequently contaminated with nonspecific sequences (i.e. other unrelated oligonucleotides). Most of the oligos that we designed to amplify clustered regularly interspersed palindromic repeats (CRISPR) guide sequences contained nonspecific CRISPR guides. These contaminants were detected in research-grade oligos procured from eight commercial oligo-suppliers located in three different geographic regions of the world. Deep sequencing of some of the oligos revealed a variety of contaminants. Given the wide range of applications of oligos, the impact of oligo cross-contamination varies greatly depending on the field and the experimental method. Incorporating appropriate control experiments in research design can help ensure that the quality of oligo reagents meets the intended purpose. This can also minimize risk depending on the purposes for which the oligos are used.
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Affiliation(s)
- Hiroshi Arakawa
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiromi Miura
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa Japan
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa Japan
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
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16
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Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold S, Novoa E, Motorin Y, Roignant JY. Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster. Nucleic Acids Res 2024; 52:2848-2864. [PMID: 38416577 PMCID: PMC11014333 DOI: 10.1093/nar/gkae139] [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] [Received: 06/02/2023] [Revised: 02/09/2024] [Accepted: 02/26/2024] [Indexed: 03/01/2024] Open
Abstract
During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2'-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. We de novo identified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable in D. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2'-O-methylation on translation and proteostasis in a whole organism.
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Affiliation(s)
- Athena Sklias
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sonia Cruciani
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Mariangela Spagnuolo
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Guillaume Lavergne
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Alessandro Brambilla
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - René Dreos
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Eva Maria Novoa
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
- University Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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17
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Chen E, Trajkovski M, Lee H, Nyovanie S, Martin K, Dean W, Tahiliani M, Plavec J, Yatsunyk L. Structure of native four-repeat satellite III sequence with non-canonical base interactions. Nucleic Acids Res 2024; 52:3390-3405. [PMID: 38381082 PMCID: PMC11014236 DOI: 10.1093/nar/gkae113] [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] [Received: 07/05/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5'-ATGGA ATGGA ATGGA ATGGA-3' using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05-0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G-G intercalation sandwiched by sheared A-G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A-T/T-A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.
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Affiliation(s)
- Erin Chen
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Hyun Kyung Lee
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Samantha Nyovanie
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - William L Dean
- Structural Biology Program JG Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Mamta Tahiliani
- Department of Biology, New York University, New York, NY 10003, USA
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
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18
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Gudkov M, Thibaut L, Giannoulatou E. Quantifying negative selection on synonymous variants. HGG Adv 2024; 5:100262. [PMID: 38192100 PMCID: PMC10835449 DOI: 10.1016/j.xhgg.2024.100262] [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: 08/21/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 01/10/2024] Open
Abstract
Widespread adoption of DNA sequencing has resulted in large numbers of genetic variants, whose contribution to disease is not easily determined. Although many types of variation are known to disrupt cellular processes in predictable ways, for some categories of variants, the effects may not be directly detectable. A particular example is synonymous variants, that is, those single-nucleotide variants that create a codon substitution, such that the produced amino acid sequence is unaffected. Contrary to the original theory suggesting that synonymous variants are benign, there is a growing volume of research showing that, despite their "silent" mechanism of action, some synonymous variation may be deleterious. Here, we studied the extent of the negative selective pressure acting on different classes of synonymous variants by analyzing the relative enrichment of synonymous singleton variants in the human exomes provided by gnomAD. Using a modification of the mutability-adjusted proportion of singletons (MAPS) metric as a measure of purifying selection, we found that some classes of synonymous variants are subject to stronger negative selection than others. For instance, variants that reduce codon optimality undergo stronger selection than optimality-increasing variants. Besides, selection affects synonymous variants implicated in splice-site-loss or splice-site-gain events. To understand what drives this negative selection, we tested a number of predictors in the aim to explain the variability in the selection scores. Our findings provide insights into the effects of synonymous variants at the population level, highlighting the specifics of the role that these variants play in health and disease.
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Affiliation(s)
- Mikhail Gudkov
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Loïc Thibaut
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia.
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19
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MacGowan SA, Madeira F, Britto-Borges T, Barton GJ. A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites. Commun Biol 2024; 7:447. [PMID: 38605212 PMCID: PMC11009406 DOI: 10.1038/s42003-024-06117-5] [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: 07/26/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions.
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Affiliation(s)
- Stuart A MacGowan
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
| | - Fábio Madeira
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thiago Britto-Borges
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Geoffrey J Barton
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK.
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20
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Lin R, Mitsuhashi H, Fiori LM, Denniston R, Ibrahim EC, Belzung C, Mechawar N, Turecki G. SNORA69 is up-regulated in the lateral habenula of individuals with major depressive disorder. Sci Rep 2024; 14:8258. [PMID: 38589409 PMCID: PMC11001866 DOI: 10.1038/s41598-024-58278-2] [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: 09/19/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Major depressive disorder (MDD) is a complex and potentially debilitating illness whose etiology and pathology remains unclear. Non-coding RNAs have been implicated in MDD, where they display differential expression in the brain and the periphery. In this study, we quantified small nucleolar RNA (snoRNA) expression by small RNA sequencing in the lateral habenula (LHb) of individuals with MDD (n = 15) and psychiatrically-healthy controls (n = 15). We uncovered five snoRNAs that exhibited differential expression between MDD and controls (FDR < 0.01). Specifically, SNORA69 showed increased expression in MDD and was technically validated via RT-qPCR. We further investigated the expression of Snora69 in the LHb and peripheral blood of an unpredicted chronic mild stress (UCMS) mouse model of depression. Snora69 was specifically up-regulated in mice that underwent the UCMS paradigm. SNORA69 is known to guide pseudouridylation onto 5.8S and 18S rRNAs. We quantified the relative abundance of pseudouridines on 5.8S and 18S rRNA in human post-mortem LHb samples and found increased abundance of pseudouridines in the MDD group. Overall, our findings indicate the importance of brain snoRNAs in the pathology of MDD. Future studies characterizing SNORA69's role in MDD pathology is warranted.
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Affiliation(s)
- Rixing Lin
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Haruka Mitsuhashi
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Laura M Fiori
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Ryan Denniston
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - El Cherif Ibrahim
- CNRS, INT, Institute Neuroscience Timone, Aix-Marseille Université, Marseille, France
| | - Catherine Belzung
- Imaging Brain and Neuropsychiatry iBraiN U1253, INSERM, Université de Tours, Tours, France
| | - Naguib Mechawar
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
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21
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Chalise JP, Hu Z, Li M, Shepphird JK, Gu Z, Gyawali P, Itakura K, Larson GP. Identification of an alternative short ARID5B isoform associated with B-ALL survival. Biochem Biophys Res Commun 2024; 703:149659. [PMID: 38382358 DOI: 10.1016/j.bbrc.2024.149659] [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: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/23/2024]
Abstract
Utilizing RNA sequence (RNA-Seq) splice junction data from a cohort of 1841 B-cell acute lymphoblastic leukemia (B-ALL) patients we define transcriptionally distinct isoforms of ARID5B, a risk-associated gene identified in genome wide association studies (GWAS), which associate with disease survival. Short (S) and long (L) ARID5B transcripts, which differ in an encoded BAH-like chromatin interaction domain, show remarkable correlation to the isoform splicing pattern. Testing of the ARID5B proximal promoter of the S & L isoforms indicated that both are functionally independent in luciferase reporter assays. Increased short isoform expression is associated with decreased event-free and overall survival. The abundance of short and long transcripts strongly correlates to B-ALL prognostic stratification, where B-ALL subtypes with poor outcomes express a higher proportion of the S-isoform. These data demonstrate that the analysis of independent promoters and alternative splicing events are essential for improved risk stratification and a more complete understanding of disease pathology.
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Affiliation(s)
- Jaya P Chalise
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Zunsong Hu
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Min Li
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Jennifer K Shepphird
- Clinical Translational Project Development, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Zhaohui Gu
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA; Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Purnima Gyawali
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Keiichi Itakura
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Garrett P Larson
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
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22
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Mondal B, Chakraborty D, Hori N, Nguyen HT, Thirumalai D. Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. J Chem Theory Comput 2024; 20:2934-2946. [PMID: 38498914 DOI: 10.1021/acs.jctc.3c01193] [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] [Indexed: 03/20/2024]
Abstract
Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the small-angle X-ray scattering profiles, which are in excellent agreement with experiments. Although ion-counting experiments mask the differences between Mg2+ and Ca2+, we find that Mg2+ binds to the minor grooves and phosphate groups, whereas Ca2+ binds specifically to the minor groove. Both Mg2+ and Ca2+ exhibit a tendency to bind to the minor groove of DNA as opposed to the major groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. The near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations. The successful applications of the TIS-ION model are poised to confront many problems in DNA biophysics.
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Affiliation(s)
- Balaka Mondal
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Hung T Nguyen
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
- Department of Physics, The University of Texas, Austin, Texas 78712, United States
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23
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Park MN, Yeo SG, Park J, Jung Y, Hwang SM. Usefulness and Limitations of PFGE Diagnosis and Nucleotide Sequencing Method in the Analysis of Food Poisoning Pathogens Found in Cooking Employees. Int J Mol Sci 2024; 25:4123. [PMID: 38612932 PMCID: PMC11012705 DOI: 10.3390/ijms25074123] [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: 02/27/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
In the case of a food poisoning outbreak, it is essential to understand the relationship between cooking workers and food poisoning. Many biological diagnostic methods have recently been developed to detect food poisoning pathogens. Among these diagnostic tools, this study presents PCR-based pulsed-field gel electrophoresis and nucleotide sequencing diagnostic analysis results for diagnosing food poisoning outbreaks associated with cooking employees in Chungcheongnam-do, Republic of Korea. Pulsed-field gel electrophoresis was useful in identifying the food poisoning outbreaks caused by Staphylococcus aureus and Enteropathogenic Escherichia coli. In the case of Norovirus, nucleotide sequencing was used to identify the relationship between cooking workers and the food poisoning outbreak. However, it is difficult to determine whether cooking employees directly caused the food poisoning outbreaks based on these molecular biological diagnostic results alone. A system is needed to integrate epidemiological and diagnostic information to identify a direct correlation between the food poisoning outbreak and cooking employees.
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Affiliation(s)
- Mi-Na Park
- Graduate School of Public Health & Welfare, Konyang University, 158 Gwanjeodong-ro, Daejeon 35365, Republic of Korea;
- Chungcheongnam-do Institute of Health and Environment Research, 8 Hongyegongwon-ro, Hongseong 32254, Republic of Korea;
| | - Sang-Gu Yeo
- Korea Disease Control and Prevention Agency, Osong Health Technology Administration Complex, 2 Osongsaengmyeong-ro, Cheongju 28159, Republic of Korea;
| | - Junhyuk Park
- Chungcheongnam-do Institute of Health and Environment Research, 8 Hongyegongwon-ro, Hongseong 32254, Republic of Korea;
| | - Yoomi Jung
- Korea Armed Forces Nursing Academy, 90 Jaun-ro, Daejeon 34059, Republic of Korea;
| | - Se-Min Hwang
- Graduate School of Public Health & Welfare, Konyang University, 158 Gwanjeodong-ro, Daejeon 35365, Republic of Korea;
- Department of Preventive Medicine, Myunggok Medical Faculty, Medical Campus, Konyang University College of Medicine, 158 Gwanjeodong-ro, Daejeon 35365, Republic of Korea
- Myunggok Medical Research Center, Konyang University College of Medicine, 158 Gwanjeodong-ro, Daejeon 35365, Republic of Korea
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24
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Wu Y, Wang S, Wang P, Nie W, Ahmad I, Sarris PF, Chen G, Zhu B. Suppression of host plant defense by bacterial small RNAs packaged in outer membrane vesicles. Plant Commun 2024; 5:100817. [PMID: 38217288 PMCID: PMC11009154 DOI: 10.1016/j.xplc.2024.100817] [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: 07/26/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Noncoding small RNAs (sRNAs) packaged in bacterial outer membrane vesicles (OMVs) function as novel mediators of interspecies communication. While the role of bacterial sRNAs in enhancing virulence is well established, the role of sRNAs in the interaction between OMVs from phytopathogenic bacteria and their host plants remains unclear. In this study, we employ RNA sequencing to characterize differentially packaged sRNAs in OMVs of the phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc). Our candidate sRNA (Xosr001) was abundant in OMVs and involved in the regulation of OsJMT1 to impair host stomatal immunity. Xoc loads Xosr001 into OMVs, which are specifically ttransferred into the mechanical tissues of rice leaves. Xosr001 suppresses OsJMT1 transcript accumulation in vivo, leading to a reduction in MeJA accumulation in rice leaves. Furthermore, the application of synthesized Xosr001 sRNA to the leaves of OsJMT1-HA-OE transgenic line results in the suppression of OsJMT1 expression by Xosr001. Notably, the OsJMT1-HA-OE transgenic line exhibited attenuated stomatal immunity and disease susceptibility upon infection with ΔXosr001 compared to Xoc. These results suggest that Xosr001 packaged in Xoc OMVs functions to suppress stomatal immunity in rice.
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Affiliation(s)
- Yan Wu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari 61100, Pakistan
| | | | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Shanghai Jiao Tong University Chongqing Research Institute, Shanghai, China.
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25
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Yesaya A, Zhang L, Wu C, Fu Y, Zhang J, An J, Xiao Y. The chromosomal-scale genome sequencing and assembly of Athetis lepigone. Sci Data 2024; 11:338. [PMID: 38580759 PMCID: PMC10997617 DOI: 10.1038/s41597-024-03136-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/11/2024] [Indexed: 04/07/2024] Open
Abstract
Athetis lepigone is an emerging highly polyphagous insect pest reported to cause crop damage in several European and Asian countries. However, our understanding of its genetic adaptation mechanisms has been limited due to lack of high-quality genetic resources. In this study, we present a chromosomal-level genome of A. lepigone, representing the first species in the genus of Athetis. We employed PacBio long-read sequencing and Hi-C technologies to generate 612.49 Mb genome assembly which contains 42.43% repeat sequences with a scaffold N50 of 20.9 Mb. The contigs were successfully clustered into 31 chromosomal-size scaffolds with 37% GC content. BUSCO assessment revealed a genome completeness of 97.4% with 96.3 identified as core Arthropoda single copy orthologs. Among the 17,322 genes that were predicted, 15,965 genes were functionally annotated, representing a coverage of 92.17%. Furthermore, we revealed 106 P450, 37 GST, 27 UGT, and 74 COE gene families in the genome of A. lepigone. This genome provides a significant and invaluable genomic resource for further research across the entire genus of Athetis.
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Affiliation(s)
- Alexander Yesaya
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Lei Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Yiheng Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005, Nanning, China
| | - Ji Zhang
- Sanya Nanfan Research Institute and College of Tropical Crops, Hainan University, Sanya, 572025, China
| | - Jingjie An
- Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Canter of Hebei Province, International Science and Technology Joint Research Canter on IPM of Hebei Province, Baoding, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
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26
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Jafar S, Jamil S, Yasin MS, Naseem A, Zahoor MY, Shehzad W, Imran M. Successful application of modified crude DNA extraction from muscle tissues for various types of PCR amplifications. Mol Biol Rep 2024; 51:490. [PMID: 38578476 DOI: 10.1007/s11033-024-09356-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND One of the most challenging aspects of nucleic acid amplification tests is the extraction of genomic DNA. However, achieving satisfactory quality and quantity of genomic DNA is not always easy, while the demand for rapid, low-cost and less laborious DNA isolation methods is ever-increasing. METHODS AND RESULTS We have developed a rapid (⁓2 min) crude DNA extraction method leading to direct-PCR that requires minimum reagents and laboratory equipment. It was developed by eliminating the time-consuming purification steps of DNA extraction, by processing the sample in optimized amounts of Taq KCl PCR buffer and DNARelease Additive/Proteinase K in only two minutes and carrying out amplification using conventional Taq DNA polymerase. The DNA preparation method was validated on muscle tissue samples from 12 different species as well as 48 cooked meat samples. Its compatibility was also successfully tested with different types of PCR amplification platforms extensively used for genetic analysis, such as simplex PCR, PCR-RFLP (Restriction Fragment Length Polymorphism), multiplex PCR, isothermal amplification, real-time PCR and DNA sequencing. CONCLUSIONS The developed protocol provides sufficient amount of crude DNA from muscle tissues of different species for PCR amplifications to identify species-of-origin via different techniques coupled with PCR. The simplicity and robustness of this protocol make nucleic acid amplification assays more accessible and affordable to researchers and authorities for both laboratory and point-of-care tests.
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Affiliation(s)
- Sana Jafar
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Salman Jamil
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Muhammad Sheraz Yasin
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Asif Naseem
- Institute of Molecular Biology and Biotechnology, The University of Lahore (Sargodha campus), 10-km Lahore road, Sargodha, Punjab, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Wasim Shehzad
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Muhammad Imran
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan.
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27
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He YB, Han L, Wang C, Fang J, Shang Y, Cai HL, Zhou Q, Zhang ZZ, Chen SL, Li JY, Liu YL. Bulk RNA-sequencing, single-cell RNA-sequencing analysis, and experimental validation reveal iron metabolism-related genes CISD2 and CYP17A1 are potential diagnostic markers for recurrent pregnancy loss. Gene 2024; 901:148168. [PMID: 38244949 DOI: 10.1016/j.gene.2024.148168] [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: 09/25/2023] [Revised: 01/06/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND Recurrent pregnancy loss (RPL) is associated with variable causes. Its etiology remains unexplained in about half of the cases, with no effective treatment available. Individuals with RPL have an irregular iron metabolism. In the present study, we identified key genes impacting iron metabolism that could be used for diagnosing and treating RPL. METHODS We obtained gene expression profiles from the Gene Expression Omnibus (GEO) database. The Molecular Signatures Database was used to identify 14 gene sets related to iron metabolism, comprising 520 iron metabolism genes. Differential analysis and a weighted gene co-expression network analysis (WGCNA) of gene expression revealed two iron metabolism-related hub genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) and immunohistochemistry were used on clinical samples to confirm our results. The receiver operating characteristic (ROC) analysis and immune infiltration analysis were conducted. In addition, we analyzed the distribution of genes and performed CellChat analysis by single-cell RNA sequencing. RESULTS The expression of two hub genes, namely, CDGSH iron sulfur domain 2 (CISD2)and Cytochrome P450 family 17 subfamily A member 1 (CYP17A1), were reduced in RPL, as verified by both qPCR and immunohistochemistry. The Gene Ontology (GO) analysis revealed the genes predominantly engaged in autophagy and iron metabolism. The area under the curve (AUC) demonstrated better diagnostic performance for RPL using CISD2 and CYP17A1. The single-cell transcriptomic analysis of RPL demonstrated that CISD2 is expressed in the majority of cell subpopulations, whereas CYP17A1 is not. The cell cycle analysis revealed highly active natural killer (NK) cells that displayed the highest communications with other cells, including the strongest interaction with macrophages through the migratory inhibitory factor (MIF) pathway. CONCLUSIONS Our study suggested that CISD2 and CYP17A1 genes are involved in abnormal iron metabolism, thereby contributing to RPL. These genes could be used as potential diagnostic and therapeutic markers for RPL.
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Affiliation(s)
- Yi-Bo He
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang Province, China
| | - Lu Han
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Cong Wang
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang Province, China
| | - Ju Fang
- Reproductive Center, Hainan Branch, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Sanya, Hainan Province, China
| | - Yue Shang
- Reproductive Center, Hainan Branch, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Sanya, Hainan Province, China
| | - Hua-Lei Cai
- Department of Emergency Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Qun Zhou
- Obstetrics and Gynecology, First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang Province, China
| | - Zhe-Zhong Zhang
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang Province, China
| | - Shi-Liang Chen
- Department of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang Province, China.
| | - Jun-Yu Li
- Pharmacy Department, Hainan Branch, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Sanya, Hainan Province, China.
| | - Yong-Lin Liu
- Reproductive Center, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China.
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28
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Remines M, Schoonover MG, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine. G3 (Bethesda) 2024; 14:jkae002. [PMID: 38184845 PMCID: PMC10989883 DOI: 10.1093/g3journal/jkae002] [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: 11/17/2023] [Revised: 11/17/2023] [Accepted: 12/16/2023] [Indexed: 01/09/2024]
Abstract
The SAM1 and SAM2 genes encode for S-Adenosylmethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1Δ/sam1Δ, and sam2Δ/sam2Δ strains in 15 different Phenotypic Microarray plates with different components and measured growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. We explored how the phenotypic growth differences are linked to the altered gene expression, and hypothesize mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact pathways and processes. We present 6 stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role in production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Makailyn G Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Kellyn M Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
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29
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Roberts JB, Boldvig OLG, Aubourg G, Kanchenapally ST, Deehan DJ, Rice SJ, Loughlin J. Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence. Arthritis Res Ther 2024; 26:78. [PMID: 38570801 PMCID: PMC10988806 DOI: 10.1186/s13075-024-03315-8] [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: 11/30/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism (SNP) rs34195470 (A > G). The OA risk-conferring G allele of this SNP associates with increased DNA methylation (DNAm) at two CpG dinucleotides within WWP2. This gene encodes a ubiquitin ligase and is the host gene of microRNA-140 (miR-140). WWP2 and miR-140 are both regulators of TGFβ signaling. METHODS Nucleic acids were extracted from adult OA (arthroplasty) and foetal cartilage. Samples were genotyped and DNAm quantified by pyrosequencing at the two CpGs plus 14 flanking CpGs. CpGs were tested for transcriptional regulatory effects using a chondrocyte cell line and reporter gene assay. DNAm was altered using epigenetic editing, with the impact on gene expression determined using RT-qPCR. In silico analysis complemented laboratory experiments. RESULTS rs34195470 genotype associates with differential methylation at 14 of the 16 CpGs in OA cartilage, forming a methylation quantitative trait locus (mQTL). The mQTL is less pronounced in foetal cartilage (5/16 CpGs). The reporter assay revealed that the CpGs reside within a transcriptional regulator. Epigenetic editing to increase their DNAm resulted in altered expression of the full-length and N-terminal transcript isoforms of WWP2. No changes in expression were observed for the C-terminal isoform of WWP2 or for miR-140. CONCLUSIONS As far as we are aware, this is the first experimental demonstration of an OA association signal targeting specific transcript isoforms of a gene. The WWP2 isoforms encode proteins with varying substrate specificities for the components of the TGFβ signaling pathway. Future analysis should focus on the substrates regulated by the two WWP2 isoforms that are the targets of this genetic risk.
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Affiliation(s)
- Jack B Roberts
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Olivia L G Boldvig
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Guillaume Aubourg
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - S Tanishq Kanchenapally
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Deehan
- Freeman Hospital, Newcastle University Teaching Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
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30
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Saunders CJ, Brunelli L, Deem MJ, Farrow EG, Hegde M, Stark Z. More Than a Decade of Rapid Genomic Sequencing: Where Are We Now? Clin Chem 2024; 70:577-583. [PMID: 38565214 PMCID: PMC10987227 DOI: 10.1093/clinchem/hvae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Affiliation(s)
- Carol J Saunders
- Director, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Luca Brunelli
- Professor of Pediatrics, Division of Neonatology, Department of Pediatrics, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT, United States
| | - Michael J Deem
- Associate Professor, Department of Human Genetics, Core Faculty, Center for Bioethics & Health Law, University of Pittsburgh, Pittsburgh, PA, United States
| | - Emily G Farrow
- Director of Genomics Operations, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Associate Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Madhuri Hegde
- Vice President and Chief Scientific Officer, Revvity Inc., Waltham, MA, United States
| | - Zornitza Stark
- Professor, Department of Paediatrics, University of Melbourne; Australian Genomics; Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
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31
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Gonzalez P, Hauck QC, Baxevanis AD. Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution. Genome Biol Evol 2024; 16:evae052. [PMID: 38502060 PMCID: PMC10988421 DOI: 10.1093/gbe/evae052] [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: 08/06/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs and reconstructed the temporal dynamics of their appearance in each lineage, as well as determining their spatial distribution across genomes. We show that CNEs evolve repeatedly around the same genes across the Metazoa, including around homeodomain genes and other transcription factors; they also evolve repeatedly around genes involved in neural development. We also show that transposons are a major source of CNEs, confirming previous observations from vertebrates and suggesting that they have played a major role in wiring developmental gene regulatory mechanisms since the dawn of animal evolution.
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Affiliation(s)
- Paul Gonzalez
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quinn C Hauck
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Hardy J, Demecheleer E, Schauvliege M, Staelens D, Mortier V, Verhofstede C. Reverse transcription of plasma-derived HIV-1 RNA generates multiple artifacts through tRNA(Lys-3)-priming. Microbiol Spectr 2024; 12:e0387223. [PMID: 38442427 DOI: 10.1128/spectrum.03872-23] [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: 11/06/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
In vitro reverse transcription of full-length HIV-1 RNA extracted from the blood plasma of people living with HIV-1 remains challenging. Here, we describe the initiation of reverse transcription of plasma-derived viral RNA in the absence of an exogenous primer. Real-time PCR and Sanger sequencing were applied to identify the source and to monitor the outcome of this reaction. Results demonstrated that during purification of viral RNA from plasma, tRNA(Lys-3) is co-extracted in a complex with the viral RNA. In the presence of a reverse transcription enzyme, this tRNA(Lys-3) can induce reverse transcription, a reaction that is not confined to transcription of the 5' end of the viral RNA. A range of cDNA products is generated, most of them indicative for the occurrence of in vitro strand transfer events that involve translocation of cDNA from the 5' end to random positions on the viral RNA. This process results in the formation of cDNAs with large internal deletions. However, near full-length cDNA and cDNA with sequence patterns resembling multiple spliced HIV-1 RNA were also detected. Despite its potential to introduce significant bias in the interpretation of results across various applications, tRNA(Lys-3)-driven reverse transcription has been overlooked thus far. A more in-depth study of this tRNA-driven in vitro reaction may provide new insight into the complex process of in vivo HIV-1 replication.IMPORTANCEThe use of silica-based extraction methods for purifying HIV-1 RNA from viral particles is a common practice, but it involves co-extraction of human tRNA(Lys-3) due to the strong interactions between these molecules. This co-extraction becomes particularly significant when the extracted RNA is used in reverse transcription reactions, as the tRNA(Lys-3) then serves as a primer. Reverse transcription from tRNA(Lys-3) is not confined to cDNA synthesis of the 5' end of the viral RNA but extends across various regions of the viral genome through in vitro strand transfer events. Co-extraction of tRNA(Lys-3) has been overlooked thus far, despite its potential to introduce bias in downstream, reverse transcription-related applications. The observed events in the tRNA(Lys-3)-induced in vitro reverse transcription resemble in vivo replication processes. Therefore, these reactions may offer a unique model to better understand the replication dynamics of HIV-1.
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Affiliation(s)
- Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Dabin A, Stirnemann G. Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence. Biophys Chem 2024; 307:107167. [PMID: 38262278 DOI: 10.1016/j.bpc.2023.107167] [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: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université de Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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Tanabe K, Miyazaki K, Umeno H, Takemoto M, Nakano S. Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes. Biochimie 2024; 219:110-117. [PMID: 37972915 DOI: 10.1016/j.biochi.2023.11.005] [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: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Affiliation(s)
- Kazuya Tanabe
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouichi Miyazaki
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hikari Umeno
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Marina Takemoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - S Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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Blandin L, Guidicelli G, Wojciechowski E, Rouzaire P, Lemal R. Characterization of the novel HLA-DQB1*02:01:01:21Q allele by sequencing-based typing. HLA 2024; 103:e15468. [PMID: 38575356 DOI: 10.1111/tan.15468] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
HLA-DQB1*02:01:01:21Q differs from HLA-DQB1*02:01:01:01 by one nucleotide substitution in the splice site in the beginning of intron 3.
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Affiliation(s)
- Lucie Blandin
- Histocompatibility and Immunogenetics Laboratory, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Elodie Wojciechowski
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Paul Rouzaire
- Histocompatibility and Immunogenetics Laboratory, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
- EA7453 CHELTER, Clermont-Auvergne University, Clermont-Ferrand, France
| | - Richard Lemal
- Histocompatibility and Immunogenetics Laboratory, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
- EA7453 CHELTER, Clermont-Auvergne University, Clermont-Ferrand, France
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36
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Dhuyser A, Pérès M, Clément S, Morel T, Aarnink A. The novel HLA-DPB1*1467:01 allele characterised by two different sequencing-based typing techniques. HLA 2024; 103:e15409. [PMID: 38575362 DOI: 10.1111/tan.15409] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
The novel allele HLA-DPB1*1467:01 differs from HLA-DPB1*09:01:01:01 by one non-synonymous nucleotide substitution in exon 2.
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Affiliation(s)
- Adèle Dhuyser
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
| | - Michaël Pérès
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Sandra Clément
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Thomas Morel
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
| | - Alice Aarnink
- HLA and Histocompatibility Laboratory, CHRU de Nancy, Vandoeuvre les Nancy, France
- IMoPA 6, UMR7365 CNRS, Université de Lorraine, Vandoeuvre-les-Nancy, France
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37
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Morishita S. A whole-genome shotgun approach to human reference genome sequencing. Nat Rev Genet 2024; 25:236. [PMID: 38307946 DOI: 10.1038/s41576-024-00703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Affiliation(s)
- Shinichi Morishita
- Department of Computational Biology and Medical Sciences, University of Tokyo, Tokyo, Japan.
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38
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Wilson HE, Wyrick JJ. Genome-wide impact of cytosine methylation and DNA sequence context on UV-induced CPD formation. Environ Mol Mutagen 2024; 65 Suppl 1:14-24. [PMID: 37554110 PMCID: PMC10853481 DOI: 10.1002/em.22569] [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: 04/05/2023] [Revised: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023]
Abstract
Exposure to ultraviolet (UV) light is the primary etiological agent for skin cancers because UV damages cellular DNA. The most frequent form of UV damage is the cyclobutane pyrimidine dimer (CPD), which consists of covalent linkages between neighboring pyrimidine bases in DNA. In human cells, the 5' position of cytosine bases in CG dinucleotides is frequently methylated, and methylated cytosines in the TP53 tumor suppressor are often sites of mutation hotspots in skin cancers. It has been argued that this is because cytosine methylation promotes UV-induced CPD formation; however, the effects of cytosine methylation on CPD formation are controversial, with conflicting results from previous studies. Here, we use a genome-wide method known as CPD-seq to map UVB- and UVC-induced CPDs across the yeast genome in the presence or absence in vitro methylation by the CpG methyltransferase M.SssI. Our data indicate that cytosine methylation increases UVB-induced CPD formation nearly 2-fold relative to unmethylated DNA, but the magnitude of induction depends on the flanking sequence context. Sequence contexts with a 5' guanine base (e.g., GCCG and GTCG) show the strongest induction due to cytosine methylation, potentially because these sequence contexts are less efficient at forming CPD lesions in the absence of methylation. We show that cytosine methylation also modulates UVC-induced CPD formation, albeit to a lesser extent than UVB. These findings can potentially reconcile previous studies, and define the impact of cytosine methylation on UV damage across a eukaryotic genome.
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Affiliation(s)
- Hannah E. Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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39
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Schmidt N, Sielemann K, Breitenbach S, Fuchs J, Pucker B, Weisshaar B, Holtgräwe D, Heitkam T. Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. Plant J 2024; 118:171-190. [PMID: 38128038 DOI: 10.1111/tpj.16599] [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: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Sarah Breitenbach
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Graz, Austria
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40
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Wang J, Wu S, Ye K. Complicated target recognition by archaeal box C/D guide RNAs. Sci China Life Sci 2024; 67:631-644. [PMID: 38041781 DOI: 10.1007/s11427-022-2412-3] [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: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 12/03/2023]
Abstract
Box C/D RNAs guide the site-specific formation of 2'-O-methylated nucleotides (Nm) of RNAs in eukaryotes and archaea. Although C/D RNAs have been profiled in several archaea, their targets have not been experimentally determined. Here, we mapped Nm in rRNAs, tRNAs, and abundant small RNAs (sRNAs) and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus. The targets of C/D RNAs were assigned by analysis of base-pairing interactions, in vitro modification assays, and gene deletion experiments, revealing a complicated landscape of C/D RNA-target interactions. C/D RNAs widely use dual antisense elements to target adjacent sites in rRNAs, enhancing modification at weakly bound sites. Two consecutive sites can be guided with the same antisense element upstream of box D or D', a phenomenon known as double-specificity that is exclusive to internal box D' in eukaryotic C/D RNAs. Several C/D RNAs guide modification at a single non-canonical site. This study reveals the global landscape of RNA-guided 2'-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.
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Affiliation(s)
- Jiayin Wang
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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41
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Hoelzel AR, Gkafas GA, Kang H, Sarigol F, Le Boeuf B, Costa DP, Beltran RS, Reiter J, Robinson PW, McInerney N, Seim I, Sun S, Fan G, Li S. Genomics of post-bottleneck recovery in the northern elephant seal. Nat Ecol Evol 2024; 8:686-694. [PMID: 38383849 PMCID: PMC11009102 DOI: 10.1038/s41559-024-02337-4] [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: 06/29/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence. Recovery was rapid and now there are over 200,000 individuals. We sequenced 260 modern and 8 historical northern elephant seal nuclear genomes to assess the impact of the population bottleneck on individual northern elephant seals and to better understand their recovery. Here we show that inbreeding, an increase in the frequency of alleles compromised by lost function, and allele frequency distortion, reduced the fitness of breeding males and females, as well as the performance of adult females on foraging migrations. We provide a detailed investigation of the impact of a severe bottleneck on fitness at the genomic level and report on the role of specific gene systems.
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Affiliation(s)
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Burney Le Boeuf
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Daniel P Costa
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Roxanne S Beltran
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Joanne Reiter
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Patrick W Robinson
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Nancy McInerney
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | | | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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42
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Zhu N, Xue WJ, An L, Yan XF, Zheng J. The novel HLA-DPB1*1500:01N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual. HLA 2024; 103:e15483. [PMID: 38605645 DOI: 10.1111/tan.15483] [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: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
HLA-DPB1*1500:01N differs from HLA-DPB1*05:01:01:01 by one nucleotide in exon 3.
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Affiliation(s)
- Ning Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Wu-Jun Xue
- Department of Kidney Transplantation, Hospital of Nephrology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lin An
- Department of Laboratory, Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Xiao-Fei Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Jin Zheng
- Department of Kidney Transplantation, Hospital of Nephrology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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43
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Ge J, Wang Z, Wu J. NAT10-mediated ac 4C modification promotes ectoderm differentiation of human embryonic stem cells via acetylating NR2F1 mRNA. Cell Prolif 2024; 57:e13577. [PMID: 38041497 PMCID: PMC10984107 DOI: 10.1111/cpr.13577] [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] [Received: 08/02/2023] [Revised: 10/11/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023] Open
Abstract
Cell fate determination in mammalian development is complex and precisely controlled and accumulating evidence indicates that epigenetic mechanisms are crucially involved. N4-acetylcytidine (ac4C) is a recently identified modification of messenger RNA (mRNA); however, its functions are still elusive in mammalian. Here, we show that N-acetyltransferase 10 (NAT10)-mediated ac4C modification promotes ectoderm differentiation of human embryonic stem cells (hESCs) by acetylating nuclear receptor subfamily 2 group F member 1 (NR2F1) mRNA to enhance translation efficiency (TE). Acetylated RNA immunoprecipitation sequencing (acRIP-seq) revealed that levels of ac4C modification were higher in ectodermal neuroepithelial progenitor (NEP) cells than in hESCs or mesoendoderm cells. In addition, integrated analysis of acRIP-seq and ribosome profiling sequencing revealed that NAT10 catalysed ac4C modification to improve TE in NEP cells. RIP-qRT-PCR analysis identified an interaction between NAT10 and NR2F1 mRNA in NEP cells and NR2F1 accelerated the nucleus-to-cytoplasm translocation of yes-associated protein 1, which contributed to ectodermal differentiation of hESCs. Collectively, these findings point out the novel regulatory role of ac4C modification in the early ectodermal differentiation of hESCs and will provide a new strategy for the treatment of neuroectodermal defects diseases.
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Affiliation(s)
- Junbang Ge
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoxia Wang
- Laboratory Animal Center of Instrumental Analysis CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Ji Wu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical SciencesNingxia Medical UniversityYinchuanChina
- Shanghai Key Laboratory of Reproductive MedicineShanghaiChina
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Hussian CHAC, Rahman RNZRA, Leow ATC, Salleh AB, Ali MSM, Latip W. Enhancement in T1 lipase purification recovery using the novel construct pGEX4T1/His-T1. Prep Biochem Biotechnol 2024; 54:526-534. [PMID: 37647127 DOI: 10.1080/10826068.2023.2252052] [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: 09/01/2023]
Abstract
The Geobacillus zalihae strain T1 produces a thermostable T1 lipase that could be used for industrial purposes. Previously, the GST-T1 lipase was purified through two chromatographic steps: affinity and ion exchange (IEX) but the recovery yield was only 33%. To improve the recovery yield to over 80%, the GST tag from the pGEX system was replaced with a poly-histidine at the N-terminal of the T1 lipase sequence. The novel construct of pGEX/His-T1 lipase was developed by site-directed mutagenesis, where the XbaI restriction site was introduced upstream of the GST tag, allowing the removal of tag via double digestion using XbaI and EcoRI (existing cutting site in the pGEX system). Fragment of 6 × His-T1 lipase fusion was synthesized, cloned into the pGEX4T1 system, and expressed in Escherichia coli BL21 (DE3) pLysS, resulting in lipase-specific activity at 236 U/mg. The single purification step of His-T1 lipase was successfully achieved using nickel Sepharose 6FF with an optimized concentration of 5 mM imidazole for binding, yielding the recovery of 98%, 1,353 U/mg lipase activity, and a 5.7-fold increase in purification fold. His-T1 lipase was characterized and was found to be stable at pH 5-9, active at 70 °C, and optimal at pH 9.
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Affiliation(s)
- Che Haznie Ayu Che Hussian
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Adam Thean Chor Leow
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
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Sun JR, Kong CF, Ye YX, Wang Q, Qu XK, Jia LQ, Wu S. Integrated analysis of single-cell and bulk RNA-sequencing reveals a novel signature based on NK cell marker genes to predict prognosis and immunotherapy response in gastric cancer. Sci Rep 2024; 14:7648. [PMID: 38561388 PMCID: PMC10985121 DOI: 10.1038/s41598-024-57714-7] [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: 12/25/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK) cells play essential roles in the tumor development, diagnosis, and prognosis of tumors. In this study, we aimed to establish a reliable signature based on marker genes in NK cells, thus providing a new perspective for assessing immunotherapy and the prognosis of patients with gastric cancer (GC). We analyzed a total of 1560 samples retrieved from the public database. We performed a comprehensive analysis of single-cell RNA-sequencing (scRNA-seq) data of gastric cancer and identified 377 marker genes for NK cells. By performing Cox regression analysis, we established a 12-gene NK cell-associated signature (NKCAS) for the Cancer Genome Atlas (TCGA) cohort, that assigned GC patients into a low-risk group (LRG) or a high-risk group (HRG). In the TCGA cohort, the areas under curve (AUC) value were 0.73, 0.81, and 0.80 at 1, 3, and 5 years. External validation of the predictive ability for the signature was then validated in the Gene Expression Omnibus (GEO) cohorts (GSE84437). The expression levels of signature genes were measured and validated in GC cell lines by real-time PCR. Moreover, NKCAS was identified as an independent prognostic factor by multivariate analysis. We combined this with a variety of clinicopathological characteristics (age, M stage, and tumor grade) to construct a nomogram to predict the survival outcomes of patients. Moreover, the LRG showed higher immune cell infiltration, especially CD8+ T cells and NK cells. The risk score was negatively associated with inflammatory activities. Importantly, analysis of the independent immunotherapy cohort showed that the LRG had a better prognosis and immunotherapy response when compared with the HRG. The identification of NK cell marker genes in this study suggests potential therapeutic targets. Additionally, the developed predictive signatures and nomograms may aid in the clinical management of GC.
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Affiliation(s)
- Jian-Rong Sun
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Chen-Fan Kong
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China
| | - Yi-Xiang Ye
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Qin Wang
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Xiang-Ke Qu
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Li-Qun Jia
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China.
| | - Song Wu
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China.
- Department of Urology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China.
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Zhuang J, Zhang R, Zhou B, Cao Z, Zhou J, Chen X, Zhang N, Zhu Y, Yang J. Mutation analysis of RHO in patients with non-syndromic retinitis pigmentosa. Ophthalmic Genet 2024; 45:147-152. [PMID: 38284172 DOI: 10.1080/13816810.2023.2294843] [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: 08/23/2023] [Accepted: 12/09/2023] [Indexed: 01/30/2024]
Abstract
PURPOSE To identify RHO mutations in patients with non-syndromic retinitis pigmentosa (NS-RP). METHODS A total of 143 probands (46 family history and 97 sporadic cases) with NS-RP were recruited from Southeast China. The coding exons and adjacent intronic regions of RHO were PCR-amplified and sequenced by Sanger sequencing. The candidate variant was evaluated by the guidelines of American College of Medical Genetics and further validated through co-segregation analysis within the family. RESULTS Five heterozygous mutations in RHO were detected in 5 out of 143 probands, where the frequency of RHO mutations in our cohort was approximately 3.5% (5/143) and 10.8% (5/46) for probands and families with NS-RP, respectively. Three known disease-causing mutations including c.C1030T (p.Q344X), c.C173G (p.T58R), and c.G266A (p.G89D) were identified in three unrelated families. The other two previously unreported mutations c.557C>A (p.S186X) and c.944delA (p.N315TfsX43) were confirmed in Family RP-087 and Family RP-139, respectively. These mutations co-segregated with available affected individuals in each family were not observed in the unaffected family members or in the 112 unrelated controls. CONCLUSIONS This report expands the mutational spectrum of RHO gene associated with NS-RP and demonstrates the frequency of RP RHO mutations in Southeast Chinese populations.
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Affiliation(s)
- Jianfu Zhuang
- Ophthalmology, Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Rongcai Zhang
- Fujian Baimeng Biotechnology Research Center, Fujian BioMed Technology Co. LTD, Fuzhou, Fujian, China
| | - Biting Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zongfu Cao
- National Human Genetic Resources Center, National Research Institute for Family Planning, Beijing, China
| | - Jie Zhou
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaole Chen
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Nanwen Zhang
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
| | - Yihua Zhu
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Juhua Yang
- Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China
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Machulin AV, Deryusheva EI, Galzitskaya OV. Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene. Biosystems 2024; 238:105196. [PMID: 38537772 DOI: 10.1016/j.biosystems.2024.105196] [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: 10/03/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024]
Abstract
Protein domain repeats are known to arise due to tandem duplications of internal genes. However, the understanding of the underlying mechanisms of this process is incomplete. The goal of this work was to investigate the mechanism of occurrence of repeat expansion based on studying the sequences of 1324 rpsA genes of bacterial S1 ribosomal proteins containing different numbers of S1 structural domains. The rpsA gene encodes ribosomal S1 protein, which is essential for cell viability as it interacts with both mRNA and proteins. Gene ontology (GO) analysis of S1 domains in ribosomal S1 proteins revealed that bacterial protein sequences in S1 mainly have 3 types of molecular functions: RNA binding activity, nucleic acid activity, and ribosome structural component. Our results show that the maximum value of rpsA gene identity for full-length proteins was found for S1 proteins containing six structural domains (58%). Analysis of consensus sequences showed that parts of the rpsA gene encoding separate S1 domains have no a strictly repetitive structure between groups containing different numbers of S1 domains. At the same time, gene regions encoding some conserved residues that form the RNA-binding site remain conserved. The detected phylogenetic similarity suggests that the proposed fold of the rpsA translation initiation region of Escherichia coli has functional value and is important for translational control of rpsA gene expression in other bacterial phyla, but not only in gamma Proteobacteria.
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Affiliation(s)
- Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290, Pushchino, Moscow Region, Russia
| | - Evgeniya I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.
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Tusseau M, Eyries M, Chatron N, Coulet F, Guichet A, Colin E, Demeer B, Maillard H, Thevenon J, Lavigne C, Saillour V, Paris C, De Sainte Agathe JM, Pujalte M, Guilhem A, Dupuis-Girod S, Lesca G. Genome sequencing identify chromosome 9 inversions disrupting ENG in 2 unrelated HHT families. Eur J Med Genet 2024; 68:104919. [PMID: 38355093 DOI: 10.1016/j.ejmg.2024.104919] [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: 07/25/2023] [Revised: 01/05/2024] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT), also known as Rendu-Osler-Weber disease, is a dominant inherited vascular disorder. The clinical diagnosis is based on the Curaçao criteria and pathogenic variants in the ENG and ACVRL1 genes are responsible for most cases of HHT. Four families with a negative targeted gene panel and selected by a multidisciplinary team were selected and whole-genome sequencing was performed according to the recommendations of the French National Plan for Genomic Medicine. Structural variations were confirmed by standard molecular cytogenetic analysis (FISH). In two families with a definite diagnosis of HHT, we identified two different paracentric inversions of chromosome 9, both disrupting the ENG gene. These inversions are considered as pathogenic and causative for the HHT phenotype of the patients. This is the first time structural variations are reported to cause HHT. As such balanced events are often missed by exon-based sequencing (panel, exome), structural variations may be an under-recognized cause of HHT. Genome sequencing for the detection of these events could be suggested for patients with a definite diagnosis of HHT and in whom no causative pathogenic variant was identified.
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Affiliation(s)
- M Tusseau
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - M Eyries
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - N Chatron
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - F Coulet
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - A Guichet
- Service de Génétique Médicale, CHU D'Angers, Angers, France
| | - E Colin
- Service de Génétique Médicale, CHU D'Angers, Angers, France
| | - B Demeer
- Genetics Department, CLAD Nord de France, CHU Amiens, France; CHIMERE, UR UPJV 7516, Université Picardie Jules Verne, Amiens, France
| | - H Maillard
- Department of Internal Medicine and Clinical Immunology, Referral Centre for Rare Systemic Autoimmune Diseases for North and North-West France (CeRAINO), CHU Lille, 59000, Lille, France
| | | | - C Lavigne
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | - V Saillour
- Laboratoire Multisites SeqOIA, Paris, France
| | - C Paris
- Laboratoire AURAGEN, Lyon, France
| | - J M De Sainte Agathe
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - M Pujalte
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - A Guilhem
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France
| | - S Dupuis-Girod
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France
| | - G Lesca
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France.
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Kuang R, Xu Z, Zhou H, Zhang Z, Peng H, Wang D, Xu X, Zhao S, Zhao Y, Zhu M. H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig. Anim Genet 2024; 55:217-229. [PMID: 38296601 DOI: 10.1111/age.13400] [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] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.
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Affiliation(s)
- Renzhuo Kuang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Honghong Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Hao Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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50
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Li B, Yang J. A twist in the tale: global insights into archaeal box C/D RNA-guided 2'-O-methylation. Sci China Life Sci 2024; 67:849-850. [PMID: 38502431 DOI: 10.1007/s11427-024-2553-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Affiliation(s)
- Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China.
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