The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals [RESOURCES]
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. symbiolongicarpus and identified cell type markers for all major...
Source: Genome Research - March 20, 2024 Category: Genetics & Stem Cells Authors: Schnitzler, C. E., Chang, E. S., Waletich, J., Quiroga-Artigas, G., Wong, W. Y., Nguyen, A.-D., Barreira, S., Doonan, L. B., Gonzalez, P., Koren, S., Gahan, J., Sanders, S., Bradshaw, B., DuBuc, T., Febrimarsa, F., de Jong, D., Nawrocki, E., Larson, A., K Tags: RESOURCES Source Type: research
Inference of selective force on house mouse genomes during secondary contact in East Asia [RESEARCH]
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 be...
Source: Genome Research - March 20, 2024 Category: Genetics & Stem Cells Authors: Fujiwara, K., Kubo, S., Endo, T., Takada, T., Shiroishi, T., Suzuki, H., Osada, N. Tags: RESEARCH Source Type: research
Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA based host defense against invading P-elements [RESEARCH]
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. A piRNA-based host defense was rapidly established ...
Source: Genome Research - March 15, 2024 Category: Genetics & Stem Cells Authors: Selvaraju, D., Wierzbicki, F., Kofler, R. Tags: RESEARCH Source Type: research
The structure, function, and evolution of plant centromeres [REVIEW]
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 kine...
Source: Genome Research - March 14, 2024 Category: Genetics & Stem Cells Authors: Naish, M., Henderson, I. R. Tags: REVIEW Source Type: research
Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes [RESEARCH]
mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechan...
Source: Genome Research - March 13, 2024 Category: Genetics & Stem Cells Authors: Wu, T.-Y., Li, Y.-R., Chang, K.-J., Fang, J.-C., Urano, D., Liu, M.-J. Tags: RESEARCH Source Type: research
Haplotype-resolved 3D chromatin architecture of the hybrid pig [RESOURCES]
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation ma...
Source: Genome Research - March 13, 2024 Category: Genetics & Stem Cells Authors: Lin, Y., Li, J., Gu, Y., Jin, L., Bai, J., Zhang, J., Wang, Y., Liu, P., Long, K., He, M., Li, D., Liu, C., Han, Z., Zhang, Y., Li, X., Zeng, B., Lu, L., Kong, F., Sun, Y., Fan, Y., Wang, X., Wang, T., Jiang, A., Ma, J., Shen, L., Zhu, L., Jiang, Y., Tang Tags: RESOURCES Source Type: research
Major impacts of widespread structural variation on sorghum [RESEARCH]
This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum. (Source: Genome Research)
Source: Genome Research - March 13, 2024 Category: Genetics & Stem Cells Authors: Zhang, Z., Gomes Viana, J. P., Zhang, B., Walden, K. K. O., Müller Paul, H., Moose, S. P., Morris, G. P., Daum, C., Barry, K. W., Shakoor, N., Hudson, M. E. Tags: RESEARCH Source Type: research
RNA Pol II-dependent transcription efficiency fine-tunes A-to-I editing levels [RESEARCH]
A-to-I RNA editing is a widespread epitranscriptomic phenomenon leading to the conversion of adenosines to inosines, which are primarily interpreted as guanosines by cellular machines. Consequently, A-to-I editing can alter splicing or lead to recoding of transcripts. As misregulation of editing can cause a variety of human diseases, A-to-I editing requires tight regulation of the extent of deamination, particularly in protein-coding regions. The bulk of A-to-I editing occurs cotranscriptionally. Thus, we studied A-to-I editing regulation in the context of transcription and pre-mRNA processing. We show that stimulation of ...
Source: Genome Research - March 12, 2024 Category: Genetics & Stem Cells Authors: Szabo, B., Mandl, T. C., Woldrich, B., Diensthuber, G., Martin, D., Jantsch, M. F., Licht, K. Tags: RESEARCH Source Type: research
Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma [RESEARCH]
Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals an uneven distribution of long molecules from across the genome. Long cfDNA molecules show overrepresentation in euchromatic regions of the genome, in sharp contrast to short DNA molecules. We observe a stronger relation...
Source: Genome Research - March 12, 2024 Category: Genetics & Stem Cells Authors: Che, H., Jiang, P., Choy, L. Y. L., Cheng, S. H., Peng, W., Chan, R. W. Y., Liu, J., Zhou, Q., Lam, W. K. J., Yu, S. C. Y., Lau, S. L., Leung, T. Y., Wong, J., Wong, V. W.-S., Wong, G. L. H., Chan, S. L., Chan, K. C. A., Lo, Y. M. D. Tags: RESEARCH Source Type: research
Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus [RESEARCH]
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can...
Source: Genome Research - March 12, 2024 Category: Genetics & Stem Cells Authors: Liu, Y., Niu, J., Ye, F., Solberg, T., Lu, B., Wang, C., Nowacki, M., Gao, S. Tags: RESEARCH Source Type: research
Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle [RESOURCES]
Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-calle...
Source: Genome Research - March 11, 2024 Category: Genetics & Stem Cells Authors: Leonard, A. S., Mapel, X. M., Pausch, H. Tags: RESOURCES Source Type: research
Tyrosine 1-phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage [RESEARCH]
In this study, we investigated global changes in transcription in response to ionizing irradiation (IR), which induces double-strand breaks in DNA. We used mNET-seq to profile nascent transcripts bound to different phosphorylated forms of the RNA polymerase II (RNA Pol II) C-terminal domain (CTD). We found that IR leads to global transcriptional repression of protein-coding genes, accompanied by an increase in antisense transcripts near promoters, called PROMPTs, transcribed by RNA Pol II phosphorylated on tyrosine 1 (Y1P) residue of the CTD. These Y1P-transcribed PROMPTs are enriched for PRC2 binding sites and associated ...
Source: Genome Research - March 11, 2024 Category: Genetics & Stem Cells Authors: Ajit, K., Alagia, A., Burger, K., Gullerova, M. Tags: RESEARCH Source Type: research
Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes [RESOURCES]
Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition a...
Source: Genome Research - March 1, 2024 Category: Genetics & Stem Cells Authors: Yu, W., Luo, H., Yang, J., Zhang, S., Jiang, H., Zhao, X., Hui, X., Sun, D., Li, L., Wei, X.-q., Lonardi, S., Pan, W. Tags: RESOURCES Source Type: research
Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors [RESEARCH]
Dozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of...
Source: Genome Research - February 28, 2024 Category: Genetics & Stem Cells Authors: Shepherdson, J. L., Friedman, R. Z., Zheng, Y., Sun, C., Oh, I. Y., Granas, D. M., Cohen, B. A., Chen, S., White, M. A. Tags: RESEARCH Source Type: research
Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA [RESEARCH]
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNAs in biological contexts was ...
Source: Genome Research - February 28, 2024 Category: Genetics & Stem Cells Authors: Bhatt, U., Cucchiarini, A., Luo, Y., Evans, C. W., Mergny, J.-L., Iyer, K. S., Smith, N. M. Tags: RESEARCH Source Type: research
