PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data [METHOD]
Available computational methods for tumor phylogeny inference via single-cell sequencing (SCS) data typically aim to identify the most likely perfect phylogeny tree satisfying the infinite sites assumption (ISA). However, the limitations of SCS technologies including frequent allele dropout and variable sequence coverage may prohibit a perfect phylogeny. In addition, ISA violations are commonly observed in tumor phylogenies due to the loss of heterozygosity, deletions, and convergent evolution. In order to address such limitations, we introduce the optimal subperfect phylogeny problem which asks to integrate SCS data with ...
Source: Genome Research - October 18, 2019 Category: Genetics & Stem Cells Authors: Malikic, S., Mehrabadi, F. R., Ciccolella, S., Rahman, M. K., Ricketts, C., Haghshenas, E., Seidman, D., Hach, F., Hajirasouliha, I., Sahinalp, S. C. Tags: METHOD Source Type: research

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data [METHOD]
Accumulation and selection of somatic mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity. Recently developed single-cell DNA sequencing (SCS) technologies promise to resolve ITH to a single-cell level. However, technical errors in SCS data sets, including false-positives (FP) and false-negatives (FN) due to allelic dropout, and cell doublets, significantly complicate these task...
Source: Genome Research - October 18, 2019 Category: Genetics & Stem Cells Authors: Zafar, H., Navin, N., Chen, K., Nakhleh, L. Tags: METHOD Source Type: research

A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations [RESEARCH]
Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from...
Source: Genome Research - October 17, 2019 Category: Genetics & Stem Cells Authors: Mai, T.-L., Chuang, T.-J. Tags: RESEARCH Source Type: research

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression [RESEARCH]
The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using global run-on sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 min. Many repressed regulatory regions reside within "hyper-ChIPable" genomic regions that ar...
Source: Genome Research - October 17, 2019 Category: Genetics & Stem Cells Authors: Sasse, S. K., Gruca, M., Allen, M. A., Kadiyala, V., Song, T., Gally, F., Gupta, A., Pufall, M. A., Dowell, R. D., Gerber, A. N. Tags: RESEARCH Source Type: research

Global analyses of the dynamics of mammalian microRNA metabolism [RESEARCH]
Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with
Source: Genome Research - October 11, 2019 Category: Genetics & Stem Cells Authors: Kingston, E. R., Bartel, D. P. Tags: RESEARCH Source Type: research

Exploration of fine-scale recombination rate variation in the domestic horse [RESOURCES]
Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using approximately 1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for ~9% of the physical map length. Regions with elevated recombination rates in the entire cohort were e...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Beeson, S. K., Mickelson, J. R., McCue, M. E. Tags: RESOURCES Source Type: research

Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks [METHOD]
Cellular identity relies on cell-type–specific gene expression controlled at the transcriptional level by cis-regulatory elements (CREs). CREs are unevenly distributed across the genome, giving rise to individual CREs and clusters of CREs (COREs). Technical and biological features hinder CORE identification. We addressed these issues by developing an unsupervised machine learning approach termed clustering of genomic regions analysis method (CREAM). CREAM automates CORE detection from chromatin accessibility profiles that are enriched in CREs strongly bound by master transcription regulators, proximal to highly expre...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Madani Tonekaboni, S. A., Mazrooei, P., Kofia, V., Haibe-Kains, B., Lupien, M. Tags: METHOD Source Type: research

A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission [METHOD]
One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations, and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partly because not all genes controlling chromosome transmission have yet been identified. To address this question, we developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen an siRNA library of protein kinases, we ...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Liskovykh, M., Goncharov, N. V., Petrov, N., Aksenova, V., Pegoraro, G., Ozbun, L. L., Reinhold, W. C., Varma, S., Dasso, M., Kumeiko, V., Masumoto, H., Earnshaw, W. C., Larionov, V., Kouprina, N. Tags: METHOD Source Type: research

RNA-seq as a tool for evaluating human embryo competence [METHOD]
The majority of embryos created through in vitro fertilization (IVF) do not implant. It seems plausible that rates of implantation would improve if we had a better understanding of molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer uses an ad hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing (RNA-seq) of embryos could yield high-dimensional data, which may provide additional insight and illuminate the discre...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Groff, A. F., Resetkova, N., DiDomenico, F., Sakkas, D., Penzias, A., Rinn, J. L., Eggan, K. Tags: METHOD Source Type: research

Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia [RESEARCH]
Can ecological changes impact somatic genome development? Efforts to resolve this question could reveal a direct link between environmental changes and somatic variability, potentially illuminating our understanding of how variation can surface from a single genotype under stress. Here, we tackle this question by leveraging the biological properties of ciliates. When Paramecium tetraurelia reproduces sexually, its polyploid somatic genome regenerates from the germline genome through a developmental process that involves the removal of thousands of ORF-interrupting sequences known as internal eliminated sequences (IESs). We...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Vitali, V., Hagen, R., Catania, F. Tags: RESEARCH Source Type: research

Fitness benefits of loss of heterozygosity in Saccharomyces hybrids [RESEARCH]
In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness eff...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Lancaster, S. M., Payen, C., Smukowski Heil, C., Dunham, M. J. Tags: RESEARCH Source Type: research

Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system [RESEARCH]
We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore, despite little methylation differentiation between sexes, extremely localized DNA methylation differences between male and female chicken Z Chromosomes have evolved and affect expression of nearby regions. Our findings offer new insights into epigenetic regulation of gene expression between sexes in female heterogametic systems. (Source: Genome Research)
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Sun, D., Maney, D. L., Layman, T. S., Chatterjee, P., Yi, S. V. Tags: RESEARCH Source Type: research

Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming [RESEARCH]
Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. Here, we use allele-specific transcriptomics to study XCR during mouse iPSC reprogramming in o...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Janiszewski, A., Talon, I., Chappell, J., Collombet, S., Song, J., De Geest, N., To, S. K., Bervoets, G., Marin-Bejar, O., Provenzano, C., Vanheer, L., Marine, J.-C., Rambow, F., Pasque, V. Tags: RESEARCH Source Type: research

Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf [RESEARCH]
The extinct marsupial Tasmanian tiger, or thylacine, and the eutherian gray wolf are among the most widely recognized examples of convergent evolution in mammals. Despite being distantly related, these large predators independently evolved extremely similar craniofacial morphologies, and evidence suggests that they filled similar ecological niches. Previous analyses revealed little evidence of adaptive convergence between their protein-coding genes. Thus, the genetic basis of their convergence is still unclear. Here, we identified candidate craniofacial cis-regulatory elements across vertebrates and compared their evolutio...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Feigin, C. Y., Newton, A. H., Pask, A. J. Tags: RESEARCH Source Type: research

Sequence determinants of polyadenylation-mediated regulation [RESEARCH]
The cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning mutagenesis data set, we g...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Vainberg Slutskin, I., Weinberger, A., Segal, E. Tags: RESEARCH Source Type: research

The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A [RESEARCH]
How individual genes are regulated from a mitochondrial polycistronic transcript to have variable expression remains an enigma. Here, through bisulfite sequencing and strand-specific mapping, we show mitochondrial genomes in humans and other animals are strongly biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene–gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic local or global changes during development and aging. Kn...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Dou, X., Boyd-Kirkup, J. D., McDermott, J., Zhang, X., Li, F., Rong, B., Zhang, R., Miao, B., Chen, P., Cheng, H., Xue, J., Bennett, D., Wong, J., Lan, F., Han, J.-D. J. Tags: RESEARCH Source Type: research

Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms [RESEARCH]
In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most tran...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Court, F., Le Boiteux, E., Fogli, A., Müller-Barthelemy, M., Vaurs-Barriere, C., Chautard, E., Pereira, B., Biau, J., Kemeny, J.-L., Khalil, T., Karayan-Tapon, L., Verrelle, P., Arnaud, P. Tags: RESEARCH Source Type: research

RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing [RESEARCH]
Alternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established that even core protein components of the spliceosome, which are required for splicing to proceed, can nonetheless contribute to splicing regulation by modulating splice site choice. We here show that the RNA components of the spliceosome likewise influence alternative splicing decisions. Although these small nuclear RNAs (snRNAs), termed U1, U2, U4, ...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Dvinge, H., Guenthoer, J., Porter, P. L., Bradley, R. K. Tags: RESEARCH Source Type: research

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly [RESEARCH]
Dysregulated endogenous retroelements (EREs) are increasingly implicated in the initiation, progression, and immune surveillance of human cancer. However, incomplete knowledge of ERE activity limits mechanistic studies. By using pan-cancer de novo transcript assembly, we uncover the extent and complexity of ERE transcription. The current assembly doubled the number of previously annotated transcripts overlapping with long-terminal repeat (LTR) elements, several thousand of which were expressed specifically in one or a few related cancer types. Exemplified in melanoma, LTR-overlapping transcripts were highly predictable, di...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Attig, J., Young, G. R., Hosie, L., Perkins, D., Encheva-Yokoya, V., Stoye, J. P., Snijders, A. P., Ternette, N., Kassiotis, G. Tags: RESEARCH Source Type: research

Pedigree-based estimation of human mobile element retrotransposition rates [RESEARCH]
Germline mutation rates in humans have been estimated for a variety of mutation types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We used three tools for calling mobile element insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the r...
Source: Genome Research - October 1, 2019 Category: Genetics & Stem Cells Authors: Feusier, J., Watkins, W. S., Thomas, J., Farrell, A., Witherspoon, D. J., Baird, L., Ha, H., Xing, J., Jorde, L. B. Tags: RESEARCH Source Type: research

Exploration of fine-scale recombination rate variation in the domestic horse [RESOURCES]
Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using approximately 1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for ~9% of the physical map length. Regions with elevated recombination rates in the entire cohort were e...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Beeson, S. K., Mickelson, J. R., McCue, M. E. Tags: RESOURCES Source Type: research

Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia [RESEARCH]
Can ecological changes impact somatic genome development? Efforts to resolve this question could reveal a direct link between environmental changes and somatic variability, potentially illuminating our understanding of how variation can surface from a single genotype under stress. Here, we tackle this question by leveraging the biological properties of ciliates. When Paramecium tetraurelia reproduces sexually, its polyploid somatic genome regenerates from the germline genome through a developmental process that involves the removal of thousands of ORF-interrupting sequences known as internal eliminated sequences (IESs). We...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Vitali, V., Hagen, R., Catania, F. Tags: RESEARCH Source Type: research

Fitness benefits of loss of heterozygosity in Saccharomyces hybrids [RESEARCH]
In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness eff...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Lancaster, S. M., Payen, C., Smukowski Heil, C., Dunham, M. J. Tags: RESEARCH Source Type: research

Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system [RESEARCH]
We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore, despite little methylation differentiation between sexes, extremely localized DNA methylation differences between male and female chicken Z Chromosomes have evolved and affect expression of nearby regions. Our findings offer new insights into epigenetic regulation of gene expression between sexes in female heterogametic systems. (Source: Genome Research)
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Sun, D., Maney, D. L., Layman, T. S., Chatterjee, P., Yi, S. V. Tags: RESEARCH Source Type: research

Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution [METHOD]
Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation and motility as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method (ddMDM; droplet digital mitochondrial DNA measur...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: O'Hara, R., Tedone, E., Ludlow, A. T., Huang, E., Arosio, B., Mari, D., Shay, J. W. Tags: METHOD Source Type: research

RNA-seq as a tool for evaluating human embryo competence [METHOD]
The majority of embryos created through in vitro fertilization (IVF) do not implant. It seems plausible that rates of implantation would improve if we had a better understanding of molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer uses an ad hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing (RNA-seq) of embryos could yield high-dimensional data, which may provide additional insight and illuminate the discre...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Groff, A. F., Resetkova, N., DiDomenico, F., Sakkas, D., Penzias, A., Rinn, J. L., Eggan, K. Tags: METHOD Source Type: research

A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission [METHOD]
One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations, and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partly because not all genes controlling chromosome transmission have yet been identified. To address this question, we developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen an siRNA library of protein kinases, we ...
Source: Genome Research - September 23, 2019 Category: Genetics & Stem Cells Authors: Liskovykh, M., Goncharov, N. V., Petrov, N., Aksenova, V., Pegoraro, G., Ozbun, L. L., Reinhold, W. C., Varma, S., Dasso, M., Kumeiko, V., Masumoto, H., Earnshaw, W. C., Larionov, V., Kouprina, N. Tags: METHOD Source Type: research

The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A [RESEARCH]
How individual genes are regulated from a mitochondrial polycistronic transcript to have variable expression remains an enigma. Here, through bisulfite sequencing and strand-specific mapping, we show mitochondrial genomes in humans and other animals are strongly biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene–gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic local or global changes during development and aging. Kn...
Source: Genome Research - September 19, 2019 Category: Genetics & Stem Cells Authors: Dou, X., Boyd-Kirkup, J. D., McDermott, J., Zhang, X., Li, F., Rong, B., Zhang, R., Miao, B., Chen, P., Cheng, H., Xue, J., Bennett, D., Wong, J., Lan, F., Han, J.-D. J. Tags: RESEARCH Source Type: research

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci [RESOURCES]
The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely-used tool to identify evolutionary signatures of protein-coding regions using multi-species genome alignments. Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. We develop a workflow that uses machine-learning to predict novel conserved protein-coding regions and efficiently guide their manual curation. We analyse over 1000 high-scoring human PhyloCSF regions, and c...
Source: Genome Research - September 19, 2019 Category: Genetics & Stem Cells Authors: Mudge, J. M., Jungreis, I., Hunt, T., Gonzalez, J. M., Wright, J. C., Kay, M., Davidson, C., Fitzgerald, S., Seal, R., Tweedie, S., He, L., Waterhouse, R. M., Li, Y., Bruford, E., Choudhary, J. S., Frankish, A., Kellis, M. Tags: RESOURCES Source Type: research

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly [RESEARCH]
Dysregulated endogenous retroelements (EREs) are increasingly implicated in the initiation, progression, and immune surveillance of human cancer. However, incomplete knowledge of ERE activity limits mechanistic studies. By using pan-cancer de novo transcript assembly, we uncover the extent and complexity of ERE transcription. The current assembly doubled the number of previously annotated transcripts overlapping with long-terminal repeat (LTR) elements, several thousand of which were expressed specifically in one or a few related cancer types. Exemplified in melanoma, LTR-overlapping transcripts were highly predictable, di...
Source: Genome Research - September 19, 2019 Category: Genetics & Stem Cells Authors: Attig, J., Young, G. R., Hosie, L., Perkins, D., Encheva-Yokoya, V., Stoye, J. P., Snijders, A. P., Ternette, N., Kassiotis, G. Tags: RESEARCH Source Type: research

Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf [RESEARCH]
The extinct marsupial Tasmanian tiger, or thylacine, and the eutherian gray wolf are among the most widely recognized examples of convergent evolution in mammals. Despite being distantly related, these large predators independently evolved extremely similar craniofacial morphologies, and evidence suggests that they filled similar ecological niches. Previous analyses revealed little evidence of adaptive convergence between their protein-coding genes. Thus, the genetic basis of their convergence is still unclear. Here, we identified candidate craniofacial cis-regulatory elements across vertebrates and compared their evolutio...
Source: Genome Research - September 18, 2019 Category: Genetics & Stem Cells Authors: Feigin, C. Y., Newton, A. H., Pask, A. J. Tags: RESEARCH Source Type: research

Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks [METHOD]
Cellular identity relies on cell-type–specific gene expression controlled at the transcriptional level by cis-regulatory elements (CREs). CREs are unevenly distributed across the genome, giving rise to individual CREs and clusters of CREs (COREs). Technical and biological features hinder CORE identification. We addressed these issues by developing an unsupervised machine learning approach termed clustering of genomic regions analysis method (CREAM). CREAM automates CORE detection from chromatin accessibility profiles that are enriched in CREs strongly bound by master transcription regulators, proximal to highly expre...
Source: Genome Research - September 18, 2019 Category: Genetics & Stem Cells Authors: Madani Tonekaboni, S. A., Mazrooei, P., Kofia, V., Haibe-Kains, B., Lupien, M. Tags: METHOD Source Type: research

Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms [RESEARCH]
In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most tran...
Source: Genome Research - September 18, 2019 Category: Genetics & Stem Cells Authors: Court, F., Le Boiteux, E., Fogli, A., Müller-Barthelemy, M., Vaurs-Barriere, C., Chautard, E., Pereira, B., Biau, J., Kemeny, J.-L., Khalil, T., Karayan-Tapon, L., Verrelle, P., Arnaud, P. Tags: RESEARCH Source Type: research

RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing [RESEARCH]
Alternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established that even core protein components of the spliceosome, which are required for splicing to proceed, can nonetheless contribute to splicing regulation by modulating splice site choice. We here show that the RNA components of the spliceosome likewise influence alternative splicing decisions. Although these small nuclear RNAs (snRNAs), termed U1, U2, U4, ...
Source: Genome Research - September 17, 2019 Category: Genetics & Stem Cells Authors: Dvinge, H., Guenthoer, J., Porter, P. L., Bradley, R. K. Tags: RESEARCH Source Type: research

Sequence determinants of polyadenylation-mediated regulation [RESEARCH]
The cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning mutagenesis data set, we g...
Source: Genome Research - September 17, 2019 Category: Genetics & Stem Cells Authors: Slutskin, I. V., Weinberger, A., Segal, E. Tags: RESEARCH Source Type: research

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ [METHOD]
RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq pro...
Source: Genome Research - September 13, 2019 Category: Genetics & Stem Cells Authors: Foley, J. W., Zhu, C., Jolivet, P., Zhu, S. X., Lu, P., Meaney, M. J., West, R. B. Tags: METHOD Source Type: research

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression [RESEARCH]
The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using Global Run-on Sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 minutes. Many repressed regulatory regions reside within 'hyper-ChIPable' genomic regions that are subj...
Source: Genome Research - September 13, 2019 Category: Genetics & Stem Cells Authors: Sasse, S. K., Gruca, M., Allen, M. A., Kadiyala, V., Song, T., Gally, F., Gupta, A., Pufall, M. A., Dowell, R. D., Gerber, A. N. Tags: RESEARCH Source Type: research

Global analyses of the dynamics of mammalian microRNA metabolism [RESEARCH]
Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell per min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with
Source: Genome Research - September 13, 2019 Category: Genetics & Stem Cells Authors: Kingston, E., Bartel, D. Tags: RESEARCH Source Type: research

A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations [RESEARCH]
Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/post-transcriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from...
Source: Genome Research - September 12, 2019 Category: Genetics & Stem Cells Authors: Mai, T.-L., Chuang, T.-J. Tags: RESEARCH Source Type: research

Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming [RESEARCH]
Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. Here, we use allele-specific transcriptomics to study XCR during mouse iPSC reprogramming in o...
Source: Genome Research - September 12, 2019 Category: Genetics & Stem Cells Authors: Janiszewski, A., Talon, I., Chappell, J., Collombet, S., Song, J., De Geest, N., To, S. K., Bervoets, G., Marin-Bejar, O., Provenzano, C., Vanheer, L., Marine, J.-C., Rambow, F., Pasque, V. Tags: RESEARCH Source Type: research

A novel assay to screen siRNA libraries identifies protein kinases as required for chromosome transmission [METHOD]
One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partially because not all genes controlling chromosome transmission have yet been identified. To address this question, we have developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen a siRNA library of protein kinase...
Source: Genome Research - September 12, 2019 Category: Genetics & Stem Cells Authors: Liskovykh, M., Goncharov, N. V., Petrov, N., Aksenova, V., Pegoraro, G., Ozbun, L. L., Reinhold, W. C., Varma, S., Dasso, M., Kumeiko, V., Masumoto, H., Earnshaw, W. C., Larionov, V., Kouprina, N. Tags: METHOD Source Type: research

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation [RESEARCH]
DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or in...
Source: Genome Research - September 11, 2019 Category: Genetics & Stem Cells Authors: Chereji, R. V., Eriksson, P. R., Ocampo, J., Prajapati, H. K., Clark, D. J. Tags: RESEARCH Source Type: research

Corrigendum: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers [CORRIGENDA]
(Source: Genome Research)
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Meier, B., Volkova, N. V., Hong, Y., Schofield, P., Campbell, P. J., Gerstung, M., Gartner, A. Tags: CORRIGENDA Source Type: research

Corrigendum: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster [CORRIGENDA]
(Source: Genome Research)
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Gao, G., Vibranovski, M. D., Zhang, L., Li, Z., Liu, M., Zhang, Y. E., Li, X., Zhang, W., Fan, Q., VanKuren, N. W., Long, M., Wei, L. Tags: CORRIGENDA Source Type: research

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants [RESOURCES]
Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Edmonson, M. N., Patel, A. N., Hedges, D. J., Wang, Z., Rampersaud, E., Kesserwan, C. A., Zhou, X., Liu, Y., Newman, S., Rusch, M. C., McLeod, C. L., Wilkinson, M. R., Rice, S. V., Soussi, T., Taylor, J. P., Benatar, M., Becksfort, J. B., Nichols, K. E., Tags: RESOURCES Source Type: research

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis [METHOD]
Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses. Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called "quasispecies." Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous genome regions. Here, we used a full-length, direct RNA sequencing (DRS) approach based on nanopores to characteriz...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Viehweger, A., Krautwurst, S., Lamkiewicz, K., Madhugiri, R., Ziebuhr, J., Hölzer, M., Marz, M. Tags: METHOD Source Type: research

Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays [METHOD]
Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false-positive and -negative predictions. To address these limitations, we developed an experimental approach based on enhanced yeast one-hybrid assays. The first variation of this approach interrogates the binding of>1000 human TFs to repetitive DNA elements, while the second evaluates TF bi...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Shrestha, S., Sewell, J. A., Santoso, C. S., Forchielli, E., Pro, S. C., Martinez, M., Bass, J. I. F. Tags: METHOD Source Type: research

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing [METHOD]
Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a "chromatin-RNA in situ reverse transcription sequencing" (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The pr...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Zhang, S., Wang, Y., Jia, L., Wen, X., Du, Z., Wang, C., Hao, Y., Yu, D., Zhou, L., Chen, N., Chen, J., Chen, H., Zhang, H., Celik, I., Gülsoy, G., Luo, J., Qin, B., Cui, X., Liu, Z., Zhang, S., Esteban, M. A., Ay, F., Xu, W., Chen, R., Li, W., Ho Tags: METHOD Source Type: research

Identifying loci under positive selection in complex population histories [METHOD]
Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective swe...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Refoyo-Martinez, A., da Fonseca, R. R., Halldorsdottir, K., Arnason, E., Mailund, T., Racimo, F. Tags: METHOD Source Type: research

Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains [RESEARCH]
How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)–producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)–encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are li...
Source: Genome Research - September 3, 2019 Category: Genetics & Stem Cells Authors: Arimizu, Y., Kirino, Y., Sato, M. P., Uno, K., Sato, T., Gotoh, Y., Auvray, F., Brugere, H., Oswald, E., Mainil, J. G., Anklam, K. S., Döpfer, D., Yoshino, S., Ooka, T., Tanizawa, Y., Nakamura, Y., Iguchi, A., Morita-Ishihara, T., Ohnishi, M., Aka Tags: RESEARCH Source Type: research