GeneticsPub Date : 2023-12-01DOI: 10.1093/genetics/iyad193
Gabor Juhász, Aashiq H. Kachroo, David Kadosh, Toshie Kai, Daniel Kalderon, Oguz Kanca, Nolan Kane, Hyun Min Kang, Si-Yong Kang, Joshua Kaplan, Martin Kapun, David Karasik, X. Karp, Gary Karpen, Cooper Kashtelyan, Yona Kassir, Judith Kassis, Prasad Kasturi, Martin Kater, Thomas Kaufman, Kerstin Kaufman, Paul Kaufman, Karla Kaun, Tadeusz Kawecki, Siraj Kayondo, Wenfan Ke, Gregory Keele, Patrick Keeling, Alex Keene, A. Keinan, Krystyna Keleman, Erin Kelleher, Christina Kelliher, Elizabeth Kellogg, John Kelly, Gavin Kelsey, Scott Kennedy, Michael Keogh, Benjamin Kerr, Oliver Kerscher, Douglas Kiel, Amy Kiger, Kyuhyung Kim, Nayun Kim, John Kim, Sarah Kim-Hellmuth, Elizabeth King, Mark Kirkpatrick, Ranjana Kishore, Satoshi Kitamura, Maiko Kitaoka, Christian Klaembt, Hannah Klein, Daniel Kliebenstein, Anke Kloock, Hisato Kobayashi, Kyunghee Koh, Chandrika Konwar, Maarten Koornneef, David Kopecky, Sergey Koren, Tom Kornberg, Katharine Korunes, Douglas Koshland, Luise Kost, Sandhya Koushika, Genevieve Kozak, Helmut
{"title":"GENETICS 2023 Reviewer Index","authors":"Gabor Juhász, Aashiq H. Kachroo, David Kadosh, Toshie Kai, Daniel Kalderon, Oguz Kanca, Nolan Kane, Hyun Min Kang, Si-Yong Kang, Joshua Kaplan, Martin Kapun, David Karasik, X. Karp, Gary Karpen, Cooper Kashtelyan, Yona Kassir, Judith Kassis, Prasad Kasturi, Martin Kater, Thomas Kaufman, Kerstin Kaufman, Paul Kaufman, Karla Kaun, Tadeusz Kawecki, Siraj Kayondo, Wenfan Ke, Gregory Keele, Patrick Keeling, Alex Keene, A. Keinan, Krystyna Keleman, Erin Kelleher, Christina Kelliher, Elizabeth Kellogg, John Kelly, Gavin Kelsey, Scott Kennedy, Michael Keogh, Benjamin Kerr, Oliver Kerscher, Douglas Kiel, Amy Kiger, Kyuhyung Kim, Nayun Kim, John Kim, Sarah Kim-Hellmuth, Elizabeth King, Mark Kirkpatrick, Ranjana Kishore, Satoshi Kitamura, Maiko Kitaoka, Christian Klaembt, Hannah Klein, Daniel Kliebenstein, Anke Kloock, Hisato Kobayashi, Kyunghee Koh, Chandrika Konwar, Maarten Koornneef, David Kopecky, Sergey Koren, Tom Kornberg, Katharine Korunes, Douglas Koshland, Luise Kost, Sandhya Koushika, Genevieve Kozak, Helmut","doi":"10.1093/genetics/iyad193","DOIUrl":"https://doi.org/10.1093/genetics/iyad193","url":null,"abstract":"Below is a list of individuals who have reviewed manuscripts for GENETICS during the preparation of Volumes 223, 224, and 225 (2023). The aim of GENETICS is to communicate significant research. To succeed, we must recognize what is significant, making sure the presentation is accurate, unambiguous","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" 21","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138616825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2023-07-11DOI: 10.1101/2023.01.23.525249
Yibing Zeng, R. Dawe, J. Gent
{"title":"Natural methylation epialleles correlate with gene expression in maize","authors":"Yibing Zeng, R. Dawe, J. Gent","doi":"10.1101/2023.01.23.525249","DOIUrl":"https://doi.org/10.1101/2023.01.23.525249","url":null,"abstract":"DNA methylation (5-methylcytosine) represses transposon activity and contributes to inaccessible chromatin structure of repetitive DNA in plants. It is depleted from cis regulatory elements in and near genes but is present in some gene bodies, including exons. Methylation in exons solely in the CG context is called gene body methylation (gbM). Methylation in exons in both CG and non-CG contexts is called TE-like methylation (teM). Assigning functions to both forms of methylation in genes has proven to be challenging. Toward that end, we utilized recent genome assemblies, gene annotations, transcription data, and methylome data to quantify common patterns of gene methylation and their relations to gene expression in maize. To compare between genomes, we analyzed each data source relative to its own genome assembly rather than the easier but less accurate method of using one assembly as reference for all. We found that gbM genes exist in a continuum of CG methylation levels without a clear demarcation between unmethylated genes and gbM genes. Analysis of expression levels across diverse maize stocks and tissues revealed a weak but highly significant positive correlation between gbM and gene expression except in endosperm. gbM epialleles were associated with an approximately 3% increase in steady-state expression level relative to unmethylated epialleles. In contrast to gbM genes, which were conserved and were broadly expressed across tissues, we found that teM genes, which make up about 12% of genes, are mainly silent, are limited to specific maize stocks, and exhibit evidence of annotation errors. We used these data to flag all teM genes in the 26 NAM founder genome assemblies. While some teM genes are likely functional, these data suggest that the majority are not, and their inclusion can confound interpretation of whole-genome studies.","PeriodicalId":12706,"journal":{"name":"Genetics","volume":"225 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45200151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.55
R. Scofield, Christina G. Bruxvoort, B. Kurien, Valerie M Lewis
{"title":"904 Lupus Sex Bias and TLR7 Signaling","authors":"R. Scofield, Christina G. Bruxvoort, B. Kurien, Valerie M Lewis","doi":"10.1136/lupus-2022-lupus21century.55","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.55","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":"1 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41423803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.56
R. Fernandez-Ruiz, Justin Shum, Ilona Nln, J. L. Paredes, T. Niewold
{"title":"905 Impact of the cGMP-dependent protein kinase I on the Rho-Kinase 2 signaling pathway and type I Interferon production","authors":"R. Fernandez-Ruiz, Justin Shum, Ilona Nln, J. L. Paredes, T. Niewold","doi":"10.1136/lupus-2022-lupus21century.56","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.56","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42231019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.54
Qiang Wang, Xiaoming Lu, M. Weirauch, P. Nigrovic
{"title":"903 Decoding genome-wide association study (GWAS) hits for lupus using massively parallel reporter assays","authors":"Qiang Wang, Xiaoming Lu, M. Weirauch, P. Nigrovic","doi":"10.1136/lupus-2022-lupus21century.54","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.54","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43450716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.57
Sarah K. Baxter, S. Gulsuner, M. Eckert, Ming K. Lee, T. Walsh, Anne Stevens, M. King
{"title":"906 De novomutations in childhood-onset systemic lupus erythematosus","authors":"Sarah K. Baxter, S. Gulsuner, M. Eckert, Ming K. Lee, T. Walsh, Anne Stevens, M. King","doi":"10.1136/lupus-2022-lupus21century.57","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.57","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43422553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.62
Ryan J Pachucki, Xinyan Zhang, L. Kohler, S. Tursi, Lauren K Nicastro, Laurie Kilpatrick, Ç. Tükel, S. Gallucci, R. Caricchio
{"title":"1002 Bacterial amyloid curli/eDNA complexes induce NETosis in lupus patients positive for anti-dsDNA","authors":"Ryan J Pachucki, Xinyan Zhang, L. Kohler, S. Tursi, Lauren K Nicastro, Laurie Kilpatrick, Ç. Tükel, S. Gallucci, R. Caricchio","doi":"10.1136/lupus-2022-lupus21century.62","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.62","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44013110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.59
Vrati M. Mehra, D. Dominguez, Nicholas Gold, A. Knight, D. Levy, FangMing Liao, E. Pullenayegum, A. Shammas, E. Sochett, Raza Vali, Declan Webber, E. Silverman, L. Hiraki
{"title":"908 The association between Systemic lupus Erythematosus (SLE) and bone mineral density (BMD) polygenic risk scores with lumbar spine BMD z-score: a retrospective cohort study","authors":"Vrati M. Mehra, D. Dominguez, Nicholas Gold, A. Knight, D. Levy, FangMing Liao, E. Pullenayegum, A. Shammas, E. Sochett, Raza Vali, Declan Webber, E. Silverman, L. Hiraki","doi":"10.1136/lupus-2022-lupus21century.59","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.59","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49575813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.58
P. Raj, C. Liang, C. Arana, N. V. Oers, Quanzhen Li, E. Wakeland, D. Karp
{"title":"907 ANA associated regulatory polymorphisms in HLA class III region downregulate complement 4 (C4) gene expression","authors":"P. Raj, C. Liang, C. Arana, N. V. Oers, Quanzhen Li, E. Wakeland, D. Karp","doi":"10.1136/lupus-2022-lupus21century.58","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.58","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43602100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticsPub Date : 2022-12-01DOI: 10.1136/lupus-2022-lupus21century.63
Haoyang Zhuang, Erin E. Hudson, Shuhong Han, Rawad Daniel Arja, Li Lu, W. Reeves
{"title":"1003 Impaired intracellular protein transport and an endothelial stress response reminiscent of COPA syndrome in SLE-associated diffuse alveolar hemorrhage","authors":"Haoyang Zhuang, Erin E. Hudson, Shuhong Han, Rawad Daniel Arja, Li Lu, W. Reeves","doi":"10.1136/lupus-2022-lupus21century.63","DOIUrl":"https://doi.org/10.1136/lupus-2022-lupus21century.63","url":null,"abstract":"","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47471152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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