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Genetics of glycosylation in mammalian development and disease Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-05-09 Pamela Stanley
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Understanding liver repair through space and time Nat. Genet. (IF 30.8) Pub Date : 2024-05-10 Lenka Belicova, Noemi Van Hul, Emma R. Andersson
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Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition Genes Dev. (IF 10.5) Pub Date : 2024-05-09 Manuel Ares, Jr., Haller Igel, Sol Katzman, John P. Donohue
Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using Saccharomyces cerevisiae, documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome
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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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Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-09 Marie-Christine Carpentier, Anne-Elodie Receveur, Alexandre Boubegtitene, Adrien Cadoudal, Cécile Bousquet-Antonelli, Rémy Merret
Until recently, the general 5′-3′ mRNA decay was placed in the cytosol after the mRNA was released from ribosomes. However, the discovery of an additional 5′ to 3′ pathway, the Co-Translational mRNA Decay (CTRD), changed this paradigm. Up to date, defining the real contribution of CTRD in the general mRNA turnover has been hardly possible as the enzyme involved in this pathway is also involved in cytosolic
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EXO1 and DNA2-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-09 Néstor García-Rodríguez, Iria Domínguez-García, María del Carmen Domínguez-Pérez, Pablo Huertas
DNA replication faces challenges from DNA lesions originated from endogenous or exogenous sources of stress, leading to the accumulation of single-stranded DNA (ssDNA) that triggers the activation of the ATR checkpoint response. To complete genome replication in the presence of damaged DNA, cells employ DNA damage tolerance mechanisms that operate not only at stalled replication forks but also at ssDNA
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Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-09 Elena Rogoulenko, Yaakov Levy
The kinetics of protein–DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shaping biological function. Protein–DNA recognition kinetics are characterized by two key elements: the time taken to locate the target site amid various nonspecific alternatives; and the kinetics involved in the recognition process, which may necessitate overcoming
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Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent cell survival Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-09 Martina Rossi, Nirad Banskota, Chang Hoon Shin, Carlos Anerillas, Dimitrios Tsitsipatis, Jen-Hao Yang, Rachel Munk, Jennifer L Martindale, Xiaoling Yang, Yulan Piao, Krystyna Mazan-Mamczarz, Jinshui Fan, Elin Lehrmann, Kwan-Wood Gabriel Lam, Supriyo De, Kotb Abdelmohsen, Myriam Gorospe
RNA modifications, including N6-methyladenosine (m6A), critically modulate protein expression programs in a range of cellular processes. Although the transcriptomes of cells undergoing senescence are strongly regulated, the landscape and impact of m6A modifications during senescence are poorly understood. Here, we report a robust m6A modification of PTCHD4 mRNA, encoding Patched Domain-Containing Protein
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Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-09 Attila Horvath, Yoshika Janapala, Katrina Woodward, Shafi Mahmud, Alice Cleynen, Elizabeth E Gardiner, Ross D Hannan, Eduardo Eyras, Thomas Preiss, Nikolay E Shirokikh
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq)
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Tandem repeat variation of human centromeres Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-05-08 Kirsty Minton
Logsdon et al. report the second complete sequence of all centromeres from a single human genome, enabling comparative analyses of the variation in tandemly repeating α-satellite DNA.
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Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-08 Aleksei Agapov, Vladimir Panteleev, Ekaterina Kropocheva, Anna Kanevskaya, Daria Esyunina, Andrey Kulbachinskiy
Argonautes are an evolutionary conserved family of programmable nucleases that identify target nucleic acids using small guide oligonucleotides. In contrast to eukaryotic Argonautes (eAgos) that act on RNA, most studied prokaryotic Argonautes (pAgos) recognize DNA targets. Similarly to eAgos, pAgos can protect prokaryotic cells from invaders, but the biogenesis of guide oligonucleotides that confer
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Fluoropyrimidines trigger decay of hypomodified tRNA in yeast Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-08 Katharina Görlitz, Larissa Bessler, Mark Helm, Raffael Schaffrath, Roland Klassen
Therapeutic fluoropyrimidines 5-fluorouracil (5-FU) and 5-fluorocytosine (5-FC) are in long use for treatment of human cancers and severe invasive fungal infections, respectively. 5-Fluorouridine triphosphate represents a bioactive metabolite of both drugs and is incorporated into target cells’ RNA. Here we use the model fungus Saccharomyces cerevisiae to define fluorinated tRNA as a key mediator of
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Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-08 Frederik Weber, Nikolas Alexander Motzkus, Leona Brandl, Marvin Möhler, Andrijana Alempijevic, Andres Jäschke
In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied, with multiple decapping enzymes identified and efficient capture and sequencing protocols developed for nicotinamide adenine dinucleotide (NAD)-RNA, which allowed for a stepwise elucidation of capping functions. Despite being identified
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Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-08 Pascal Hirsch, Leidy-Alejandra G Molano, Annika Engel, Jens Zentgraf, Sven Rahmann, Matthias Hannig, Rolf Müller, Fabian Kern, Andreas Keller, Georges P Schmartz
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional
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Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-08 Mao Chen, Bo Wu, Yuhuan Huang, Weiting Wang, Yudi Zheng, Samina Shabbir, Panting Liu, Yonghua Dai, Mengli Xia, Guoquan Hu, Mingxiong He
Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome may also play an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutation and ambient stimuli (acetic
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The emerging role of tandem repeats in complex traits Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-05-07 Michael Lamkin, Melissa Gymrek
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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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Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia Genome Biol. (IF 12.3) Pub Date : 2024-05-07 Xiaoli Gong, Wei He, Wan Jin, Hongwei Ma, Gang Wang, Jiaxin Li, Yu Xiao, Yangyu Zhao, Qiong Chen, Huanhuan Guo, Jiexia Yang, Yiming Qi, Wei Dong, Meng Fu, Xiaojuan Li, Jiusi Liu, Xinghui Liu, Aihua Yin, Yi Zhang, Yuan Wei
Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia
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Mapping and functional characterization of structural variation in 1060 pig genomes Genome Biol. (IF 12.3) Pub Date : 2024-05-07 Liu Yang, Hongwei Yin, Lijing Bai, Wenye Yao, Tan Tao, Qianyi Zhao, Yahui Gao, Jinyan Teng, Zhiting Xu, Qing Lin, Shuqi Diao, Zhangyuan Pan, Dailu Guan, Bingjie Li, Huaijun Zhou, Zhongyin Zhou, Fuping Zhao, Qishan Wang, Yuchun Pan, Zhe Zhang, Kui Li, Lingzhao Fang, George E. Liu
Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break
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Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome Genome Biol. (IF 12.3) Pub Date : 2024-05-06 Georgi K. Marinov, Xinyi Chen, Matthew P. Swaffer, Tingting Xiang, Arthur R. Grossman, William J. Greenleaf
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of
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Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions Genome Res. (IF 7.0) Pub Date : 2024-05-06 Stacey E.P. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintaş, Yongsoo Kim, Sander Canisius, Cathy B. Moelans, Paul J. van Diest, Gozde Korkmaz, Nathan A. Lack, Michiel Vermeulen, Sabine C. Linn, Wilbert Zwart
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications
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Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription Genome Res. (IF 7.0) Pub Date : 2024-05-06 Christine R. Keenan, Hannah D. Coughlan, Nadia Iannarella, Andres Tapia del Fierro, Andrew Keniry, Timothy M. Johanson, Wing Fuk Chan, Alexandra L. Garnham, Lachlan W. Whitehead, Marnie E. Blewitt, Gordon K. Smyth, Rhys S. Allan
H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences of heterochromatin loss in cells deficient in both SUV39H1 and SUV39H2 (Suv39DKO), the major mammalian histone methyltransferase enzymes
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Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy Genome Res. (IF 7.0) Pub Date : 2024-05-06 Dhanur P. Iyer, Lambert Moyon, Lars Wittler, Chieh-Yu Cheng, Francisca R. Ringeling, Stefan Canzar, Annalisa Marsico, Aydan Bulut-Karslioğlu
Dormancy is a key feature of stem cell function in adult tissues as well as in embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state remains unclear. Here we show that microRNA activity
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A new framework for exploratory network mediator analysis in omics data Genome Res. (IF 7.0) Pub Date : 2024-05-07 Qingpo Cai, Yinghao Fu, Cheng Lyu, Zihe Wang, Shun Rao, Jessica A. Alvarez, Yun Bai, Jian Kang, Tianwei Yu
Omics methods are widely used in basic biology and translational medicine research. More and more omics data are collected to explain the impact of certain risk factors on clinical outcomes. To explain the mechanism of the risk factors, a core question is how to find the genes/proteins/metabolites that mediate their effects on the clinical outcome. Mediation analysis is a modeling framework to study
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Ribosome decision graphs for the representation of eukaryotic RNA translation complexity Genome Res. (IF 7.0) Pub Date : 2024-05-07 Jack A.S. Tierney, Michał Świrski, Håkon Tjeldnes, Jonathan M. Mudge, Joanna Kufel, Nicola Whiffin, Eivind Valen, Pavel V. Baranov
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, within both annotated protein-coding and noncoding regions. The biological significance of this translation is a matter of intensive
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Oct4 redox sensitivity potentiates reprogramming and differentiation Genes Dev. (IF 10.5) Pub Date : 2024-05-07 Zuolian Shen, Yifan Wu, Asit Manna, Chongil Yi, Bradley R. Cairns, Kimberley J. Evason, Mahesh B. Chandrasekharan, Dean Tantin
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes
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A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Terry Kipkorir, Peter Polgar, Declan Barker, Alexandre D’Halluin, Zaynah Patel, Kristine B Arnvig
Vitamin B12 is an essential cofactor in all domains of life and B12-sensing riboswitches are some of the most widely distributed riboswitches. Mycobacterium tuberculosis, the causative agent of tuberculosis, harbours two B12-sensing riboswitches. One controls expression of metE, encoding a B12-independent methionine synthase, the other controls expression of ppe2 of uncertain function. Here, we analysed
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Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Daniela Tarău, Felix Grünberger, Michael Pilsl, Robert Reichelt, Florian Heiß, Sabine König, Henning Urlaub, Winfried Hausner, Christoph Engel, Dina Grohmann
Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic
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Structural snapshots of phenuivirus cap-snatching and transcription Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Harry M Williams, Sigurdur R Thorkelsson, Dominik Vogel, Carola Busch, Morlin Milewski, Stephen Cusack, Kay Grünewald, Emmanuelle R J Quemin, Maria Rosenthal
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a human pathogen that is now endemic to several East Asian countries. The viral large (L) protein catalyzes viral transcription by stealing host mRNA caps via a process known as cap-snatching. Here, we establish an in vitro cap-snatching assay and present three high-quality electron cryo-microscopy (cryo-EM) structures of the SFTSV L protein
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LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Chia-Hsin Liu, Pei-Chun Shen, Wen-Jen Lin, Hsiu-Cheng Liu, Meng-Hsin Tsai, Tzu-Ya Huang, I-Chieh Chen, Yo-Liang Lai, Yu-De Wang, Mien-Chie Hung, Wei-Chung Cheng
In the field of lipidomics, where the complexity of lipid structures and functions presents significant analytical challenges, LipidSig stands out as the first web-based platform providing integrated, comprehensive analysis for efficient data mining of lipidomic datasets. The upgraded LipidSig 2.0 (https://lipidsig.bioinfomics.org/) simplifies the process and empowers researchers to decipher the complex
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IsoVis – a webserver for visualization and annotation of alternative RNA isoforms Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Ching Yin Wan, Jack Davis, Manveer Chauhan, Josie Gleeson, Yair D J Prawer, Ricardo De Paoli-Iseppi, Christine A Wells, Jarny Choi, Michael B Clark
Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely
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SCTC: inference of developmental potential from single-cell transcriptional complexity Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Hai Lin, Huan Hu, Zhen Feng, Fei Xu, Jie Lyu, Xiang Li, Liyu Liu, Gen Yang, Jianwei Shuai
Inferring the developmental potential of single cells from scRNA-Seq data and reconstructing the pseudo-temporal path of cell development are fundamental but challenging tasks in single-cell analysis. Although single-cell transcriptional diversity (SCTD) measured by the number of expressed genes per cell has been widely used as a hallmark of developmental potential, it may lead to incorrect estimation
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PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Anitha Vijayakumar, Mrinmoyee Majumder, Shasha Yin, Charles Brobbey, Joseph Karam, Breege Howley, Philip H Howe, Stefano Berto, Lalima K Madan, Wenjian Gan, Viswanathan Palanisamy
Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1’s nuclear
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A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Xin Fang, Ruiqi Zhao, Yafen Wang, Mei Sun, Jin Xu, Shengrong Long, Jing Mo, Hudan Liu, Xiang Li, Fang Wang, Xiang Zhou, Xiaocheng Weng
Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named
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mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Hansi Weissensteiner, Lukas Forer, Florian Kronenberg, Sebastian Schönherr
Over the past decade, mtDNA-Server established itself as one of the most widely used variant calling web-services for human mitochondrial genomes. The service accepts sequencing data in BAM format and returns an annotated variant analysis report for both homoplasmic and heteroplasmic variants. In this work we present mtDNA-Server 2, which includes several new features highly requested by the community
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Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Weiyi Li, Darach Miller, Xianan Liu, Lorenzo Tosi, Lamia Chkaiban, Han Mei, Po-Hsiang Hung, Biju Parekkadan, Gavin Sherlock, Sasha F Levy
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput
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Imputation Server PGS: an automated approach to calculate polygenic risk scores on imputation servers Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Lukas Forer, Daniel Taliun, Jonathon LeFaive, Albert V Smith, Andrew P Boughton, Stefan Coassin, Claudia Lamina, Florian Kronenberg, Christian Fuchsberger, Sebastian Schönherr
Polygenic scores (PGS) enable the prediction of genetic predisposition for a wide range of traits and diseases by calculating the weighted sum of allele dosages for genetic variants associated with the trait or disease in question. Present approaches for calculating PGS from genotypes are often inefficient and labor-intensive, limiting transferability into clinical applications. Here, we present ‘Imputation
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GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yu Xue
Small ubiquitin-like modifiers (SUMOs) are tiny but important protein regulators involved in orchestrating a broad spectrum of biological processes, either by covalently modifying protein substrates or by noncovalently interacting with other proteins. Here, we report an updated server, GPS-SUMO 2.0, for the prediction of SUMOylation sites and SUMO-interacting motifs (SIMs). For predictor training,
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SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Niek R Scholten, Dennis Haandrikman, Joshua O Tolhuis, Edoardo Morandi, Danny Incarnato
RNA molecules perform a variety of functions in cells, many of which rely on their secondary and tertiary structures. Chemical probing methods coupled with high-throughput sequencing have significantly accelerated the mapping of RNA structures, and increasingly large datasets of transcriptome-wide RNA chemical probing data are becoming available. Analogously to what has been done for decades in the
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UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2 Nucleic Acids Res. (IF 14.9) Pub Date : 2024-05-06 Lukas M Langer, Katharina Kurscheidt, Jérôme Basquin, Fabien Bonneau, Iuliia Iermak, Claire Basquin, Elena Conti
Nonsense-mediated mRNA decay (NMD) is a conserved co-translational mRNA surveillance and turnover pathway across eukaryotes. NMD has a central role in degrading defective mRNAs and also regulates the stability of a significant portion of the transcriptome. The pathway is organized around UPF1, an RNA helicase that can interact with several NMD-specific factors. In human cells, degradation of the targeted
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Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice Genome Res. (IF 7.0) Pub Date : 2024-05-03 Leandros Boukas, Teresa Romeo Luperchio, Afrooz Razi, Kasper D. Hansen, Hans T. Bjornsson
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically exhibits phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption - the root of the pathogenesis - is similar in the different disease-relevant cell
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Navigating the landscape of epitranscriptomics and host immunity Genome Res. (IF 7.0) Pub Date : 2024-05-03 Elaine Huang, Clara Frydman, Xinshu Xiao
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic
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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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Kernel-based testing for single-cell differential analysis Genome Biol. (IF 12.3) Pub Date : 2024-05-03 A. Ozier-Lafontaine, C. Fourneaux, G. Durif, P. Arsenteva, C. Vallot, O. Gandrillon, S. Gonin-Giraud, B. Michel, F. Picard
Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and epigenomic modifications. Our method allows feature-wise and global transcriptome/epigenome comparisons, revealing cell population heterogeneities. Using a classifier based
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Simulation of nanopore sequencing signal data with tunable parameters Genome Res. (IF 7.0) Pub Date : 2024-05-01 Hasindu Gamaarachchi, James Ferguson, Hiruna Samarakoon, Kisaru Liyanage, Sri Parameswaran, Ira Deveson
In silico simulation of high-throughput sequencing data is a technique used widely in the genomics field. However, there is currently a lack of effective tools for creating simulated data from nanopore sequencing devices, which measure DNA or RNA molecules in the form of time-series current signal data. Here, we introduce Squigulator, a fast and simple tool for simulation of realistic nanopore signal
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mi-Mic: a novel multi-layer statistical test for microbiota-disease associations Genome Biol. (IF 12.3) Pub Date : 2024-05-01 Oshrit Shtossel, Shani Finkelstein, Yoram Louzoun
mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical tests: a large number of tests, sparsity, varying abundance scales, and taxonomic relationships. mi-Mic first converts microbial counts to a cladogram of means. It then applies a priori tests on the upper levels of the cladogram to detect overall relationships. Finally, it performs
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DISSECT: deep semi-supervised consistency regularization for accurate cell type fraction and gene expression estimation Genome Biol. (IF 12.3) Pub Date : 2024-04-30 Robin Khatri, Pierre Machart, Stefan Bonn
Cell deconvolution is the estimation of cell type fractions and cell type-specific gene expression from mixed data. An unmet challenge in cell deconvolution is the scarcity of realistic training data and the domain shift often observed in synthetic training data. Here, we show that two novel deep neural networks with simultaneous consistency regularization of the target and training domains significantly
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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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The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons Genes Dev. (IF 10.5) Pub Date : 2024-04-30 Wen Xiao, Reem Halabi, Chia-Ho Lin, Mohammad Nazim, Kyu-Hyeon Yeom, Douglas L. Black
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The metastasis‐associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion
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An unexpected path for Malat1 in neurons: trafficking out of the nucleus for translation Genes Dev. (IF 10.5) Pub Date : 2024-04-30 Bradley W. Wright, Jeremy E. Wilusz
The Malat1 (metastasis-associated lung adenocarcinoma transcript 1) long noncoding RNA is highly and broadly expressed in mammalian tissues, accumulating in the nucleus where it modulates expression and pre-mRNA processing of many protein-coding genes. In this issue of Genes & Development, Xiao and colleagues (doi:10.1101/gad.351557.124) report that a significant fraction of Malat1 transcripts in cultured
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The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids Nucleic Acids Res. (IF 14.9) Pub Date : 2024-04-30 Xueping Sun, Meenu Singla-Rastogi, Jingwen Wang, Chuanzhi Zhao, Xingjun Wang, Pengcheng Li
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis
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RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Nucleic Acids Res. (IF 14.9) Pub Date : 2024-04-30 Alessio Del Conte, Giorgia F Camagni, Damiano Clementel, Giovanni Minervini, Alexander Miguel Monzon, Carlo Ferrari, Damiano Piovesan, Silvio C E Tosatto
Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters
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SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina Nucleic Acids Res. (IF 14.9) Pub Date : 2024-04-30 Marine Bugnon, Ute F Röhrig, Mathilde Goullieux, Marta A S Perez, Antoine Daina, Olivier Michielin, Vincent Zoete
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign