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 RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes...
May 3, 2024: Genome Research
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 types. This is possible in principle, since all these cell types are subject to effects from the same causative gene, that has the same kind of function (e...
May 3, 2024: Genome Research
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 data. Squigulator takes a reference genome, transcriptome or read sequences and generates corresponding raw nanopore signal data...
May 1, 2024: Genome Research
Brian S Roberts, Ashlyn G Anderson, Chris Partridge, Gregory M Cooper, Richard M Myers
Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis -regulatory elements (CREs) with their target genes is a challenging task that is essential to address many biological and mechanistic questions. Many current approaches rely on chromatin conformation capture techniques or single-cell correlational methods to establish CRE-to-gene associations. These methods can be effective but have limitations, including resolution, gaps in detectable association distances, and cost...
April 17, 2024: Genome Research
Karan K Smith, Jesse D Moreira, Callum R Wilson, June O Padera, Ashlee N Lamason, Liying Xue, Deepa M Gopal, David B Flynn, Jessica L Fetterman
Mitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect occurs, termed the biochemical threshold. Whether the often-cited biochemical threshold of >60% VAF is similar across mtDNA variants and cell types is unclear. In our systematic review, we sought to identify the biochemical threshold of mtDNA variants in relation to VAF by human tissue/cell type...
April 16, 2024: Genome Research
Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh Olsen, Brandy McNulty, David Porubsky, Tessa Montague, Julian Lucas, Chris Condon, Jordan M Eizenga, Sissel Juul, Sean McKenzie, Sara E Simmonds, Jimin Park, Mobin Asri, Sergey Koren, Evan Eichler, Richard Axel, Bruce Martin, Paolo Carnevali, Karen Miga, Benedict Paten
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse...
April 16, 2024: Genome Research
Charles Plessy, Michael J Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W Liu, Jan Grašič, María Sara Del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M Luscombe
Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals...
April 15, 2024: Genome Research
Yinchun Zhong, Yan Yang, Xiaolin Wang, Bingbing Ren, Xueren Wang, Ge Shan, Liang Chen
Exon-intron circRNAs (EIciRNAs) are a circRNA subclass with retained introns. Global features of EIciRNAs remain largely unexplored, mainly owing to the lack of bioinformatic tools. The regulation of intron retention (IR) in EIciRNAs and the associated functionality also require further investigation. We developed a framework, FEICP, which efficiently detected EIciRNAs from high-throughput sequencing (HTS) data. EIciRNAs are distinct from exonic circRNAs (EcircRNAs) in aspects such as with larger length, localization in the nucleus, high tissue specificity, and enrichment mostly in the brain...
April 12, 2024: Genome Research
João L Reis-Cunha, Samuel A Pimenta-Carvalho, Laila V Almeida, Anderson Coqueiro-Dos-Santos, Catarina A Marques, Jennifer A Black, Jeziel Damasceno, Richard McCulloch, Daniella C Bartholomeu, Daniel C Jeffares
Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation...
April 11, 2024: Genome Research
Hassan Bukhari, Vanitha Nithianadam, Rachel A Battaglia, Anthony Cicalo, Souvarish Sarkar, Aram Comjean, Yanhui Hu, Matthew J Leventhal, Xianjun Dong, Mel B Feany
Missense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, including Drosophila , have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenous Drosophila tau gene...
April 10, 2024: Genome Research
Scott Ferguson, Ashley Jones, Kevin Murray, Rose Andrew, Benjamin Schwessinger, Justin O Borevitz
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described...
April 8, 2024: Genome Research
Shuangxi Ji, Wenyi Wang, Tong Zhu, Ankit Sethia
Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenge was overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE 2, powered by multi-step parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times than MuSE 1 and 8-80 times than other popular callers...
April 8, 2024: Genome Research
Muyoung Lee, Qingqing Guo, Mijeong Kim, Joonhyuk Choi, Alia Segura, Alper Genceroglu, Lucy LeBlanc, Nereida Ramirez, Yu Jin Jang, Yeejin Jang, Bum-Kyu Lee, Edward M Marcotte, Jonghwan Kim
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes...
April 5, 2024: Genome Research
Mehdi Foroozandeh Shahraki, Marjan Farahbod, Maxwell W Libbrecht
With the goal of mapping genomic activity, international projects have recently measured epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations produced by segmentation and genome annotation (SAGA) methods have emerged as the predominant way to summarize these epigenomic data sets in order to annotate the genome. These chromatin state annotations are essential for many genomic tasks, including identifying active regulatory elements and interpreting disease-associated genetic variation...
March 21, 2024: Genome Research
Blandine C Mercier, Emmanuel Labaronne, David Cluet, Laura Guiguettaz, Nicolas Fontrodona, Alicia Bicknell, Antoine Corbin, Melanie Wencker, Fabien Aube, Laurent Modolo, Karina Jouravleva, Didier Auboeuf, Melissa J Moore, Emiliano P Ricci
mRNA translation and decay are tightly interconnected processes both in the context of mRNA quality control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions and through the recruitment of specific proteins to ribosomes are important determinants of mRNA turnover. However, the extent to which translation-dependent (TDD) and independent (TID) mRNA decay pathways participate in the degradation of mRNAs has not been studied yet. Here we describe a comprehensive analysis of basal and signal-induced TDD and TID in mouse primary CD4+ T cells...
March 20, 2024: Genome Research
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James Gahan, Steven Sanders, Brian Bradshaw, Timothy DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian Gornik, R Travis Moreland, Tyra Wolfsberg, Adam M Phillippy, James Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew Nicotra, Uri Frank, Andreas D Baxevanis
Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata , placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H...
March 20, 2024: Genome Research
Kazumichi Fujiwara, Shunpei Kubo, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada
The house mouse ( Mus musculus ), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspecies castaneus and musculus , particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to the musculus -type haplogroup, potentially explained by genomic conflict under sex-ratio distortion due to varying copy numbers of ampliconic genes on sex chromosomes, Slx and Sly Our computer simulations, designed to replicate the observed scenario, demonstrate that the preferential fixation of musculus -type Y Chromosomes can be achieved with a 10-20% increase in the male-to-female birth ratio...
March 20, 2024: Genome Research
Fei Qin, Guoshuai Cai, Christopher I Amos, Feifei Xiao
No abstract text is available yet for this article.
April 25, 2024: Genome Research
Divya Selvaraju, Filip Wierzbicki, Robert Kofler
To prevent the spread of transposable elements (TEs) hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defence we introduced the P-element , one of the most widely studied eukaryotic transposons, into naive lines of Drosophila erecta We monitored the invasion in 3 replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs and the transcriptome at regular intervals...
March 15, 2024: Genome Research
Matthew Naish, Ian R Henderson
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation...
March 14, 2024: Genome Research
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