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Direct transposition of native DNA for sensitive multimodal single-molecule sequencing Nat. Genet. (IF 30.8) Pub Date : 2024-05-09 Arjun S. Nanda, Ke Wu, Iryna Irkliyenko, Brian Woo, Megan S. Ostrowski, Andrew S. Clugston, Leanne C. Sayles, Lingru Xu, Ansuman T. Satpathy, Hao G. Nguyen, E. Alejandro Sweet-Cordero, Hani Goodarzi, Sivakanthan Kasinathan, Vijay Ramani
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Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications Nat. Genet. (IF 30.8) Pub Date : 2024-05-09 Cristina Policarpi, Marzia Munafò, Stylianos Tsagkris, Valentina Carlini, Jamie A. Hackett
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Contraction or sequence variant of an intergenic repeat-Alu element leads to inherited thyroid disease Nat. Genet. (IF 30.8) Pub Date : 2024-05-07 Andrea Cortese, Elisa Vegezzi, Henry Houlden
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STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179 Nat. Genet. (IF 30.8) Pub Date : 2024-05-07 Helmut Grasberger, Alexandra M. Dumitrescu, Xiao-Hui Liao, Elliott G. Swanson, Roy E. Weiss, Panudda Srichomkwun, Theodora Pappa, Junfeng Chen, Takashi Yoshimura, Phillip Hoffmann, Monica Malheiros França, Rebecca Tagett, Kazumichi Onigata, Sabine Costagliola, Jane Ranchalis, Mitchell R. Vollger, Andrew B. Stergachis, Jessica X. Chong, Michael J. Bamshad, Guillaume Smits, Gilbert Vassart, Samuel Refetoff
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Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower Nat. Genet. (IF 30.8) Pub Date : 2024-05-07 Rui Chen, Ke Chen, Xingwei Yao, Xiaoli Zhang, Yingxia Yang, Xiao Su, Mingjie Lyu, Qian Wang, Guan Zhang, Mengmeng Wang, Yanhao Li, Lijin Duan, Tianyu Xie, Haichao Li, Yuyao Yang, Hong Zhang, Yutong Guo, Guiying Jia, Xianhong Ge, Panagiotis F. Sarris, Tao Lin, Deling Sun
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Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities Nat. Genet. (IF 30.8) Pub Date : 2024-05-07 Satoshi Narumi, Keisuke Nagasaki, Mitsuo Kiriya, Erika Uehara, Kazuhisa Akiba, Kanako Tanase-Nakao, Kazuhiro Shimura, Kiyomi Abe, Chiho Sugisawa, Tomohiro Ishii, Kenichi Miyako, Yukihiro Hasegawa, Yoshihiro Maruo, Koji Muroya, Natsuko Watanabe, Eijun Nishihara, Yuka Ito, Takahiko Kogai, Kaori Kameyama, Kazuhiko Nakabayashi, Kenichiro Hata, Maki Fukami, Hirohito Shima, Atsuo Kikuchi, Jun Takayama, Gen
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The 1+Million Genomes Minimal Dataset for Cancer Nat. Genet. (IF 30.8) Pub Date : 2024-05-03 Michela Riba, Cinzia Sala, Aedin C. Culhane, Åsmund Flobak, Attila Patocs, Kjetil Boye, Karla Plevova, Šárka Pospíšilová, Giorgia Gandolfi, Marco J. Morelli, Gabriele Bucci, Anders Edsjö, Ulrik Lassen, Fátima Al-Shahrour, Nuria Lopez-Bigas, Randi Hovland, Edwin Cuppen, Alfonso Valencia, Helene A. Poirel, Richard Rosenquist, Serena Scollen, Juan Arenas Marquez, Jeroen Belien, Arcangela De Nicolo, Ruggero
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Genomes of multicellular algal sisters to land plants illuminate signaling network evolution Nat. Genet. (IF 30.8) Pub Date : 2024-05-01 Xuehuan Feng, Jinfang Zheng, Iker Irisarri, Huihui Yu, Bo Zheng, Zahin Ali, Sophie de Vries, Jean Keller, Janine M. R. Fürst-Jansen, Armin Dadras, Jaccoline M. S. Zegers, Tim P. Rieseberg, Amra Dhabalia Ashok, Tatyana Darienko, Maaike J. Bierenbroodspot, Lydia Gramzow, Romy Petroll, Fabian B. Haas, Noe Fernandez-Pozo, Orestis Nousias, Tang Li, Elisabeth Fitzek, W. Scott Grayburn, Nina Rittmeier, Charlotte
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Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits Nat. Genet. (IF 30.8) Pub Date : 2024-04-30 Jacob M. Keaton, Zoha Kamali, Tian Xie, Ahmad Vaez, Ariel Williams, Slavina B. Goleva, Alireza Ani, Evangelos Evangelou, Jacklyn N. Hellwege, Loic Yengo, William J. Young, Matthew Traylor, Ayush Giri, Zhili Zheng, Jian Zeng, Daniel I. Chasman, Andrew P. Morris, Mark J. Caulfield, Shih-Jen Hwang, Jaspal S. Kooner, David Conen, John R. Attia, Alanna C. Morrison, Ruth J. F. Loos, Kati Kristiansson, Reinhold
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Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries Nat. Genet. (IF 30.8) Pub Date : 2024-04-30 Zhili Zheng, Shouye Liu, Julia Sidorenko, Ying Wang, Tian Lin, Loic Yengo, Patrick Turley, Alireza Ani, Rujia Wang, Ilja M. Nolte, Harold Snieder, Jian Yang, Naomi R. Wray, Michael E. Goddard, Peter M. Visscher, Jian Zeng
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New genes are involved in the adaptation of acorn barnacles to sessile life Nat. Genet. (IF 30.8) Pub Date : 2024-04-29
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Experimental evolution of cancer chromosomal changes Nat. Genet. (IF 30.8) Pub Date : 2024-04-29 Molly A. Guscott, Sarah E. McClelland
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The Egypt Genome Project Nat. Genet. (IF 30.8) Pub Date : 2024-04-29 Mohamed A. Elmonem, Neveen A. Soliman, Ahmed Moustafa, Yehia Z. Gad, Wael A. Hassan, Tarek Taha, Gina El-Feky, Mahmoud Sakr, Khaled Amer
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A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy Nat. Genet. (IF 30.8) Pub Date : 2024-04-29 Karla P. Figueroa, Caspar Gross, Elena Buena-Atienza, Sharan Paul, Mandi Gandelman, Naseebullah Kakar, Marc Sturm, Nicolas Casadei, Jakob Admard, Joohyun Park, Christine Zühlke, Yorck Hellenbroich, Jelena Pozojevic, Saranya Balachandran, Kristian Händler, Simone Zittel, Dagmar Timmann, Friedrich Erdlenbruch, Laura Herrmann, Thomas Feindt, Martin Zenker, Thomas Klopstock, Claudia Dufke, Daniel R. Scoles
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Long noncoding RNAs underlie multiple domestication traits and leafhopper resistance in soybean Nat. Genet. (IF 30.8) Pub Date : 2024-04-29 Weidong Wang, Jingbo Duan, Xutong Wang, Xingxing Feng, Liyang Chen, Chancelor B. Clark, Stephen A. Swarm, Jinbin Wang, Sen Lin, Randall L. Nelson, Blake C. Meyers, Xianzhong Feng, Jianxin Ma
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Advancing genomics to improve health equity Nat. Genet. (IF 30.8) Pub Date : 2024-04-29 Ebony B. Madden, Lucia A. Hindorff, Vence L. Bonham, Tabia Henry Akintobi, Esteban G. Burchard, Kellan E. Baker, Rene L. Begay, John D. Carpten, Nancy J. Cox, Valentina Di Francesco, Denise A. Dillard, Faith E. Fletcher, Stephanie M. Fullerton, Nanibaa’ A. Garrison, Catherine M. Hammack-Aviran, Vanessa Y. Hiratsuka, James E. K. Hildreth, Carol R. Horowitz, Chanita A. Hughes Halbert, Michael Inouye
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Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions Nat. Genet. (IF 30.8) Pub Date : 2024-04-26 Mark P. Purdue, Diptavo Dutta, Mitchell J. Machiela, Bryan R. Gorman, Timothy Winter, Dayne Okuhara, Sara Cleland, Aida Ferreiro-Iglesias, Paul Scheet, Aoxing Liu, Chao Wu, Samuel O. Antwi, James Larkin, Stênio C. Zequi, Maxine Sun, Keiko Hikino, Ali Hajiran, Keith A. Lawson, Flavio Cárcano, Odile Blanchet, Brian Shuch, Kenneth G. Nepple, Gaëlle Margue, Debasish Sundi, W. Ryan Diver, Maria A. A. K
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Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification Nat. Genet. (IF 30.8) Pub Date : 2024-04-24 Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I. Love, Vineel Bhat, Guillaume Lettre, David B. Ascher, Christopher A. Cassa, Richard I. Sherwood, Luca Pinello
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Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits Nat. Genet. (IF 30.8) Pub Date : 2024-04-24 Qiong Lu, Hainan Zhao, Zhengquan Zhang, Yuhe Bai, Haiming Zhao, Guoqing Liu, Minxuan Liu, Yunxiao Zheng, Haiyue Zhao, Huihui Gong, Lingwei Chen, Xizhen Deng, Xiangde Hong, Tianxiang Liu, Baichuan Li, Ping Lu, Feng Wen, Lun Wang, Zhijiang Li, Hai Li, Haiquan Li, Like Zhang, Wenhui Ma, Chunqing Liu, Yan Bai, Beibei Xin, Jian Chen, Lizhu E., Jinsheng Lai, Weibin Song
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New genes helped acorn barnacles adapt to a sessile lifestyle Nat. Genet. (IF 30.8) Pub Date : 2024-04-23 Zhaofang Han, Zhixuan Wang, Daniel Rittschof, Zekun Huang, Liying Chen, Huanhuan Hao, Shanshan Yao, Pei Su, Miaoqin Huang, Yuan-Ye Zhang, Caihuan Ke, Danqing Feng
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Finding the lost sister: mirror-image mutation phasing in mammalian mitotic sister cells Nat. Genet. (IF 30.8) Pub Date : 2024-04-22
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Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement Nat. Genet. (IF 30.8) Pub Date : 2024-04-22 Xinyi Wu, Zhongyuan Hu, Yan Zhang, Mao Li, Nanqiao Liao, Junyang Dong, Baogen Wang, Jian Wu, Xiaohua Wu, Ying Wang, Jian Wang, Zhongfu Lu, Yi Yang, Yuyan Sun, Wenqi Dong, Mingfang Zhang, Guojing Li
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Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits Nat. Genet. (IF 30.8) Pub Date : 2024-04-19 Qianqian Peng, Xinxuan Liu, Wenran Li, Han Jing, Jiarui Li, Xingjian Gao, Qi Luo, Charles E. Breeze, Siyu Pan, Qiwen Zheng, Guochao Li, Jiaqiang Qian, Liyun Yuan, Na Yuan, Chenglong You, Siyuan Du, Yuanting Zheng, Ziyu Yuan, Jingze Tan, Peilin Jia, Jiucun Wang, Guoqing Zhang, Xianping Lu, Leming Shi, Shicheng Guo, Yun Liu, Ting Ni, Bo Wen, Changqing Zeng, Li Jin, Andrew E. Teschendorff, Fan Liu, Sijia
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Constants and variations in 69 diverse genomes of Arabidopsis thaliana Nat. Genet. (IF 30.8) Pub Date : 2024-04-18
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Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder Nat. Genet. (IF 30.8) Pub Date : 2024-04-18 Caroline M. Nievergelt, Adam X. Maihofer, Elizabeth G. Atkinson, Chia-Yen Chen, Karmel W. Choi, Jonathan R. I. Coleman, Nikolaos P. Daskalakis, Laramie E. Duncan, Renato Polimanti, Cindy Aaronson, Ananda B. Amstadter, Soren B. Andersen, Ole A. Andreassen, Paul A. Arbisi, Allison E. Ashley-Koch, S. Bryn Austin, Esmina Avdibegoviç, Dragan Babić, Silviu-Alin Bacanu, Dewleen G. Baker, Anthony Batzler,
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Genetic modifiers of rare variants in monogenic developmental disorder loci Nat. Genet. (IF 30.8) Pub Date : 2024-04-18 Rebecca Kingdom, Robin N. Beaumont, Andrew R. Wood, Michael N. Weedon, Caroline F. Wright
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Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis Nat. Genet. (IF 30.8) Pub Date : 2024-04-17 Jonas Ghouse, Gardar Sveinbjörnsson, Marijana Vujkovic, Anne-Sofie Seidelin, Helene Gellert-Kristensen, Gustav Ahlberg, Vinicius Tragante, Søren A. Rand, Joseph Brancale, Silvia Vilarinho, Pia Rengtved Lundegaard, Erik Sørensen, Christian Erikstrup, Mie Topholm Bruun, Bitten Aagaard Jensen, Søren Brunak, Karina Banasik, Henrik Ullum, Niek Verweij, Luca Lotta, Aris Baras, Tooraj Mirshahi, David J. Carey
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Single-mitosis dissection of acute and chronic DNA mutagenesis and repair Nat. Genet. (IF 30.8) Pub Date : 2024-04-16 Paul Adrian Ginno, Helena Borgers, Christina Ernst, Anja Schneider, Mikaela Behm, Sarah J. Aitken, Martin S. Taylor, Duncan T. Odom
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A spatiotemporal atlas of cholestatic injury and repair in mice Nat. Genet. (IF 30.8) Pub Date : 2024-04-16 Baihua Wu, Xinyi Shentu, Haitao Nan, Pengcheng Guo, Shijie Hao, Jiangshan Xu, Shuncheng Shangguan, Lei Cui, Jin Cen, Qiuting Deng, Yan Wu, Chang Liu, Yumo Song, Xiumei Lin, Zhifeng Wang, Yue Yuan, Wen Ma, Ronghai Li, Yikang Li, Qiwei Qian, Wensi Du, Tingting Lai, Tao Yang, Chuanyu Liu, Xiong Ma, Ao Chen, Xun Xu, Yiwei Lai, Longqi Liu, Miguel A. Esteban, Lijian Hui
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A spatiotemporal atlas of mouse liver homeostasis and regeneration Nat. Genet. (IF 30.8) Pub Date : 2024-04-16 Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shiping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer
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Genetic associations of human metabolic traits Nat. Genet. (IF 30.8) Pub Date : 2024-04-15 Wei Li
Metabolomics has been integrated with genome-wide association studies and yielded insights into the genetic regulation of human metabolism. Using an updated NMR metabolomics platform, Karjalainen et al. conducted a genome-wide association meta-analysis of 233 metabolic traits in up to 136,016 participants from 33 cohorts, across multiple ancestry groups including non-Finnish European, Finnish, South
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Quantitative proteomics of protein–nucleosome interactions Nat. Genet. (IF 30.8) Pub Date : 2024-04-15 Michael Fletcher
One mechanism of gene regulation is the recognition of histone post-translational modifications (PTMs) by chromatin-binding proteins, which then recruit the core transcriptional machinery. Although the concept of a ‘histone code’ that corresponds to varying chromatin functional states is established, it remains unclear how combinations of these PTMs are recognized by chromatin binders, which often
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Role of gene–gene loops in fine-tuning cross-regulation Nat. Genet. (IF 30.8) Pub Date : 2024-04-15 Petra Gross
Prominent chromatin loops have been observed in both flies and vertebrates, and these often involve genes either with related functions or that are paralogs, pointing to a functional relevance for their co-regulation. Pollex et al. dissected the contribution of three loops formed between genes with related functions to the regulation of their own expression during Drosophila embryogenesis. They achieved
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Implementing polygenic risk scores in the clinic Nat. Genet. (IF 30.8) Pub Date : 2024-04-15 Kyle Vogan
Clinical use of polygenic risk scores (PRSs) can potentially improve health outcomes, but there are many open questions about how to implement PRSs effectively and equitably in primary care. To further these goals, Lennon et al. developed a pipeline within the Electronic Medical Records and Genomics (eMERGE) Network, consisting of diverse patients drawn from the US population, to perform polygenic
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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars Nat. Genet. (IF 30.8) Pub Date : 2024-04-15 Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J. Krabbenhoft, Zhen Qin Wang, Steven J. Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah
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A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range Nat. Genet. (IF 30.8) Pub Date : 2024-04-11 Qichao Lian, Bruno Huettel, Birgit Walkemeier, Baptiste Mayjonade, Céline Lopez-Roques, Lisa Gil, Fabrice Roux, Korbinian Schneeberger, Raphael Mercier
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Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles Nat. Genet. (IF 30.8) Pub Date : 2024-04-09 Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K. Dey, Karthik Jagadeesh, Masahiro Kanai, Gerald F. M. Watts, Zhu Zhu, Michael B. Brenner, Andrew McDavid, Laura T. Donlin, Kevin Wei, Alkes L. Price, Soumya Raychaudhuri
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Identifying regulatory loci across 38 lung cell types Nat. Genet. (IF 30.8) Pub Date : 2024-04-03
Using single-cell RNA-sequencing (scRNA-seq) of lung tissue, expression quantitative trait loci (eQTLs) were mapped across 38 cell types, revealing both shared and cell-type-specific effects. Highly cell-type-specific disease-interaction eQTLs were linked to cellular dysregulation in lung disease and lung disease risk variants were connected to their regulatory targets in relevant cell types.
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Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response Nat. Genet. (IF 30.8) Pub Date : 2024-04-02 Zhe Hu, Zimeng Wu, Wei Liu, Yan Ning, Jingbo Liu, Wencheng Ding, Junpeng Fan, Shuyan Cai, Qinlan Li, Wenting Li, Xiaohang Yang, Yingyu Dou, Wei Wang, Wenju Peng, Funian Lu, Xucui Zhuang, Tianyu Qin, Xiaoyan Kang, Chenzhao Feng, Zhiying Xu, Qiaoying Lv, Qian Wang, Chao Wang, Xinyu Wang, Zhiqi Wang, Jianliu Wang, Jie Jiang, Beibei Wang, Gordon B. Mills, Ding Ma, Qinglei Gao, Kezhen Li, Gang Chen, Xiaojun
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive desire and capacity. To illuminate the molecular characteristics of EEEC, we undertook a large-scale
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Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease Nat. Genet. (IF 30.8) Pub Date : 2024-04-04 Yajie Zhao, Maria Chukanova, Katherine A. Kentistou, Zammy Fairhurst-Hunter, Anna Maria Siegert, Raina Y. Jia, Georgina K. C. Dowsett, Eugene J. Gardner, Katherine Lawler, Felix R. Day, Lena R. Kaisinger, Yi-Chun Loraine Tung, Brian Yee Hong Lam, Hsiao-Jou Cortina Chen, Quanli Wang, Jaime Berumen-Campos, Pablo Kuri-Morales, Roberto Tapia-Conyer, Jesus Alegre-Diaz, Inês Barroso, Jonathan Emberson, Jason
Obesity is a major risk factor for many common diseases and has a substantial heritable component. To identify new genetic determinants, we performed exome-sequence analyses for adult body mass index (BMI) in up to 587,027 individuals. We identified rare loss-of-function variants in two genes (BSN and APBA1) with effects substantially larger than those of well-established obesity genes such as MC4R
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Mapping single-cell gene expression in the healthy human breast Nat. Genet. (IF 30.8) Pub Date : 2024-03-29
We have curated a comprehensive single-cell reference map of the human breast. Our data explore how age, parity and germline mutations might influence cellular dynamics, revealing unexpected signs of immune exhaustion in healthy tissues from carriers of BRCA1 or BRCA2 germline mutations.
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Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy Nat. Genet. (IF 30.8) Pub Date : 2024-03-29 Darcy L. Fehlings, Mehdi Zarrei, Worrawat Engchuan, Neal Sondheimer, Bhooma Thiruvahindrapuram, Jeffrey R. MacDonald, Edward J. Higginbotham, Ritesh Thapa, Tarannum Behlim, Sabrina Aimola, Lauren Switzer, Pamela Ng, John Wei, Prakroothi S. Danthi, Giovanna Pellecchia, Sylvia Lamoureux, Karen Ho, Sergio L. Pereira, Jill de Rijke, Wilson W. L. Sung, Alireza Mowjoodi, Jennifer L. Howe, Thomas Nalpathamkalam
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Protein-altering variants at copy number-variable regions influence diverse human phenotypes Nat. Genet. (IF 30.8) Pub Date : 2024-03-28 Margaux L. A. Hujoel, Robert E. Handsaker, Maxwell A. Sherman, Nolan Kamitaki, Alison R. Barton, Ronen E. Mukamel, Chikashi Terao, Steven A. McCarroll, Po-Ru Loh
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Cell-type-specific and disease-associated expression quantitative trait loci in the human lung Nat. Genet. (IF 30.8) Pub Date : 2024-03-28 Heini M. Natri, Christina B. Del Azodi, Lance Peter, Chase J. Taylor, Sagrika Chugh, Robert Kendle, Mei-i Chung, David K. Flaherty, Brittany K. Matlock, Carla L. Calvi, Timothy S. Blackwell, Lorraine B. Ware, Matthew Bacchetta, Rajat Walia, Ciara M. Shaver, Jonathan A. Kropski, Davis J. McCarthy, Nicholas E. Banovich
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A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast Nat. Genet. (IF 30.8) Pub Date : 2024-03-28 Austin D. Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J. Kunz, Linsey J. Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J. Q. Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J. Gomm, Valerie Speirs, J Louise Jones, John C. Marioni, Walid T. Khaled
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Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation Nat. Genet. (IF 30.8) Pub Date : 2024-03-25 Daniel M. Ibrahim
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Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis Nat. Genet. (IF 30.8) Pub Date : 2024-03-21 Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J. Hartemink, Yuri Pritykin, Kushal K. Dey, Christina S. Leslie
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Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain Nat. Genet. (IF 30.8) Pub Date : 2024-03-21 Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C. White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V. Pearse, Atlas Khan, Badri N. Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A. Schneider, Yanling Wang, Tracy Young-Pearse, Sara Mostafavi, David A. Bennett
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Increased enhancer–promoter interactions during developmental enhancer activation in mammals Nat. Genet. (IF 30.8) Pub Date : 2024-03-20 Zhuoxin Chen, Valentina Snetkova, Grace Bower, Sandra Jacinto, Benjamin Clock, Atrin Dizehchi, Iros Barozzi, Brandon J. Mannion, Ana Alcaina-Caro, Javier Lopez-Rios, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Evgeny Z. Kvon
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The homeobox transcription factor DUXBL controls exit from totipotency Nat. Genet. (IF 30.8) Pub Date : 2024-03-20 Maria Vega-Sendino, Felipe F. Lüttmann, Teresa Olbrich, Yanpu Chen, Carsten Kuenne, Paula Stein, Desiree Tillo, Grace I. Carey, Jiasheng Zhong, Virginia Savy, Lenka Radonova, Tianlin Lu, Bechara Saykali, Kee-Pyo Kim, Catherine N. Domingo, Leah Schüler, Stefan Günther, Mette Bentsen, Darko Bosnakovski, Hans Schöler, Michael Kyba, Tapan K. Maity, Lisa M. Jenkins, Mario Looso, Carmen J. Williams, Johnny
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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance Nat. Genet. (IF 30.8) Pub Date : 2024-03-15 Peng-Fei Ma, Yun-Long Liu, Cen Guo, Guihua Jin, Zhen-Hua Guo, Ling Mao, Yi-Zhou Yang, Liang-Zhong Niu, Yu-Jiao Wang, Lynn G. Clark, Elizabeth A. Kellogg, Zu-Chang Xu, Xia-Ying Ye, Jing-Xia Liu, Meng-Yuan Zhou, Yan Luo, Yang Yang, Douglas E. Soltis, Jeffrey L. Bennetzen, Pamela S. Soltis, De-Zhu Li
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MYC activates transcriptional enhancers to drive cancer progression Nat. Genet. (IF 30.8) Pub Date : 2024-03-13
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Genetic contribution to heterogeneity in type 2 diabetes Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Wei Li
Genome-wide association studies of type 2 diabetes (T2D) have led to the identification of hundreds of risk loci. Through the Type 2 Diabetes Global Genomics Initiative, Suzuki et al. performed a multi-ancestry meta-analysis of T2D in 2,535,601 individuals (428,452 cases of T2D) from diverse ancestry groups: European (60.3%), East Asian (19.8%), admixed African American (10.5%), admixed Hispanic (5
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How transposable elements are spliced out Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Chiara Anania
A large part of the human genome consists of transposable elements (TEs). Most TEs do not contribute to mature transcripts, which suggests that cells might have evolved a strategy to skip TE sequences by splicing them as introns. In a study published in Nature, Ilık et al. studied 33 RNA-binding proteins involved in splicing, and found that SAFB, hnRNPC and DHX9 associated with sense LINE1 elements
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Implicating XIST in sex-biased autoimmunity Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Kyle Vogan
Autoimmune diseases exhibit a strong female sex bias in incidence, but the mechanistic basis for this differential susceptibility is poorly understood. Given previous evidence that X chromosome dosage, and specifically the long non-coding RNA XIST produced from the inactive X chromosome and its associated proteins, could be key factors underlying the increased autoimmune disease risk in females and
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Transcription factor binding site affinity and the link to phenotype Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Michael Fletcher
Genetic variation, such as single-nucleotide variants (SNVs), can alter transcription factor binding and thus phenotypes. However, the exact mechanistic bases of this process remain poorly understood. Lim et al. examine the classic model enhancer, ZRS, which regulates expression of SHH during limb development and contains SNVs that are causal for polydactyly. Using protein-binding microarray data,
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Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 W. Gregory Feero, Robert D. Steiner, Anne Slavotinek, Tiago Faial, Michael J. Bamshad, Jehannine Austin, Bruce R. Korf, Annette Flanagin, Kirsten Bibbins-Domingo
In March 2023, the National Academies of Sciences, Engineering, and Medicine (NASEM) released a consensus study report titled Using Population Descriptors in Genetics and Genomics Research1. Sponsored by the US National Institutes of Health, the report is more than a discussion of the use of terminology; the authors of the NASEM report suggest a tectonic shift away from current models that use race
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Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation Nat. Genet. (IF 30.8) Pub Date : 2024-03-11 Tim Pollex, Adam Rabinowitz, Maria Cristina Gambetta, Raquel Marco-Ferreres, Rebecca R. Viales, Aleksander Jankowski, Christoph Schaub, Eileen E. M. Furlong
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MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch Nat. Genet. (IF 30.8) Pub Date : 2024-03-07 Simon T. Jakobsen, Rikke A. M. Jensen, Maria S. Madsen, Tina Ravnsborg, Christian S. Vaagenso, Majken S. Siersbæk, Hjorleifur Einarsson, Robin Andersson, Ole N. Jensen, Rasmus Siersbæk