Advanced genetics (Hoboken, N.J.)最新文献

(Advanced Genetics 3/05) (高级遗传学 3/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-09-17 DOI: 10.1002/ggn2.202470015

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Editorial Board: (Advanced Genetics 3/05) 编辑委员会：（高级遗传学 3/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-09-17 DOI: 10.1002/ggn2.202470016

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(Advanced Genetics 2/05) (高级遗传学 2/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-06-13 DOI: 10.1002/ggn2.202470013

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Editorial Board: (Advanced Genetics 2/05) 编辑委员会：（高级遗传学 2/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-06-13 DOI: 10.1002/ggn2.202470014

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Validated Negative Regions (VNRs) in the VISTA Database might be Truncated Forms of Bona Fide Enhancers VISTA 数据库中的验证负区 (VNR) 可能是真正增强子的截断形式

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-05-16 DOI: 10.1002/ggn2.202300209

Pengyu Ni, Siwen Wu, Zhengchang Su

{"title":"Validated Negative Regions (VNRs) in the VISTA Database might be Truncated Forms of Bona Fide Enhancers","authors":"Pengyu Ni, Siwen Wu, Zhengchang Su","doi":"10.1002/ggn2.202300209","DOIUrl":"10.1002/ggn2.202300209","url":null,"abstract":"The VISTA enhancer database is a valuable resource for evaluating predicted enhancers in humans and mice. In addition to thousands of validated positive regions (VPRs) in the human and mouse genomes, the database also contains similar numbers of validated negative regions (VNRs). It is previously shown that the VPRs are on average half as long as predicted overlapping enhancers that are highly conserved and hypothesize that the VPRs may be truncated forms of long bona fide enhancers. Here, it is shown that like the VPRs, the VNRs also are under strong evolutionary constraints and overlap predicted enhancers in the genomes. The VNRs are also on average half as long as predicted overlapping enhancers that are highly conserved. Moreover, the VNRs and the VPRs display similar cell/tissue-specific modification patterns of key epigenetic marks of active enhancers. Furthermore, the VNRs and the VPRs show similar impact score spectra of in silico mutagenesis. These highly similar properties between the VPRs and the VNRs suggest that like the VPRs, the VNRs may also be truncated forms of long bona fide enhancers.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202300209","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140971956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India 通过高通量测序揭示南印度独特队列中合并聋哑和男性不育表型的遗传基础

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-05-08 DOI: 10.1002/ggn2.202300206

Jeffrey Justin Margret, Chandru Jayasankaran, Pavithra Amritkumar, Hela Azaiez, C. R. Srikumari Srisailapathy

{"title":"Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India","authors":"Jeffrey Justin Margret, Chandru Jayasankaran, Pavithra Amritkumar, Hela Azaiez, C. R. Srikumari Srisailapathy","doi":"10.1002/ggn2.202300206","DOIUrl":"10.1002/ggn2.202300206","url":null,"abstract":"The co-occurrence of sensorineural hearing loss and male infertility has been reported in several instances, suggesting potential shared genetic underpinnings. One such example is the contiguous gene deletion of CATSPER2 and STRC genes, previously associated with deafness-infertility syndrome (DIS) in males. Fifteen males with both hearing loss and infertility from southern India after exclusion for the DIS contiguous gene deletion and the FOXI1 gene mutations are subjected to exome sequencing. This resolves the genetic etiology in four probands for both the phenotypes; In the remaining 11 probands, two each conclusively accounted for deafness and male infertility etiologies. Genetic heterogeneity is well reflected in both phenotypes. Four recessive (TRIOBP, SLC26A4, GJB2, COL4A3) and one dominant (SOX10) for the deafness; six recessive genes (LRGUK, DNAH9, ARMC4, DNAH2, RSPH6A, and ACE) for male infertility can be conclusively ascribed. LRGUK and RSPH6A genes are implicated earlier only in mice models, while the ARMC4 gene is implicated in chronic destructive airway diseases due to primary ciliary dyskinesia. This study would be the first to document the role of these genes in the male infertility phenotype in humans. The result suggests that deafness and infertility are independent events and do not segregate together among the probands.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202300206","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140999553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth-Promoting Bacteria 研究寄主植物与植物生长促进细菌之间相互作用的生态相关遗传学

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-03-21 DOI: 10.1002/ggn2.202300210

Rémi Duflos, Fabienne Vailleau, Fabrice Roux

{"title":"Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth-Promoting Bacteria","authors":"Rémi Duflos, Fabienne Vailleau, Fabrice Roux","doi":"10.1002/ggn2.202300210","DOIUrl":"10.1002/ggn2.202300210","url":null,"abstract":"The social movement to reduce reliance on pesticides and synthesized fertilizers and the growing global demand for sustainable food supplies require the development of eco-friendly and sustainable agricultural practices. In line, plant growth-promoting bacteria (PGPB) can participate in creating innovative agroecological systems. While the effectiveness of PGPB is highly influenced by abiotic conditions and microbe–microbe interactions, beneficial plant–PGPB interactions can also highly depend on both host and PGPB genotype. Here, the state of the art on the extent of natural genetic variation of plant–PGPB interactions and the underlying genetic architecture, in particular in Arabidopsis thaliana is reviewed. Extensive natural plant genetic variation in response to PGPB is associated with a polygenic architecture and genetic pathways rarely mentioned as being involved in the response to PGPB. To date, natural genetic variation within PGPB is little explored, which may in turn allow the identification of new genetic pathways underlying benefits to plants. Accordingly, several avenues to better understand the genomic and molecular landscape of plant–PGPB interactions are introduced. Finally, the need for establishing thorough functional studies of candidate genes underlying Quantitative Trait Loci and estimating the extent of genotype-by-genotype-by-environment interactions within the context of realistic (agro-)ecological conditions is advocated.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"5 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202300210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140223324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Editorial Board: (Advanced Genetics 1/05) 编辑委员会：（高级遗传学 1/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-03-07 DOI: 10.1002/ggn2.202470012

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(Advanced Genetics 1/05) (高级遗传学 1/05）

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-03-07 DOI: 10.1002/ggn2.202470011

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The Surprising Diversity of UV-Induced Mutations 紫外线诱导突变的惊人多样性

Advanced genetics (Hoboken, N.J.) Pub Date : 2024-03-07 DOI: 10.1002/ggn2.202300205

Marian F. Laughery, Hannah E. Wilson, Allysa Sewell, Scott Stevison, John J. Wyrick

{"title":"The Surprising Diversity of UV-Induced Mutations","authors":"Marian F. Laughery, Hannah E. Wilson, Allysa Sewell, Scott Stevison, John J. Wyrick","doi":"10.1002/ggn2.202300205","DOIUrl":"https://doi.org/10.1002/ggn2.202300205","url":null,"abstract":"Ultraviolet (UV) light is the most pervasive environmental mutagen and the primary cause of skin cancer. Genome sequencing of melanomas and other skin cancers has revealed that the vast majority of somatic mutations in these tumors are cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which, together with tandem CC>TT substitutions, comprise the canonical UV mutation “signature”. These mutation classes are caused by DNA damage directly induced by UV absorption, namely cyclobutane pyrimidine dimers (CPDs) or 6-4 pyrimidine-pyrimidone photoproducts (6-4PP), which form between neighboring pyrimidine bases. However, many of the key driver mutations in melanoma do not fit this mutation signature, but instead are caused by T>A, T>C, C>A, or AC>TT substitutions, frequently occurring in non-dipyrimidine sequence contexts. This article describes recent studies indicating that UV light causes a more diverse spectrum of mutations than previously appreciated, including many of the mutation classes observed in melanoma driver mutations. Potential mechanisms for these diverse mutation signatures are discussed, including UV-induced pyrimidine-purine photoproducts and indirect DNA damage induced by UVA light. Finally, the article reviews recent findings indicating that human DNA polymerase eta normally suppresses these non-canonical UV mutation classes, which can potentially explain why canonical C>T substitutions predominate in human skin cancers.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202300205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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