Gene expression imputation and cell type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders [RESOURCES]
In this study, we developed a tensor-based approach to impute gene expression on a transcriptome-wide level. After rigorous computational benchmarking, we applied our approach to infer missing data points in the widely used BrainSpan resource and completed the entire grid of spatiotemporal transcriptomics. Next, we conducted deconvolutional analyses to comprehensively characterize major cell type dynamics across the entire BrainSpan resource to estimate the cellular temporal changes and distinct neocortical areas across development. Moreover, integration of these results with GWAS summary statistics for 13 brain associated...
Source: Genome Research - December 3, 2020 Category: Genetics & Stem Cells Authors: Pei, G., Wang, Y.-Y., Simon, L. M., Dai, Y., Zhao, Z., Jia, P. Tags: RESOURCES Source Type: research

Reviewer Index, Volume 30, 2020 [REVIEWER INDEX]
(Source: Genome Research)
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Tags: REVIEWER INDEX Source Type: research

Corrigendum: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians [CORRIGENDUM]
(Source: Genome Research)
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Tags: CORRIGENDUM Source Type: research

Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time [METHOD]
The levels and subcellular localizations of proteins regulate critical aspects of many cellular processes and can become targets of therapeutic intervention. However, high-throughput methods for the discovery of proteins that change localization either by shuttling between compartments, by binding larger complexes, or by localizing to distinct membraneless organelles are not available. Here we describe a scalable strategy to characterize effects on protein localizations and levels in response to different perturbations. We use CRISPR-Cas9-based intron tagging to generate cell pools expressing hundreds of GFP-fusion protein...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Reicher, A., Koren, A., Kubicek, S. Tags: METHOD Source Type: research

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model [METHOD]
Transcriptional enhancers commonly work over long genomic distances to precisely regulate spatiotemporal gene expression patterns. Dissecting the promoters physically contacted by these distal regulatory elements is essential for understanding developmental processes as well as the role of disease-associated risk variants. Modern proximity-ligation assays, like HiChIP and ChIA-PET, facilitate the accurate identification of long-range contacts between enhancers and promoters. However, these assays are technically challenging, expensive, and time-consuming, making it difficult to investigate enhancer topologies, especially i...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Tang, L., Hill, M. C., Wang, J., Wang, J., Martin, J. F., Li, M. Tags: METHOD Source Type: research

Cross-species analysis of enhancer logic using deep learning [METHOD]
Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a d...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., Primot, A., Cadieu, E., van Rooijen, E., Marine, J.-C., Egidy, G., Ghanem, G.-E., Zon, L., Wouters, J., Ae Tags: METHOD Source Type: research

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits [METHOD]
Recombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions in Drosophila ...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Ruiz-Arenas, C., Caceres, A., Lopez, M., Pelegri-Siso, D., Gonzalez, J., Gonzalez, J. R. Tags: METHOD Source Type: research

Ultrafast and scalable variant annotation and prioritization with big functional genomics data [METHOD]
The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel ...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Huang, D., Yi, X., Zhou, Y., Yao, H., Xu, H., Wang, J., Zhang, S., Nong, W., Wang, P., Shi, L., Xuan, C., Li, M., Wang, J., Li, W., Kwan, H. S., Sham, P. C., Wang, K., Li, M. J. Tags: METHOD Source Type: research

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region [RESEARCH]
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Maurano, M. T., Ramaswami, S., Zappile, P., Dimartino, D., Boytard, L., Ribeiro-dos-Santos, A. M., Vulpescu, N. A., Westby, G., Shen, G., Feng, X., Hogan, M. S., Ragonnet-Cronin, M., Geidelberg, L., Marier, C., Meyn, P., Zhang, Y., Cadley, J., Ordonez, R. Tags: RESEARCH Source Type: research

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans [RESEARCH]
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profile...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritisanac, I., Zhang, Y., Calarco, J. A. Tags: RESEARCH Source Type: research

Distinctive regulatory architectures of germline-active and somatic genes in C. elegans [RESEARCH]
RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ~90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters ha...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Serizay, J., Dong, Y., Jänes, J., Chesney, M., Cerrato, C., Ahringer, J. Tags: RESEARCH Source Type: research

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans [RESEARCH]
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation, and fertility. Here, we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and ...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Strobino, M., Wenda, J. M., Padayachy, L., Steiner, F. A. Tags: RESEARCH Source Type: research

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids [RESEARCH]
Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied a...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Mugal, C. F., Wang, M., Backström, N., Wheatcroft, D., Alund, M., Semon, M., McFarlane, S. E., Dutoit, L., Qvarnström, A., Ellegren, H. Tags: RESEARCH Source Type: research

Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages [RESEARCH]
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X–Y crossing-over unleashed a second dynamic: selfish X–Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked ho...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Hughes, J. F., Skaletsky, H., Pyntikova, T., Koutseva, N., Raudsepp, T., Brown, L. G., Bellott, D. W., Cho, T.-J., Dugan-Rocha, S., Khan, Z., Kremitzki, C., Fronick, C., Graves-Lindsay, T. A., Fulton, L., Warren, W. C., Wilson, R. K., Owens, E., Womack, J Tags: RESEARCH Source Type: research

Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains [RESEARCH]
The GGGGCC hexanucleotide expansion in C9orf72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet a clear understanding of how C9 fits into the broader context of ALS/FTD pathology has remained lacking. The repetitive RNA derived from the C9 repeat is known to sequester hnRNPH, a splicing regulator, into insoluble aggregates, resulting in aberrant alternative splicing. Furthermore, hnRNPH insolubility and altered splicing of a robust set of targets have been observed to correlate in C9 and sporadic ALS/FTD patients alike, suggesting that changes along this ax...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Wang, Q., Conlon, E. G., Manley, J. L., Rio, D. C. Tags: RESEARCH Source Type: research

Complex mosaic structural variations in human fetal brains [RESEARCH]
Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200–400 mosaic SNVs per cell in three human fetal brains (15–21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of...
Source: Genome Research - December 1, 2020 Category: Genetics & Stem Cells Authors: Sekar, S., Tomasini, L., Proukakis, C., Bae, T., Manlove, L., Jang, Y., Scuderi, S., Zhou, B., Kalyva, M., Amiri, A., Mariani, J., Sedlazeck, F. J., Urban, A. E., Vaccarino, F. M., Abyzov, A. Tags: RESEARCH Source Type: research

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules [RESEARCH]
In this study, the oral microbiome, and 38 host cytokines and chemokines, were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. 42 of these species had no genomes in public repositories, therefore representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understo...
Source: Genome Research - November 25, 2020 Category: Genetics & Stem Cells Authors: Baker, J. L., Morton, J. T., Dinis, M., Alvarez, R., Tran, N. C., Knight, R., Edlund, A. Tags: RESEARCH Source Type: research

Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV) [RESOURCES]
The National Center for Biotechnology Information (NCBI) is an archive providing free access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation, is integrated with other NCBI resources such as Gene, dbGaP, and BLAST, and provides a platform for customized analysis and visualization. Here, we describe how members of the biomedical research community can use GDV...
Source: Genome Research - November 25, 2020 Category: Genetics & Stem Cells Authors: Rangwala, S. H., Kuznetsov, A., Ananiev, V., Asztalos, A., Borodin, E., Evgeniev, V., Joukov, V., Lotov, V., Pannu, R., Rudnev, D., Shkeda, A., Weitz, E. M., Schneider, V. A. Tags: RESOURCES Source Type: research

The origin and evolution of a distinct mechanism of transcription initiation in yeasts [RESEARCH]
The molecular process of transcription by RNA Polymerase II is highly conserved among eukaryotes ("classic model"). A distinct way of locating transcription start sites (TSSs) has been identified in a budding yeast Saccharomyces cerevisiae ("scanning model"). Herein, we applied genomic approaches to elucidate the origin of the "scanning model" and its underlying genetic mechanisms. We first identified TSSs at single-nucleotide resolution for 12 yeast species using the nAnT-iCAGE technique, which significantly improved the annotations of these genomes by providing accurate 5' boundaries for pro...
Source: Genome Research - November 20, 2020 Category: Genetics & Stem Cells Authors: Lu, Z., Lin, Z. Tags: RESEARCH Source Type: research

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data [METHOD]
Single-cell DNA methylation data has become increasingly abundant and has uncovered many genes with a positive correlation between expression and promoter methylation, challenging the common dogma based on bulk data. However, computational tools for analyzing single-cell methylome data are lagging far behind. A number of tasks, including cell type calling and integration with transcriptome data, requires the construction of a robust gene activity matrix as the prerequisite but challenging task. The advent of multi-omics data enables measurement of both DNA methylation and gene expression for the same single cells. Although...
Source: Genome Research - November 20, 2020 Category: Genetics & Stem Cells Authors: Uzun, Y., Wu, H., Tan, K. Tags: METHOD Source Type: research

Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared to mice and Drosophila melanogaster [METHOD]
Quantifying and comparing the amount of adaptive evolution among different species is key to understanding how evolution works. Previous studies have shown differences in adaptive evolution across species; however, their specific causes remain elusive. Here, we use improved modeling of weakly deleterious mutations and the demographic history of the outgroup species and ancestral population and estimate that at least 20% of nonsynonymous substitutions between humans and an outgroup species were fixed by positive selection. This estimate is much higher than previous estimates, which did not correct for the sizes of the outgr...
Source: Genome Research - November 18, 2020 Category: Genetics & Stem Cells Authors: Zhen, Y., Huber, C. D., Davies, R. W., Lohmueller, K. E. Tags: METHOD Source Type: research

MAnorm2 for quantitatively comparing groups of ChIP-seq samples [METHOD]
We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 employs a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples b...
Source: Genome Research - November 18, 2020 Category: Genetics & Stem Cells Authors: Tu, S., Li, M., Chen, H., Tan, F., Xu, J., Waxman, D. J., Zhang, Y., Shao, Z. Tags: METHOD Source Type: research

Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages [RESEARCH]
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X–Y crossing-over unleashed a second dynamic: selfish X–Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked ho...
Source: Genome Research - November 18, 2020 Category: Genetics & Stem Cells Authors: Hughes, J. F., Skaletsky, H., Pyntikova, T., Koutseva, N., Raudsepp, T., Brown, L. G., Bellott, D. W., Cho, T.-J., Dugan-Rocha, S., Khan, Z., Kremitzki, C., Fronick, C., Graves-Lindsay, T. A., Fulton, L., Warren, W. C., Wilson, R. K., Owens, E., Womack, J Tags: RESEARCH Source Type: research

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits [METHOD]
Recombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions in Drosophila ...
Source: Genome Research - November 17, 2020 Category: Genetics & Stem Cells Authors: Ruiz-Arenas, C., Caceres, A., Lopez, M., Pelegri-Siso, D., Gonzalez, J., Gonzalez, J. R. Tags: METHOD Source Type: research

Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time [METHOD]
The levels and subcellular localizations of proteins regulate critical aspects of many cellular processes and can become targets of therapeutic intervention. However, high-throughput methods for the discovery of proteins that change localization either by shuttling between compartments, by binding larger complexes, or by localizing to distinct membraneless organelles are not available. Here we describe a scalable strategy to characterize effects on protein localizations and levels in response to different perturbations. We use CRISPR-Cas9-based intron tagging to generate cell pools expressing hundreds of GFP-fusion protein...
Source: Genome Research - November 17, 2020 Category: Genetics & Stem Cells Authors: Reicher, A., Koren, A., Kubicek, S. Tags: METHOD Source Type: research

Ultrafast and scalable variant annotation and prioritization with big functional genomics data [METHOD]
The advances of large-scale genomics studies have enabled compilation of cell type–specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel ...
Source: Genome Research - November 17, 2020 Category: Genetics & Stem Cells Authors: Huang, D., Yi, X., Zhou, Y., Yao, H., Xu, H., Wang, J., Zhang, S., Nong, W., Wang, P., Shi, L., Xuan, C., Li, M., Wang, J., Li, W., Kwan, H. S., Sham, P. C., Wang, K., Li, M. J. Tags: METHOD Source Type: research

Distinctive regulatory architectures of germline-active and somatic genes in C. elegans [RESEARCH]
RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ~90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters ha...
Source: Genome Research - November 16, 2020 Category: Genetics & Stem Cells Authors: Serizay, J., Dong, Y., Jänes, J., Chesney, M., Cerrato, C., Ahringer, J. Tags: RESEARCH Source Type: research

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans [RESEARCH]
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profile...
Source: Genome Research - November 16, 2020 Category: Genetics & Stem Cells Authors: Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritisanac, I., Zhang, Y., Calarco, J. A. Tags: RESEARCH Source Type: research

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids [RESEARCH]
Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied a...
Source: Genome Research - November 13, 2020 Category: Genetics & Stem Cells Authors: Mugal, C. F., Wang, M., Backström, N., Wheatcroft, D., Alund, M., Semon, M., McFarlane, S. E., Dutoit, L., Qvarnström, A., Ellegren, H. Tags: RESEARCH Source Type: research

Cross-species analysis of enhancer logic using deep learning [METHOD]
Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a d...
Source: Genome Research - November 13, 2020 Category: Genetics & Stem Cells Authors: Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., Primot, A., Cadieu, E., van Rooijen, E., Marine, J.-C., Egidy, G., Ghanem, G.-E., Zon, L., Wouters, J., Ae Tags: METHOD Source Type: research

Complex mosaic structural variations in human fetal brains [RESEARCH]
Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200–400 mosaic SNVs per cell in three human fetal brains (15–21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of...
Source: Genome Research - November 13, 2020 Category: Genetics & Stem Cells Authors: Sekar, S., Tomasini, L., Proukakis, C., Bae, T., Manlove, L., Jang, Y., Scuderi, S., Zhou, B., Kalyva, M., Amiri, A., Mariani, J., Sedlazeck, F. J., Urban, A. E., Vaccarino, F. M., Abyzov, A. Tags: RESEARCH Source Type: research

Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains [RESEARCH]
The GGGGCC hexanucleotide expansion in C9orf72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet a clear understanding of how C9 fits into the broader context of ALS/FTD pathology has remained lacking. The repetitive RNA derived from the C9 repeat is known to sequester hnRNPH, a splicing regulator, into insoluble aggregates, resulting in aberrant alternative splicing. Furthermore, hnRNPH insolubility and altered splicing of a robust set of targets have been observed to correlate in C9 and sporadic ALS/FTD patients alike, suggesting that changes along this ax...
Source: Genome Research - November 13, 2020 Category: Genetics & Stem Cells Authors: Wang, Q., Conlon, E. G., Manley, J. L., Rio, D. C. Tags: RESEARCH Source Type: research

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model [METHOD]
Transcriptional enhancers commonly work over long genomic distances to precisely regulate spatiotemporal gene expression patterns. Dissecting the promoters physically contacted by these distal regulatory elements is essential for understanding developmental processes as well as the role of disease-associated risk variants. Modern proximity-ligation assays, like HiChIP and ChIA-PET, facilitate the accurate identification of long-range contacts between enhancers and promoters. However, these assays are technically challenging, expensive, and time-consuming, making it difficult to investigate enhancer topologies, especially i...
Source: Genome Research - November 12, 2020 Category: Genetics & Stem Cells Authors: Tang, L., Hill, M. C., Wang, J., Wang, J., Martin, J. F., Li, M. Tags: METHOD Source Type: research

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans [RESEARCH]
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation, and fertility. Here, we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and ...
Source: Genome Research - November 10, 2020 Category: Genetics & Stem Cells Authors: Strobino, M., Wenda, J. M., Padayachy, L., Steiner, F. A. Tags: RESEARCH Source Type: research

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region [RESEARCH]
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed...
Source: Genome Research - November 10, 2020 Category: Genetics & Stem Cells Authors: Maurano, M. T., Ramaswami, S., Zappile, P., Dimartino, D., Boytard, L., Ribeiro-dos-Santos, A. M., Vulpescu, N. A., Westby, G., Shen, G., Feng, X., Hogan, M. S., Ragonnet-Cronin, M., Geidelberg, L., Marier, C., Meyn, P., Zhang, Y., Cadley, J., Ordonez, R. Tags: RESEARCH Source Type: research

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally-occurring F1 hybrids [RESEARCH]
Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to mis-expression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analysed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally-occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied ...
Source: Genome Research - November 3, 2020 Category: Genetics & Stem Cells Authors: Mugal, C. F., Wang, M., Backstrom, N., Wheatcroft, D., Alund, M., Semon, M., McFarlane, S. E., Dutoit, L., Qvarnstrom, A., Ellegren, H. Tags: RESEARCH Source Type: research

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution [RESOURCES]
This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species. (Source: Genome Research)
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Maggiolini, F. A. M., Sanders, A. D., Shew, C. J., Sulovari, A., Mao, Y., Puig, M., Catacchio, C. R., Dellino, M., Palmisano, D., Mercuri, L., Bitonto, M., Porubsky, D., Caceres, M., Eichler, E. E., Ventura, M., Dennis, M. Y., Korbel, J. O., Antonacci, F. Tags: RESOURCES Source Type: research

Accurate reconstruction of bacterial pan- and core genomes with PEPPAN [METHOD]
Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene an...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Zhou, Z., Charlesworth, J., Achtman, M. Tags: METHOD Source Type: research

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments [METHOD]
Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by joint analysis of large collections of RNA-seq data sets has emerged as one such analysis. Current methods for transcript discovery rely on a ‘2-Step’ approach where the first step encompasses building transcripts from individual data sets, followed by the second step that merges predicted transcripts across data sets. To increase the power of transcript discovery from large collections of RNA-seq data sets, we developed a novel ‘1-Step’ approach named Pooling ...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Liu, P., Soukup, A. A., Bresnick, E. H., Dewey, C. N., Keles, S. Tags: METHOD Source Type: research

Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus [METHOD]
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the s...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Linker, S. B., Randolph-Moore, L., Kottilil, K., Qiu, F., Jaeger, B. N., Barron, J., Gage, F. H. Tags: METHOD Source Type: research

Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain [METHOD]
To gain better insight into the dynamic interaction between cells and their environment, we developed the agonist-induced functional analysis and cell sorting (aiFACS) technique, which allows the simultaneous recording and sorting of cells in real-time according to their immediate and individual response to a stimulus. By modulating the aiFACS selection parameters, testing different developmental times, using various stimuli, and multiplying the analysis of readouts, it is possible to analyze cell populations of any normal or pathological tissue. The association of aiFACS with single-cell transcriptomics allows the constru...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Castagnola, S., Cazareth, J., Lebrigand, K., Jarjat, M., Magnone, V., Delhaye, S., Brau, F., Bardoni, B., Maurin, T. Tags: METHOD Source Type: research

Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease [METHOD]
It is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times that of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals; and some variants are related to each other not by affecting the same gene but by affecting the binding of the same u...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Fu, A. X., Lui, K. N.-C., Tang, C. S.-M., Ng, R. K., Lai, F. P.-L., Lau, S.-T., Li, Z., Garcia-Barcelo, M.-M., Sham, P.-C., Tam, P. K.-H., Ngan, E. S.-W., Yip, K. Y. Tags: METHOD Source Type: research

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation [RESEARCH]
Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light-activated nuclear shuttle (LANS) domain. Light activation resulted in efficient Set2-LANS nuclear localization followed by H3K36me3 deposition in vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Lerner, A. M., Hepperla, A. J., Keele, G. R., Meriesh, H. A., Yumerefendi, H., Restrepo, D., Zimmerman, S., Bear, J. E., Kuhlman, B., Davis, I. J., Strahl, B. D. Tags: RESEARCH Source Type: research

A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize [RESEARCH]
The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic, and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analy...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Blein-Nicolas, M., Negro, S. S., Balliau, T., Welcker, C., Cabrera-Bosquet, L., Nicolas, S. D., Charcosset, A., Zivy, M. Tags: RESEARCH Source Type: research

Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response [RESEARCH]
In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we inve...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Picart-Picolo, A., Grob, S., Picault, N., Franek, M., Llauro, C., Halter, T., Maier, T. R., Jobet, E., Descombin, J., Zhang, P., Paramasivan, V., Baum, T. J., Navarro, L., Dvorackova, M., Mirouze, M., Pontvianne, F. Tags: RESEARCH Source Type: research

Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division [RESEARCH]
Retrotransposons are populated in vertebrate genomes, and when active, are thought to cause genome instability with potential benefit to genome evolution. Retrotransposon-derived RNAs are also known to give rise to small endo-siRNAs to help maintain heterochromatin at their sites of transcription; however, as not all heterochromatic regions are equally active in transcription, it remains unclear how heterochromatin is maintained across the genome. Here, we address these problems by defining the origins of repeat-derived RNAs and their specific chromatin locations in Drosophila S2 cells. We demonstrate that repeat RNAs are ...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Hao, Y., Wang, D., Wu, S., Li, X., Shao, C., Zhang, P., Chen, J.-Y., Lim, D.-H., Fu, X.-D., Chen, R., He, S. Tags: RESEARCH Source Type: research

Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome [RESEARCH]
Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophila midbrain and found that transposon expression patterns are highly stereotyped. Every detected transposon is resident in at least one cellular gene with a matching expression pattern. Bulk RNA sequencing from fly heads of the same strain revealed that coexpression is a physical link in the form of abundant c...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Treiber, C. D., Waddell, S. Tags: RESEARCH Source Type: research

V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s [RESEARCH]
The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that thes...
Source: Genome Research - November 2, 2020 Category: Genetics & Stem Cells Authors: Safonova, Y., Pevzner, P. A. Tags: RESEARCH Source Type: research

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans [RESEARCH]
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. While many documented examples of splicing differences between broad tissue-types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. Using Translating Ribosome Affinity Purification coupled with deep-sequencing (TRAP-seq) in C. elegans, we have obtained high coverage profiles of ribosome-asso...
Source: Genome Research - October 30, 2020 Category: Genetics & Stem Cells Authors: Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritišanac, I., Zhang, Y., Calarco, J. A. Tags: RESEARCH Source Type: research

Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus [METHOD]
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the s...
Source: Genome Research - October 29, 2020 Category: Genetics & Stem Cells Authors: Linker, S. B., Randolph-Moore, L., Kottilil, K., Qiu, F., Jaeger, B. N., Barron, J., Gage, F. H. Tags: METHOD Source Type: research