-
The evolutionary tale of lactase persistence in humans Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Luis B. Barreiro
Luis Barreiro highlights a 2007 paper by Tishkoff et al. that identified genetic variants associated with lactose persistence in East African populations, representing one of the first examples of convergent evolution in humans.
-
An organism-wide ATAC-seq peak catalogue for the bovine and its use to identify regulatory variants Genome Res. (IF 7.0) Pub Date : 2023-09-26 Can Yuan, Lijing Tang, Thomas Lopdell, Vyacheslav A Petrov, Claire Oget-Ebrad, Gabriel Costa Monteiro Moreira, José Luis Gualdrón Duarte, Arnaud Sartelet, Zhangrui Cheng, Mazdak Salavati, Claire D Wathes, Mark A Crowe, GplusE Consortium, Wouter Coppieters, Mathew Littlejohn, Carole Charlier, Tom Druet, Michel Georges, Haruko Takeda
We herein report the generation of an organism-wide catalogue of 976,813 cis-acting regulatory elements for the bovine detected by the Assay for Transposase Accessible Chromatin using sequencing (ATAC-Seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlations between the genome-wide density of peaks and transcription start sites, between peak accessibility
-
Mapping the recognition pathway of cyclobutane pyrimidine dimer in DNA by Rad4/XPC Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-27 Nikhil Jakhar, Akshay Prabhakant, Marimuthu Krishnan
UV radiation-induced DNA damages have adverse effects on genome integrity and cellular function. The most prevalent UV-induced DNA lesion is the cyclobutane pyrimidine dimer (CPD), which can cause skin disorders and cancers in humans. Rad4/XPC is a damage sensing protein that recognizes and repairs CPD lesions with high fidelity. However, the molecular mechanism of how Rad4/XPC interrogates CPD lesions
-
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-27 Rong Zhao, Wang Luo, You Wu, Li Zhang, Xin Liu, Junjie Li, Yujun Yang, Li Wang, Luojia Wang, Xiaole Han, Zhongzhong Wang, Jianhong Zhang, Ke Lv, Tingmei Chen, Guoming Xie
As CRISPR technology is promoted to more fine-divided molecular biology applications, its inherent performance finds it increasingly difficult to cope with diverse needs in these different fields, and how to more accurately control the performance has become a key issue to develop CRISPR technology to a new stage. Herein, we propose a CRISPR/Cas12a regulation strategy based on the powerful programmability
-
Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-26 Binglan Li, Katrin Sangkuhl, Ryan Whaley, Mark Woon, Karl Keat, Michelle Whirl-Carrillo, Marylyn D. Ritchie, Teri E. Klein
Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads
-
Genomic surveillance for antimicrobial resistance — a One Health perspective Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Steven P. Djordjevic, Veronica M. Jarocki, Torsten Seemann, Max L. Cummins, Anne E. Watt, Barbara Drigo, Ethan R. Wyrsch, Cameron J. Reid, Erica Donner, Benjamin P. Howden
-
Pioneer factors — key regulators of chromatin and gene expression Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-22 Martha L. Bulyk, Jacques Drouin, Melissa M. Harrison, Jussi Taipale, Kenneth S. Zaret
Pioneer factors are a group of transcription factors with important roles in gene regulation during development. Their unique ability to bind to compacted chromatin, promoting its remodelling for gene expression, sets them apart from other regulatory proteins and makes them essential players in cellular differentiation, fate determination and reprogramming. Here, we have tasked five experts with discussing
-
PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-25 Florence Petit, Mauro Longoni, Julie Wells, Richard S. Maser, Eric L. Bogenschutz, Matthew J. Dysart, Hannah T.M. Contreras, Frederic Frénois, Barbara R. Pober, Robin D. Clark, Philip F. Giampietro, Hilger H. Ropers, Hao Hu, Maria Loscertales, Richard Wagner, Xingbin Ai, Harrison Brand, Anne-Sophie Jourdain, Marie-Ange Delrue, Brigitte Gilbert-Dussardier, Frances A. High
Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense
-
Sequencing to save the Kākāpō Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Michael Attwaters
Guhlin et al. sequenced the genomes of almost the entire extant population of the critically-endangered kākāpō, revealing genetic variants for fitness-related traits that can inform conservation strategies.
-
Hyperactivation of oncogenic driver pathways as a precision therapeutic strategy Nat. Genet. (IF 30.8) Pub Date : 2023-09-25 Kris C. Wood
-
Linking non-coding variants to function in microglia in Alzheimer’s disease Nat. Genet. (IF 30.8) Pub Date : 2023-09-25
-
A new method for multiancestry polygenic prediction improves performance across diverse populations Nat. Genet. (IF 30.8) Pub Date : 2023-09-25 Haoyu Zhang, Jianan Zhan, Jin Jin, Jingning Zhang, Wenxuan Lu, Ruzhang Zhao, Thomas U. Ahearn, Zhi Yu, Jared O’Connell, Yunxuan Jiang, Tony Chen, Dayne Okuhara, Montserrat Garcia-Closas, Xihong Lin, Bertram L. Koelsch, Nilanjan Chatterjee
-
Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities Nat. Genet. (IF 30.8) Pub Date : 2023-09-25 Liang Chang, Nancy Y. Jung, Adel Atari, Diego J. Rodriguez, Devishi Kesar, Tian-Yu Song, Matthew G. Rees, Melissa Ronan, Ruitong Li, Paloma Ruiz, Saireudee Chaturantabut, Takahiro Ito, Laurens M. van Tienen, Yuen-Yi Tseng, Jennifer A. Roth, William R. Sellers
-
Functional characterization of Alzheimer’s disease genetic variants in microglia Nat. Genet. (IF 30.8) Pub Date : 2023-09-21 Xiaoyu Yang, Jia Wen, Han Yang, Ian R. Jones, Xiaodong Zhu, Weifang Liu, Bingkun Li, Claire D. Clelland, Wenjie Luo, Man Ying Wong, Xingjie Ren, Xiekui Cui, Michael Song, Hongjiang Liu, Cady Chen, Nicolas Eng, Mirunalini Ravichandran, Yang Sun, David Lee, Eric Van Buren, Min-Zhi Jiang, Candace S. Y. Chan, Chun Jimmie Ye, Rushika M. Perera, Li Gan, Yun Li, Yin Shen
-
Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-25 Stuart McQuarrie, Januka S Athukoralage, Stephen A McMahon, Shirley Graham, Katrin Ackermann, Bela E Bode, Malcolm F White, Tracey M Gloster
Type III CRISPR systems synthesize cyclic oligoadenylate (cOA) second messengers as part of a multi-faceted immune response against invading mobile genetic elements (MGEs). cOA activates non-specific CRISPR ancillary defence nucleases to create a hostile environment for MGE replication. Csm6 ribonucleases bind cOA using a CARF (CRISPR-associated Rossmann Fold) domain, resulting in activation of a fused
-
Literature-based predictions of Mendelian disease therapies Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-22 Cole A. Deisseroth, Won-Seok Lee, Jiyoen Kim, Hyun-Hwan Jeong, Ryan S. Dhindsa, Julia Wang, Huda Y. Zoghbi, Zhandong Liu
In the effort to treat Mendelian disorders, correcting the underlying molecular imbalance may be more effective than symptomatic treatment. Identifying treatments that might accomplish this goal requires extensive and up-to-date knowledge of molecular pathways—including drug-gene and gene-gene relationships. To address this challenge, we present “parsing modifiers via article annotations” (PARMESAN)
-
The COPD GWAS gene ADGRG6 instructs function and injury response in human iPSC-derived type II alveolar epithelial cells Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-20 Rhiannon B. Werder, Kayleigh A. Berthiaume, Carly Merritt, Marissa Gallagher, Carlos Villacorta-Martin, Feiya Wang, Pushpinder Bawa, Vidhi Malik, Shawn M. Lyons, Maria C. Basil, Edward E. Morrisey, Darrell N. Kotton, Xiaobo Zhou, Michael H. Cho, Andrew A. Wilson
-
Telomeric i-motifs and C-strands inhibit parallel G-quadruplex extension by telomerase Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-24 Roberto El-Khoury, Morgane Roman, Hala Abou Assi, Aaron L Moye, Tracy M Bryan, Masad J Damha
Telomeric C-rich repeated DNA sequences fold into tetrahelical i-motif structures in vitro at acidic pH. While studies have suggested that i-motifs may form in cells, little is known about their potential role in human telomere biology. In this study, we explore the effect of telomeric C-strands and i-motifs on the ability of human telomerase to extend G-rich substrates. To promote i-motif formation
-
Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-24 Jinjing Ni, Shuxian Li, Yanan Lai, Zuoqiang Wang, Danni Wang, Yongcong Tan, Yongqiang Fan, Jie Lu, Yu-Feng Yao
Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues
-
-1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-24 Anna A Mikkelsen, Feng Gao, Elizabeth Carino, Sayanta Bera, Anne E Simon
Plus-strand RNA viruses frequently employ -1 programmed ribosomal frameshifting (-1 PRF) to maximize their coding capacity. Ribosomes can frameshift at a slippery sequence if progression is impeded by a frameshift stimulating element (FSE), which is generally a stable, complex, dynamic structure with multiple conformations that contribute to the efficiency of -1 PRF. As FSE are usually analyzed separate
-
Coordination between aminoacylation and editing to protect against proteotoxicity Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-24 Hong Zhang, Parker Murphy, Jason Yu, Sukyeong Lee, Francis T F Tsai, Ambro van Hoof, Jiqiang Ling
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study,
-
Predicting the effects of multigene perturbations Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-19 Henry Ertl
Roohani et al. have developed a deep learning tool called GEARS that predicts the effects of multigene perturbations.
-
600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges Genome Res. (IF 7.0) Pub Date : 2023-09-22 John Sproul, Scott Hotaling, Jacqueline Heckenhauer, Ashlyn Powell, Dez Marshall, Amanda M Larracuente, Joanna Kelley, Steffen U Pauls, Paul B Frandsen
Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in REs dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across
-
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-23 Ze Liu, Justin Wang, Yi Shi, Brian A Yee, Markus Terrey, Qian Zhang, Jenq-Chang Lee, Kuo-I Lin, Andrew H-J Wang, Susan L Ackerman, Gene W Yeo, Haissi Cui, Xiang-Lei Yang
Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). Here we found that components of the human selenocysteine incorporation machinery (SerRS
-
Unequal global implementation of genomic newborn screening Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-18 Ahmad N. Abou Tayoun
Studies of genomic newborn screening are highly skewed towards populations in high-income countries. The evidence generated by these studies will be similarly biased and is likely to lead to disparate global implementation. Studies inclusive of historically under-represented populations are needed for equitable global access to genomic newborn screening. In this Comment, Ahmad Abou Tayoun advocates
-
Transposable elements: McClintock’s legacy revisited Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-18 Cédric Feschotte
-
More than a decade of genetic research on the Denisovans Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-18 Stéphane Peyrégne, Viviane Slon, Janet Kelso
-
Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-22 Sangwoo Park, Giovanni B Brandani, Taekjip Ha, Gregory D Bowman
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout
-
Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-19 Warren van Loggerenberg, Shahin Sowlati-Hashjin, Jochen Weile, Rayna Hamilton, Aditya Chawla, Dayag Sheykhkarimli, Marinella Gebbia, Nishka Kishore, Laure Frésard, Sami Mustajoki, Elena Pischik, Elena Di Pierro, Michela Barbaro, Ylva Floderus, Caroline Schmitt, Laurent Gouya, Alexandre Colavin, Robert Nussbaum, Edith C.H. Friesema, Raili Kauppinen, Frederick P. Roth
Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as “variants of uncertain significance” (VUSs). Using saturation mutagenesis, en masse selection, and sequencing
-
Demographic modeling of admixed Latin American populations from whole genomes Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-18 Santiago G. Medina-Muñoz, Diego Ortega-Del Vecchyo, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Lourdes García-García, Andrés Moreno-Estrada, Aaron P. Ragsdale
Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole-genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models
-
APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer Nat. Genet. (IF 30.8) Pub Date : 2023-09-21 Jennifer L. McCann, Agnese Cristini, Emily K. Law, Seo Yun Lee, Michael Tellier, Michael A. Carpenter, Chiara Beghè, Jae Jin Kim, Anthony Sanchez, Matthew C. Jarvis, Bojana Stefanovska, Nuri A. Temiz, Erik N. Bergstrom, Daniel J. Salamango, Margaret R. Brown, Shona Murphy, Ludmil B. Alexandrov, Kyle M. Miller, Natalia Gromak, Reuben S. Harris
-
Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury Genome Res. (IF 7.0) Pub Date : 2023-09-20 Qiuyun Yang, Lingxuan Zhang, Manrui Li, Yang Xu, Xiaogang Chen, Ruixuan Yuan, Xiaofeng Ou, Min He, Miao Liao, Lin Zhang, Hao Dai, Meili Lv, Xiaoqi Xie, Weibo Liang, Xiameng Chen
The subventricular zone (SVZ) is a neurogenic niche that contributes to homeostasis and repair after brain injury. However, the effects of mild traumatic brain injury (mTBI) on the divergence of the regulatory DNA landscape within the SVZ and its link to functional alterations remain unexplored. In this study, we meticulously mapped the transcriptome atlas of murine SVZ and its responses to mTBI at
-
Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing Genes Dev. (IF 10.5) Pub Date : 2023-09-21 Elsa Franco-Echevarría, Mathias Nielsen, Anna Schulten, Jitender Cheema, Tomos E. Morgan, Mariann Bienz, Caroline Dean
Polycomb repressive complex 2 (PRC2) mediates epigenetic silencing of target genes in animals and plants. In Arabidopsis, PRC2 is required for the cold-induced epigenetic silencing of the FLC floral repressor locus to align flowering with spring. During this process, PRC2 relies on VEL accessory factors, including the constitutively expressed VRN5 and the cold-induced VIN3. The VEL proteins are physically
-
Rice heterosis: quantitatively characterized and optimized hybrid breeding Nat. Genet. (IF 30.8) Pub Date : 2023-09-18
-
Boosting the power of genome-wide association studies within and across ancestries by using polygenic scores Nat. Genet. (IF 30.8) Pub Date : 2023-09-18 Adrian I. Campos, Shinichi Namba, Shu-Chin Lin, Kisung Nam, Julia Sidorenko, Huanwei Wang, Yoichiro Kamatani, Ling-Hua Wang, Seunggeun Lee, Yen-Feng Lin, Yen-Chen Anne Feng, Yukinori Okada, Peter M. Visscher, Loic Yengo
-
Molecular basis for maternal inheritance of human mitochondrial DNA Nat. Genet. (IF 30.8) Pub Date : 2023-09-18 William Lee, Angelica Zamudio-Ochoa, Gina Buchel, Petar Podlesniy, Nuria Marti Gutierrez, Margalida Puigròs, Anna Calderon, Hsin-Yao Tang, Li Li, Aleksei Mikhalchenko, Amy Koski, Ramon Trullas, Shoukhrat Mitalipov, Dmitry Temiakov
-
Dosage compensation of Z sex chromosome genes in avian fibroblast cells Genome Biol. (IF 12.3) Pub Date : 2023-09-20 Ruslan Deviatiiarov, Hiroki Nagai, Galym Ismagulov, Anastasia Stupina, Kazuhiro Wada, Shinji Ide, Noriyuki Toji, Heng Zhang, Woranop Sukparangsi, Sittipon Intarapat, Oleg Gusev, Guojun Sheng
In birds, sex is genetically determined; however, the molecular mechanism is not well-understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in contrast to the mammalian chrX. To investigate chrZ dosage compensation and its role in sex specification, we use a highly quantitative method and analyze transcriptional activities of male and female fibroblast cells from seven
-
DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection Genome Biol. (IF 12.3) Pub Date : 2023-09-20 Fabian Hausmann, Can Ergen, Robin Khatri, Mohamed Marouf, Sonja Hänzelmann, Nicola Gagliani, Samuel Huber, Pierre Machart, Stefan Bonn
Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering and cell type identification. Here, we present DISCERN, a novel deep generative network that
-
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment Genome Biol. (IF 12.3) Pub Date : 2023-09-18 Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Hubert Pausch, Alexander S. Leonard, Danang Crysnanto, Shikang Wang, Bin Tong, Johannes A. Lenstra, Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu, Liangliang Jin, Ruihua Dang, Yongzhen Huang, Xianyong Lan, Gang Ren, Yu Wang, Yuanpeng Gao, Zhijie Ma, Haijian Cheng, Yun Ma, Hong Chen, Weijun Pang, Chuzhao Lei, Ningbo Chen
Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental
-
Author Correction: Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem Genome Biol. (IF 12.3) Pub Date : 2023-09-18 Xiangqian Zhu, Zhongping Xu, Guanying Wang, Yulong Cong, Lu Yu, Ruoyu Jia, Yuan Qin, Guangyu Zhang, Bo Li, Daojun Yuan, Lili Tu, Xiyan Yang, Keith Lindsey, Xianlong Zhang, Shuangxia Jin
Correction: Genome Biol 24, 194 (2023) https://doi.org/10.1186/s13059-023-03032-6 Following publication of the original article [1], the authors reported an error in Fig. 9, namely a missing significant difference symbol for JCR1 and a redundant significant difference symbol for JOE1. The updated Fig. 9 is available in this Correction. Fig. 9 Phenotype of GhLAX1, GhLAX2, GhLOX3 knock out and overexpression
-
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods Genome Biol. (IF 12.3) Pub Date : 2023-09-18 Natalie Charitakis, Agus Salim, Adam T. Piers, Kevin I. Watt, Enzo R. Porrello, David A. Elliott, Mirana Ramialison
Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable using RNA-sequencing technologies. However, the increasing number of published tools designed to define SVG sets currently lack benchmarking methods to accurately
-
RNA modifications in physiology and disease: towards clinical applications Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-15 Sylvain Delaunay, Mark Helm, Michaela Frye
-
mtPGS: Leverage multiple correlated traits for accurate polygenic score construction Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-15 Chang Xu, Santhi K. Ganesh, Xiang Zhou
Accurate polygenic scores (PGSs) facilitate the genetic prediction of complex traits and aid in the development of personalized medicine. Here, we develop a statistical method called multi-trait assisted PGS (mtPGS), which can construct accurate PGSs for a target trait of interest by leveraging multiple traits relevant to the target trait. Specifically, mtPGS borrows SNP effect size similarity information
-
Illuminating the human yolk sac through single-cell omics Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-15 Kirsty Minton
A paper in Science reports a time-resolved multiomic atlas of the human yolk sac, expanding knowledge of this poorly resolved structure in humans.
-
Imprinted genes and the manipulation of parenting in mammals Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-15 Rosalind M. John, Matthew J. Higgs, Anthony R. Isles
-
Genome-wide association meta-analysis identifies 17 loci associated with nonalcoholic fatty liver disease Nat. Genet. (IF 30.8) Pub Date : 2023-09-14 Yanhua Chen, Xiaomeng Du, Annapurna Kuppa, Mary F. Feitosa, Lawrence F. Bielak, Jeffrey R. O’Connell, Solomon K. Musani, Xiuqing Guo, Bratati Kahali, Vincent L. Chen, Albert V. Smith, Kathleen A. Ryan, Gudny Eirksdottir, Matthew A. Allison, Donald W. Bowden, Matthew J. Budoff, John Jeffrey Carr, Yii-Der I. Chen, Kent D. Taylor, Antonino Oliveri, Adolfo Correa, Breland F. Crudup, Sharon L. R. Kardia
-
Somatic SLC30A1 mutations altering zinc transporter ZnT1 cause aldosterone-producing adenomas and primary aldosteronism Nat. Genet. (IF 30.8) Pub Date : 2023-09-14 Juilee Rege, Sascha Bandulik, Kazutaka Nanba, Carla Kosmann, Amy R. Blinder, Allein Plain, Pankaj Vats, Chandan Kumar-Sinha, Antonio M. Lerario, Tobias Else, Yuto Yamazaki, Fumitoshi Satoh, Hironobu Sasano, Thomas J. Giordano, Tracy Ann Williams, Martin Reincke, Adina F. Turcu, Aaron M. Udager, Richard Warth, William E. Rainey
-
Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity Nat. Genet. (IF 30.8) Pub Date : 2023-09-14 Peter M. K. Westcott, Francesc Muyas, Haley Hauck, Olivia C. Smith, Nathan J. Sacks, Zackery A. Ely, Alex M. Jaeger, William M. Rideout, Daniel Zhang, Arjun Bhutkar, Mary C. Beytagh, David A. Canner, Grissel C. Jaramillo, Roderick T. Bronson, Santiago Naranjo, Abbey Jin, J. J. Patten, Amanda M. Cruz, Sean-Luc Shanahan, Isidro Cortes-Ciriano, Tyler Jacks
-
Mary Lyon and the birth of X-inactivation research Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-13 Marnie E. Blewitt
Marnie Blewitt highlights the visionary 1961 paper by Mary Lyon in which she proposed that dosage compensation in female mammals involves X-inactivation and recognized its implications for sex-specific phenotypes in X-linked disorders.
-
Quantifying fitness effects and mutation rates of mCAs in blood Nat. Genet. (IF 30.8) Pub Date : 2023-09-11
-
Mutation rates and fitness consequences of mosaic chromosomal alterations in blood Nat. Genet. (IF 30.8) Pub Date : 2023-09-11 Caroline J. Watson, Jamie R. Blundell
-
ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data Genome Biol. (IF 12.3) Pub Date : 2023-09-11 Yang Li, Mingcong Wu, Shuangge Ma, Mengyun Wu
Clustering is a critical component of single-cell RNA sequencing (scRNA-seq) data analysis and can help reveal cell types and infer cell lineages. Despite considerable successes, there are few methods tailored to investigating cluster-specific genes contributing to cell heterogeneity, which can promote biological understanding of cell heterogeneity. In this study, we propose a zero-inflated negative
-
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees Genome Biol. (IF 12.3) Pub Date : 2023-09-11 Kenneth A. Barr, Katherine L. Rhodes, Yoav Gilad
Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation
-
Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis Genome Biol. (IF 12.3) Pub Date : 2023-09-11 Sixian Zhou, Fengli Zhao, Danling Zhu, Qiqi Zhang, Ziwei Dai, Zhe Wu
In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. Here, we analyze Pol II dynamics at 3’ ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated
-
PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution Genome Biol. (IF 12.3) Pub Date : 2023-09-11 Barbara Poszewiecka, Krzysztof Gogolewski, Justyna A. Karolak, Paweł Stankiewicz, Anna Gambin
Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich regions of interest iteratively. We validate its robustness and efficiency using a golden-standard set of human BAC clones and in silico-generated SDs with predefined
-
COLLAGENE enables privacy-aware federated and collaborative genomic data analysis Genome Biol. (IF 12.3) Pub Date : 2023-09-11 Wentao Li, Miran Kim, Kai Zhang, Han Chen, Xiaoqian Jiang, Arif Harmanci
Growing regulatory requirements set barriers around genetic data sharing and collaborations. Moreover, existing privacy-aware paradigms are challenging to deploy in collaborative settings. We present COLLAGENE, a tool base for building secure collaborative genomic data analysis methods. COLLAGENE protects data using shared-key homomorphic encryption and combines encryption with multiparty strategies
-
Nucleosome repositioning in chronic lymphocytic leukaemia Genome Res. (IF 7.0) Pub Date : 2023-09-12 Kristan V Piroeva, Charlotte McDonald, Charalampos Xanthopoulos, Chelsea Fox, Christopher T Clarkson, Jan-Philipp Mallm, Yevhen Vainshtein, Luminita Ruje, Lara C Klett, Stephan Stilgenbauer, Daniel Mertens, Efterpi Kostareli, Karsten Rippe, Vladimir B. Teif
The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral-blood B cells from patients with chronic lymphocytic
-
Characterization of a promiscuous DNA sulfur binding domain and application in site-directed RNA base editing Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-13 Wenyue Hu, Bingxu Yang, Qingjie Xiao, Yuli Wang, Yuting Shuai, Gong Zhao, Lixin Zhang, Zixin Deng, Xinyi He, Guang Liu
Phosphorothioate (PT)-modification was discovered in prokaryotes and is involved in many biological functions such as restriction-modification systems. PT-modification can be recognized by the sulfur binding domains (SBDs) of PT-dependent restriction endonucleases, through coordination with the sulfur atom, accompanied by interactions with the DNA backbone and bases. The unique characteristics of PT
-
FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues Nucleic Acids Res. (IF 14.9) Pub Date : 2023-09-12 Qili Shi, Xinrong Li, Yizhe Liu, Zhiao Chen, Xianghuo He
Regulatory processes at the RNA transcript level play a crucial role in generating transcriptome diversity and proteome composition in human cells, impacting both physiological and pathological states. This study introduces FLIBase (www.FLIBase.org), a specialized database that focuses on annotating full-length isoforms using long-read sequencing techniques. We collected and integrated long-read (351
-
Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension Am. J. Hum. Genet. (IF 9.8) Pub Date : 2023-09-07 Stefan van Duijvenboden, Julia Ramírez, William J. Young, Kaya J. Olczak, Farah Ahmed, Mohammed J.A.Y. Alhammadi, , Christopher G. Bell, Andrew P. Morris, Patricia B. Munroe