PR-DUB maintains expression of critical genes through FOXK1/2 and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination [RESEARCH]
Polycomb group proteins are important for maintaining gene expression patterns and cell identity in metazoans. The mammalian Polycomb repressive de-ubiquitinase (PR-DUB) complexes catalyze removal of monoubiquitination on lysine 119 of histone H2A (H2AK119Ub1) through a multi-protein core comprised of BAP1, HCFC1, FOXK1/2, and OGT in combination with either of ASXL1, 2 or 3. Mutations in PR-DUB components are frequent in cancer. However, mechanistic understanding of PR-DUB function in gene regulation is limited. Here, we show that BAP1 is dependent on the ASXL proteins and FOXK1/2 in facilitating gene activation across the...
Source: Genome Research - August 3, 2020 Category: Genetics & Stem Cells Authors: Kolovos, P., Nishimura, K., Sankar, A., Sidoli, S., Cloos, P. A., Helin, K., Christensen, J. 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 as 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 due to the presence of distinct melanoma cell states. We trained and validated a deep learning ...
Source: Genome Research - July 30, 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

Recounting the FANTOM CAGE-Associated Transcriptome [RESOURCES]
In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs. (Source: Genome Research)
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Imada, E. L., Sanchez, D. F., Collado-Torres, L., Wilks, C., Matam, T., Dinalankara, W., Stupnikov, A., Lobo-Pereira, F., Yip, C.-W., Yasuzawa, K., Kondo, N., Itoh, M., Suzuki, H., Kasukawa, T., Hon, C.-C., de Hoon, M. J. L., Shin, J. W., Carninci, P., Ja Tags: RESOURCES Source Type: research

Functional annotation of human long noncoding RNAs via molecular phenotyping [RESOURCES]
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected ge...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonet Tags: RESOURCES Source Type: research

A limited set of transcriptional programs define major cell types [RESOURCES]
We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the cont...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Breschi, A., Munoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martin, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigo, R. Tags: RESOURCES Source Type: research

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence [METHOD]
Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors (TFs) can bind. Thus, identification of TF binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches used for TFBS prediction, such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq), are widely used but have their drawbacks, including high false-positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating c...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Ouyang, N., Boyle, A. P. Tags: METHOD Source Type: research

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility [METHOD]
Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human ...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Xing, Q. R., Farran, C. A. E., Zeng, Y. Y., Yi, Y., Warrier, T., Gautam, P., Collins, J. J., Xu, J., Dröge, P., Koh, C.-G., Li, H., Zhang, L.-F., Loh, Y.-H. Tags: METHOD Source Type: research

System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA-protein complexes [METHOD]
Large RNA-binding complexes play a central role in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA–protein crosslinking data provide information on the organization of RNA–protein complexes. To evaluate the relative enrichment of cellular RBPs on poly(A)+ RNA, we combine poly(A)+ RNA interactome capture with a whole-cell extract normalization procedure. Th...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Kilchert, C., Kecman, T., Priest, E., Hester, S., Aydin, E., Kus, K., Rossbach, O., Castello, A., Mohammed, S., Vasiljeva, L. Tags: METHOD Source Type: research

Independent evolution of transcript abundance and gene regulatory dynamics [RESEARCH]
Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Krieger, G., Lupo, O., Levy, A. A., Barkai, N. Tags: RESEARCH Source Type: research

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing [RESEARCH]
Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ~10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals....
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Arpat, A. B., Liechti, A., De Matos, M., Dreos, R., Janich, P., Gatfield, D. Tags: RESEARCH Source Type: research

Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context [RESEARCH]
Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes continues the mRNA probing. We explored the relationship between the context of AUG codons annotated as starts of protein-coding sequences and the next AUG codon occurrence. We found that AUG codons downstream from weak starts ...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Benitez-Cantos, M. S., Yordanova, M. M., O'Connor, P. B. F., Zhdanov, A. V., Kovalchuk, S. I., Papkovsky, D. B., Andreev, D. E., Baranov, P. V. Tags: RESEARCH Source Type: research

Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences [RESEARCH]
RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-throughput RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequences, whereas ~30% preferred struc...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Jolma, A., Zhang, J., Mondragon, E., Morgunova, E., Kivioja, T., Laverty, K. U., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, T. R., Maher, L. J., Taipale, J. Tags: RESEARCH Source Type: research

Comparative transcriptomics of primary cells in vertebrates [RESEARCH]
Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type man...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., Shen Tags: RESEARCH Source Type: research

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations [RESEARCH]
In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an ...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Ramaker, R. C., Hardigan, A. A., Goh, S.-T., Partridge, E. C., Wold, B., Cooper, S. J., Myers, R. M. Tags: RESEARCH Source Type: research

ADAR-deficiency perturbs the global splicing landscape in mouse tissues [RESEARCH]
Adenosine to inosine RNA-editing and pre-mRNA splicing largely occur co-transcriptionally and influence each other. Here we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA-editing on splicing across different tissues. We find that ADAR has a 100x higher impact on splicing than ADARB1, although both enzymes target a similar number of substrates with a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Kapoor, U., Licht, K., Amman, F., Jakobi, T., Martin, D., Dieterich, C., Jantsch, M. Tags: RESEARCH Source Type: research

The multi-comparative 2-n-way genome suite [METHOD]
To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite is comprised of two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multip...
Source: Genome Research - July 29, 2020 Category: Genetics & Stem Cells Authors: Churakov, G., Zhang, F., Grundmann, N., Makalowski, W., Noll, A., Doronina, L., Schmitz, J. Tags: METHOD Source Type: research

Functional annotation of human long noncoding RNAs via molecular phenotyping [RESOURCES]
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected ge...
Source: Genome Research - July 27, 2020 Category: Genetics & Stem Cells Authors: Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonet Tags: RESOURCES Source Type: research

Recounting the FANTOM CAGE-Associated Transcriptome [RESOURCES]
In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs. (Source: Genome Research)
Source: Genome Research - July 27, 2020 Category: Genetics & Stem Cells Authors: Imada, E. L., Sanchez, D. F., Collado-Torres, L., Wilks, C., Matam, T., Dinalankara, W., Stupnikov, A., Lobo-Pereira, F., Yip, C.-W., Yasuzawa, K., Kondo, N., Itoh, M., Suzuki, H., Kasukawa, T., Hon, C.-C., de Hoon, M. J. L., Shin, J. W., Carninci, P., Ja Tags: RESOURCES Source Type: research

Comparative transcriptomics of primary cells in vertebrates [RESEARCH]
Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type man...
Source: Genome Research - July 27, 2020 Category: Genetics & Stem Cells Authors: Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., Shen Tags: RESEARCH Source Type: research

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing [RESEARCH]
Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ~10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals....
Source: Genome Research - July 23, 2020 Category: Genetics & Stem Cells Authors: Arpat, A. B., Liechti, A., De Matos, M., Dreos, R., Janich, P., Gatfield, D. Tags: RESEARCH Source Type: research

Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences [RESEARCH]
RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-throughput RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequences, whereas ~30% preferred struc...
Source: Genome Research - July 23, 2020 Category: Genetics & Stem Cells Authors: Jolma, A., Zhang, J., Mondragon, E., Morgunova, E., Kivioja, T., Laverty, K. U., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, T. R., Maher, L. J., Taipale, J. Tags: RESEARCH Source Type: research

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility [METHOD]
Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human ...
Source: Genome Research - July 22, 2020 Category: Genetics & Stem Cells Authors: Xing, Q. R., El Farran, C. A., Zeng, Y. Y., Yi, Y., Warrier, T., Gautam, P., Collins, J. J., Xu, J., Dröge, P., Koh, C.-G., Li, H., Zhang, L.-F., Loh, Y.-H. Tags: METHOD Source Type: research

Independent evolution of transcript abundance and gene regulatory dynamics [RESEARCH]
Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels...
Source: Genome Research - July 22, 2020 Category: Genetics & Stem Cells Authors: Krieger, G., Lupo, O., Levy, A. A., Barkai, N. Tags: RESEARCH Source Type: research

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence [METHOD]
Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors (TFs) can bind. Thus, identification of TF binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches used for TFBS prediction, such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq), are widely used but have their drawbacks, including high false-positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating c...
Source: Genome Research - July 17, 2020 Category: Genetics & Stem Cells Authors: Ouyang, N., Boyle, A. P. Tags: METHOD Source Type: research

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations [RESEARCH]
In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an ...
Source: Genome Research - July 17, 2020 Category: Genetics & Stem Cells Authors: Ramaker, R. C., Hardigan, A. A., Goh, S.-T., Partridge, E. C., Wold, B., Cooper, S. J., Myers, R. M. Tags: RESEARCH Source Type: research

Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context [RESEARCH]
Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes continues the mRNA probing. We explored the relationship between the context of AUG codons annotated as starts of protein-coding sequences and the next AUG codon occurrence. We found that AUG codons downstream from weak starts ...
Source: Genome Research - July 15, 2020 Category: Genetics & Stem Cells Authors: Benitez-Cantos, M. S., Yordanova, M. M., O'Connor, P. B. F., Zhdanov, A. V., Kovalchuk, S. I., Papkovsky, D. B., Andreev, D. E., Baranov, P. V. Tags: RESEARCH Source Type: research

Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes [CORRIGENDUM]
(Source: Genome Research)
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Altenhoff, A. M., Levy, J., Zarowiecki, M., Tomiczek, B., Vesztrocy, A. W., Dalquen, D. A., Müller, S., Telford, M. J., Glover, N. M., Dylus, D., Dessimoz, C. Tags: CORRIGENDUM Source Type: research

Corrigendum: Human auditory ossicles as an alternative optimal source of ancient DNA [CORRIGENDUM]
(Source: Genome Research)
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Sirak, K., Fernandes, D., Cheronet, O., Harney, E., Mah, M., Mallick, S., Rohland, N., Adamski, N., Broomandkhoshbacht, N., Callan, K., Candilio, F., Lawson, A. M., Mandl, K., Oppenheimer, J., Stewardson, K., Zalzala, F., Anders, A., Bartik, J., Coppa, A. Tags: CORRIGENDUM Source Type: research

Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis [RESOURCES]
Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including abou...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Li, Y., Liu, Y., Yang, H., Zhang, T., Naruse, K., Tu, Q. Tags: RESOURCES Source Type: research

Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq [METHOD]
We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a stra...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Policastro, R. A., Raborn, R. T., Brendel, V. P., Zentner, G. E. Tags: METHOD Source Type: research

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information [METHOD]
Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded be...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Chen, Z., Pham, L., Wu, T.-C., Mo, G., Xia, Y., Chang, P. L., Porter, D., Phan, T., Che, H., Tran, H., Bansal, V., Shaffer, J., Belda-Ferre, P., Humphrey, G., Knight, R., Pevzner, P., Pham, S., Wang, Y., Lei, M. Tags: METHOD Source Type: research

A long-read RNA-seq approach to identify novel transcripts of very large genes [METHOD]
RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts. Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential expression studies. We used long-read isoform sequencing combined with a novel analysis approach to compare alternative splicing of large, repetitive structural genes in muscles. Analysis of muscle structural genes that produc...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Uapinyoying, P., Goecks, J., Knoblach, S. M., Panchapakesan, K., Bonnemann, C. G., Partridge, T. A., Jaiswal, J. K., Hoffman, E. P. Tags: METHOD Source Type: research

The evolution of sex-biased gene expression in the Drosophila brain [RESEARCH]
Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using population-scale RNA sequencing data, we show that sex-biased genes in the Drosophila brain are highly enriched on the X Chromosome and that most are biased in a species-specific manner. We show that X-linked male-biased genes, and to a lesser extent female-biased genes, are enriched for signatures of directional sele...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Khodursky, S., Svetec, N., Durkin, S. M., Zhao, L. Tags: RESEARCH Source Type: research

Quantitative analysis of Y-Chromosome gene expression across 36 human tissues [RESEARCH]
Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX. Evolutio...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Godfrey, A. K., Naqvi, S., Chmatal, L., Chick, J. M., Mitchell, R. N., Gygi, S. P., Skaletsky, H., Page, D. C. Tags: RESEARCH Source Type: research

Untangling the effects of cellular composition on coexpression analysis [RESEARCH]
Coexpression analysis is widely used for inferring regulatory networks, predicting gene function, and interpretation of transcriptome profiling studies, based on methods such as clustering. The majority of such studies use data collected from bulk tissue, where the effects of cellular composition present a potential confound. However, the impact of composition on coexpression analysis has not been studied in detail. Here, we examine this issue for the case of human RNA analysis. Focusing on brain tissue, we found that, for most genes, differences in expression levels across cell types account for a large fraction of the va...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Farahbod, M., Pavlidis, P. Tags: RESEARCH Source Type: research

Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders [RESEARCH]
A large number of genes have been implicated in neurodevelopmental disorders (NDDs), but their contributions to NDD pathology are difficult to decipher without understanding their diverse roles in different brain cell types. Here, we integrated NDD genetics with single-cell RNA sequencing data to assess coexpression enrichment patterns of various NDD gene sets. We identified midfetal cortical neural progenitor cell development—more specifically, the ventricular radial glia-to-intermediate progenitor cell transition at gestational week 10—as a key point of convergence in autism spectrum disorder (ASD) and epilep...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Pang, K., Wang, L., Wang, W., Zhou, J., Cheng, C., Han, K., Zoghbi, H. Y., Liu, Z. Tags: RESEARCH Source Type: research

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability [RESEARCH]
Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents and offspring. Studies in humans have revealed that the paternal age at conception explains most of the variation in mutation rate: Each additional year of paternal age in humans leads to approximately 1.5 additional inheri...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Wang, R. J., Thomas, G. W. C., Raveendran, M., Harris, R. A., Doddapaneni, H., Muzny, D. M., Capitanio, J. P., Radivojac, P., Rogers, J., Hahn, M. W. Tags: RESEARCH Source Type: research

Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism [RESEARCH]
Less than half of human zygotes survive to birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors generate chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and impacts of mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of few embryonic cells. Single-cell genomic data provide an opportunity to quantify mosaicism on an embryo-wide scale. To this end, we extended an approach to infer aneuploidies based on dosage-associated changes in gene expression by ...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Starostik, M. R., Sosina, O. A., McCoy, R. C. Tags: RESEARCH Source Type: research

Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types [RESEARCH]
Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who presented with oral bacterial infections showed novel mutational signatures. One of these novel signatures, SBS_AnT, is characterized by a preponderance of thymine mutations, strong transcriptional strand bias, and enrichment f...
Source: Genome Research - July 14, 2020 Category: Genetics & Stem Cells Authors: Boot, A., Ng, A. W. T., Chong, F. T., Ho, S.-C., Yu, W., Tan, D. S. W., Iyer, N. G., Rozen, S. G. Tags: RESEARCH Source Type: research

Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism [RESEARCH]
Less than half of human zygotes survive to birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors generate chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and impacts of mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of few embryonic cells. Single-cell genomic data provide an opportunity to quantify mosaicism on an embryo-wide scale. To this end, we extended an approach to infer aneuploidies based on dosage-associated changes in gene expression by ...
Source: Genome Research - July 8, 2020 Category: Genetics & Stem Cells Authors: Starostik, M. R., Sosina, O. A., McCoy, R. C. Tags: RESEARCH Source Type: research

Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders [RESEARCH]
A large number of genes have been implicated in neurodevelopmental disorders (NDDs), but their contributions to NDD pathology are difficult to decipher without understanding their diverse roles in different brain cell types. Here, we integrated NDD genetics with single-cell RNA sequencing data to assess coexpression enrichment patterns of various NDD gene sets. We identified midfetal cortical neural progenitor cell development—more specifically, the ventricular radial glia-to-intermediate progenitor cell transition at gestational week 10—as a key point of convergence in autism spectrum disorder (ASD) and epilep...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Pang, K., Wang, L., Wang, W., Zhou, J., Cheng, C., Han, K., Zoghbi, H. Y., Liu, Z. Tags: RESEARCH Source Type: research

Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types [RESEARCH]
Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who presented with oral bacterial infections showed novel mutational signatures. One of these novel signatures, SBS_AnT, is characterized by a preponderance of thymine mutations, strong transcriptional strand bias, and enrichment f...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Boot, A., Ng, A. W. T., Chong, F. T., Ho, S.-C., Yu, W., Tan, D. S. W., Iyer, N. G., Rozen, S. G. Tags: RESEARCH Source Type: research

Untangling the effects of cellular composition on coexpression analysis [RESEARCH]
Coexpression analysis is widely used for inferring regulatory networks, predicting gene function, and interpretation of transcriptome profiling studies, based on methods such as clustering. The majority of such studies use data collected from bulk tissue, where the effects of cellular composition present a potential confound. However, the impact of composition on coexpression analysis has not been studied in detail. Here, we examine this issue for the case of human RNA analysis. Focusing on brain tissue, we found that, for most genes, differences in expression levels across cell types account for a large fraction of the va...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Farahbod, M., Pavlidis, P. Tags: RESEARCH Source Type: research

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence [METHOD]
Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors can bind. Thus, identification of transcription factor binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches used for TFBS prediction, such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq), are widely used, but have their drawbacks including high false positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by inv...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Ouyang, N., Boyle, A. P. Tags: METHOD Source Type: research

Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis [RESOURCES]
Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including abou...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Li, Y., Liu, Y., Yang, H., Zhang, T., Naruse, K., Tu, Q. Tags: RESOURCES Source Type: research

The evolution of sex-biased gene expression in the Drosophila brain [RESEARCH]
Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using population-scale RNA sequencing data, we show that sex-biased genes in the Drosophila brain are highly enriched on the X Chromosome and that most are biased in a species-specific manner. We show that X-linked male-biased genes, and to a lesser extent female-biased genes, are enriched for signatures of directional sele...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Khodursky, S., Svetec, N., Durkin, S. M., Zhao, L. Tags: RESEARCH Source Type: research

A long-read RNA-seq approach to identify novel transcripts of very large genes [METHOD]
RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts. Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential expression studies. We used long-read isoform sequencing combined with a novel analysis approach to compare alternative splicing of large, repetitive structural genes in muscles. Analysis of muscle structural genes that produc...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Uapinyoying, P., Goecks, J., Knoblach, S. M., Panchapakesan, K., Bonnemann, C. G., Partridge, T. A., Jaiswal, J. K., Hoffman, E. P. Tags: METHOD Source Type: research

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information [METHOD]
Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded be...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Chen, Z., Pham, L., Wu, T.-C., Mo, G., Xia, Y., Chang, P. L., Porter, D., Phan, T., Che, H., Tran, H., Bansal, V., Shaffer, J., Belda-Ferre, P., Humphrey, G., Knight, R., Pevzner, P., Pham, S., Wang, Y., Lei, M. Tags: METHOD Source Type: research

Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq [METHOD]
We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a stra...
Source: Genome Research - July 6, 2020 Category: Genetics & Stem Cells Authors: Policastro, R. A., Raborn, R. T., Brendel, V. P., Zentner, G. E. Tags: METHOD Source Type: research

LEMMI: A continuous benchmarking platform for metagenomics classifiers [RESOURCES]
Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the method's release and its adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark design...
Source: Genome Research - July 2, 2020 Category: Genetics & Stem Cells Authors: Seppey, M., Manni, M., Zdobnov, E. M. Tags: RESOURCES Source Type: research