1
|
Pinglay S, Lalanne JB, Daza RM, Koeppel J, Li X, Lee DS, Shendure J. Multiplex generation and single cell analysis of structural variants in a mammalian genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576756. [PMID: 38405830 PMCID: PMC10888807 DOI: 10.1101/2024.01.22.576756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The functional consequences of structural variants (SVs) in mammalian genomes are challenging to study. This is due to several factors, including: 1) their numerical paucity relative to other forms of standing genetic variation such as single nucleotide variants (SNVs) and short insertions or deletions (indels); 2) the fact that a single SV can involve and potentially impact the function of more than one gene and/or cis regulatory element; and 3) the relative immaturity of methods to generate and map SVs, either randomly or in targeted fashion, in in vitro or in vivo model systems. Towards addressing these challenges, we developed Genome-Shuffle-seq, a straightforward method that enables the multiplex generation and mapping of several major forms of SVs (deletions, inversions, translocations) throughout a mammalian genome. Genome-Shuffle-seq is based on the integration of "shuffle cassettes" to the genome, wherein each shuffle cassette contains components that facilitate its site-specific recombination (SSR) with other integrated shuffle cassettes (via Cre-loxP), its mapping to a specific genomic location (via T7-mediated in vitro transcription or IVT), and its identification in single-cell RNA-seq (scRNA-seq) data (via T7-mediated in situ transcription or IST). In this proof-of-concept, we apply Genome-Shuffle-seq to induce and map thousands of genomic SVs in mouse embryonic stem cells (mESCs) in a single experiment. Induced SVs are rapidly depleted from the cellular population over time, possibly due to Cre-mediated toxicity and/or negative selection on the rearrangements themselves. Leveraging T7 IST of barcodes whose positions are already mapped, we further demonstrate that we can efficiently genotype which SVs are present in association with each of many single cell transcriptomes in scRNA-seq data. Finally, preliminary evidence suggests our method may be a powerful means of generating extrachromosomal circular DNAs (ecDNAs). Looking forward, we anticipate that Genome-Shuffle-seq may be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and 3D nuclear architecture. We further anticipate potential uses for in vitro modeling of ecDNAs, as well as in paving the path to a minimal mammalian genome.
Collapse
Affiliation(s)
- Sudarshan Pinglay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David S Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
2
|
Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
Collapse
Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
| |
Collapse
|
3
|
Li Y, Zhai H, Tong L, Wang C, Xie Z, Zheng K. LncRNA Functional Screening in Organismal Development. Noncoding RNA 2023; 9:36. [PMID: 37489456 PMCID: PMC10366883 DOI: 10.3390/ncrna9040036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.
Collapse
Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiming Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
4
|
Di-Battista A, Favilla BP, Zamariolli M, Nunes N, Defelicibus A, Armelin-Correa L, da Silva IT, Reymond A, Moyses-Oliveira M, Melaragno MI. Premature ovarian insufficiency is associated with global alterations in the regulatory landscape and gene expression in balanced X-autosome translocations. Epigenetics Chromatin 2023; 16:19. [PMID: 37202802 DOI: 10.1186/s13072-023-00493-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/04/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Patients with balanced X-autosome translocations and premature ovarian insufficiency (POI) constitute an interesting paradigm to study the effect of chromosome repositioning. Their breakpoints are clustered within cytobands Xq13-Xq21, 80% of them in Xq21, and usually, no gene disruption can be associated with POI phenotype. As deletions within Xq21 do not cause POI, and since different breakpoints and translocations with different autosomes lead to this same gonadal phenotype, a "position effect" is hypothesized as a possible mechanism underlying POI pathogenesis. OBJECTIVE AND METHODS To study the effect of the balanced X-autosome translocations that result in POI, we fine-mapped the breakpoints in six patients with POI and balanced X-autosome translocations and addressed gene expression and chromatin accessibility changes in four of them. RESULTS We observed differential expression in 85 coding genes, associated with protein regulation, multicellular regulation, integrin signaling, and immune response pathways, and 120 differential peaks for the three interrogated histone marks, most of which were mapped in high-activity chromatin state regions. The integrative analysis between transcriptome and chromatin data pointed to 12 peaks mapped less than 2 Mb from 11 differentially expressed genes in genomic regions not related to the patients' chromosomal rearrangement, suggesting that translocations have broad effects on the chromatin structure. CONCLUSION Since a wide impact on gene regulation was observed in patients, our results observed in this study support the hypothesis of position effect as a pathogenic mechanism for premature ovarian insufficiency associated with X-autosome translocations. This work emphasizes the relevance of chromatin changes in structural variation, since it advances our knowledge of the impact of perturbations in the regulatory landscape within interphase nuclei, resulting in the position effect pathogenicity.
Collapse
Affiliation(s)
- Adriana Di-Battista
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Bianca Pereira Favilla
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Natália Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Alexandre Defelicibus
- Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Lucia Armelin-Correa
- Department of Biological Sciences, Universidade Federal São Paulo, Diadema, Brazil
| | - Israel Tojal da Silva
- Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Mariana Moyses-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
- Sleep Institute, Associação Fundo de Incentivo à Pesquisa, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil.
| |
Collapse
|
5
|
Tóth A, Székvölgyi L, Vellai T. The genome loading model for the origin and maintenance of sex in eukaryotes. Biol Futur 2022; 73:345-357. [PMID: 36534301 DOI: 10.1007/s42977-022-00148-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Understanding why sexual reproduction-which involves syngamy (union of gametes) and meiosis-emerged and how it has subsisted for millions of years remains a fundamental problem in biology. Considered as the essence of sex, meiotic recombination is initiated by a DNA double-strand break (DSB) that forms on one of the pairing homologous chromosomes. This DNA lesion is subsequently repaired by gene conversion, the non-reciprocal transfer of genetic information from the intact homolog. A major issue is which of the pairing homologs undergoes DSB formation. Accumulating evidence shows that chromosomal sites where the pairing homologs locally differ in size, i.e., are heterozygous for an insertion or deletion, often display disparity in gene conversion. Biased conversion tends to duplicate insertions and lose deletions. This suggests that DSB is preferentially formed on the "shorter" homologous region, which thereby acts as the recipient for DNA transfer. Thus, sex primarily functions as a genome (re)loading mechanism. It ensures the restoration of formerly lost DNA sequences (deletions) and allows the efficient copying and, mainly in eukaryotes, subsequent spreading of newly emerged sequences (insertions) arising initially in an individual genome, even if they confer no advantage to the host. In this way, sex simultaneously repairs deletions and increases genetic variability underlying adaptation. The model explains a remarkable increase in DNA content during the evolution of eukaryotic genomes.
Collapse
Affiliation(s)
- András Tóth
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary.
| |
Collapse
|
6
|
Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations. PLoS Comput Biol 2022; 18:e1010710. [DOI: 10.1371/journal.pcbi.1010710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/05/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the benefits and costs of recombination under different scenarios of evolutionary adaptation remains an open problem for theoretical and experimental research. In this study, we focus on finite populations evolving on neutral networks comprising viable and unfit genotypes. We provide a comprehensive overview of the effects of recombination by jointly considering different measures of evolvability and mutational robustness over a broad parameter range, such that many evolutionary regimes are covered. We find that several of these measures vary non-monotonically with the rates of mutation and recombination. Moreover, the presence of unfit genotypes that introduce inhomogeneities in the network of viable states qualitatively alters the effects of recombination. We conclude that conflicting trends induced by recombination can be explained by an emerging trade-off between evolvability on the one hand, and mutational robustness on the other. Finally, we discuss how different implementations of the recombination scheme in theoretical models can affect the observed dependence on recombination rate through a coupling between recombination and genetic drift.
Collapse
|
7
|
Extreme purifying selection against point mutations in the human genome. Nat Commun 2022; 13:4312. [PMID: 35879308 PMCID: PMC9314448 DOI: 10.1038/s41467-022-31872-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
Large-scale genome sequencing has enabled the measurement of strong purifying selection in protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring such selection in noncoding as well as coding regions of the human genome. ExtRaINSIGHT estimates the prevalence of “ultraselection” by the fractional depletion of rare single-nucleotide variants, after controlling for variation in mutation rates. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find abundant ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. By contrast, we find much less ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest levels in ultraconserved elements. We estimate that ~0.4–0.7% of the human genome is ultraselected, implying ~ 0.26–0.51 strongly deleterious mutations per generation. Overall, our study sheds new light on the genome-wide distribution of fitness effects by combining deep sequencing data and classical theory from population genetics. Previous work has investigated selection in the coding genome, but it is not as well characterized in the non-coding genome. By analyzing rare variants in 70k genome sequences from gnomAD, the authors detect very strong purifying selection ("ultraselection”) across the human genome, finding it in some microRNAs and coding sequences but generally rare in regulatory sequences.
Collapse
|
8
|
Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| |
Collapse
|
9
|
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun 2020; 11:6053. [PMID: 33247132 PMCID: PMC7695720 DOI: 10.1038/s41467-020-19879-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.
Collapse
|
10
|
Abstract
Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized as biologically meaningful, the fraction of such transcripts out of the entire collection of lncRNAs remains a subject of vigorous debate. Here we review the evidence for and against biological functionalities of lncRNAs and attempt to arrive at potential modes of lncRNA functionality that would reconcile the contradictory conclusions. Finally, we discuss different strategies of phenotypic analyses that could be used to investigate such modes of lncRNA functionality.
Collapse
Affiliation(s)
- Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
| |
Collapse
|
11
|
White ND, Braun MJ. Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores). Mol Phylogenet Evol 2019; 141:106611. [DOI: 10.1016/j.ympev.2019.106611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
|
12
|
He Y, Tian S, Tian P. Fundamental asymmetry of insertions and deletions in genomes size evolution. J Theor Biol 2019; 482:109983. [PMID: 31445016 DOI: 10.1016/j.jtbi.2019.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/18/2019] [Accepted: 08/21/2019] [Indexed: 12/01/2022]
Abstract
The origin of large genomes that underlies the long standing "C-value enigma" is only partially explained by selfish DNA. We investigated insertions and deletions (indels) of nucleotides and discussed their relevance in size evolution of random biological sequences (RBS) and genomes. By developing a probabilistic model of RBS based on size evolution of expandable sites in a thought perfect genome, it was found that insertion bias engenders exponential increase of average RBS sizes. When combined with existing large segments of genome that are not subject to selection pressure (e.g. selfish DNA), such insertion bias results in explosive expansion of genomes, and therefore helps explain the "C value enigma" besides selfish DNA. Such increase of RBS size is caused by the fundamental asymmetry of indels, with insertions result in more available sites and deletions result in less deletable nucleotides. In qualitative agreement with the size distribution of known genomes, tails of RBS size distributions exhibit exponential decay with probabilities of larger RBS segments being smaller. Unsurprisingly, a slight deletion bias (higher deletions probabilities) results in a slow decrease of average RBS size and may lead to their eventual vanishing. Contrary to intuition, strictly balanced insertion and deletion results in linearly increasing instead of completely fixed RBS size. Nonetheless, such slow linear increase of average RBS sizes with time are small in magnitude and are consequently not influential on genome size evolution, and certainly not a major contributor for the "C-value enigma". Our model suggested that insertion bias of nucleotides may provide complementary explanation for large genomes besides selfish DNA. The fundamental indel asymmetry is applicable for all forms of genomic insertions and deletions. Long-lasting exponential increase of genome size present energy and material requirement that is impossible to sustain. We therefore concluded that if there were explosively accelerating expansion caused by significant effective insertion bias for any survival species, it must have occurred sporadically. Our model also provided an explanation for the observed proportional evolution of genome size.
Collapse
Affiliation(s)
- Yang He
- School of Life Sciences, Jilin University Changchun, 2699 Qianjin Street, China 130012
| | - Suyan Tian
- Division of Clinical Epidemiology, First Hospital of The Jilin University, 71 Xinmin Street, Changchun, China, 130021.
| | - Pu Tian
- School of Life Sciences and MOE Key laboratory of Molecular Enzymology and Engineering, Jilin University 2699 Qianjin Street, Changchun, China 130012.
| |
Collapse
|
13
|
Abstract
One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.
Collapse
Affiliation(s)
- Warren R Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
| |
Collapse
|
14
|
An Ultraconserved Element Containing lncRNA Preserves Transcriptional Dynamics and Maintains ESC Self-Renewal. Stem Cell Reports 2018; 10:1102-1114. [PMID: 29456181 PMCID: PMC5918197 DOI: 10.1016/j.stemcr.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/16/2022] Open
Abstract
Ultraconserved elements (UCEs) show the peculiar feature to retain extended perfect sequence identity among human, mouse, and rat genomes. Most of them are transcribed and represent a new family of long non-coding RNAs (lncRNAs), the transcribed UCEs (T-UCEs). Despite their involvement in human cancer, the physiological role of T-UCEs is still unknown. Here, we identify a lncRNA containing the uc.170+, named T-UCstem1, and provide in vitro and in vivo evidence that it plays essential roles in embryonic stem cells (ESCs) by modulating cytoplasmic miRNA levels and preserving transcriptional dynamics. Specifically, while T-UCstem1::miR-9 cytoplasmic interplay regulates ESC proliferation by reducing miR-9 levels, nuclear T-UCstem1 maintains ESC self-renewal and transcriptional identity by stabilizing polycomb repressive complex 2 on bivalent domains. Altogether, our findings provide unprecedented evidence that T-UCEs regulate physiological cellular functions and point to an essential role of T-UCstem1 in preserving ESC identity. The transcribed ultraconserved element T-UCstem1 exerts a dual function in ESCs T-UCstem1 controls ESC proliferation by regulating the miR-9/Lin28b molecular axis T-UCstem1 maintains ESC self-renewal T-UCstem1 preserves ESC transcriptional identity by stabilizing PRC2
Collapse
|
15
|
Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018; 45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.
Collapse
Affiliation(s)
- Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - James W D King
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander J Nash
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| |
Collapse
|
16
|
Qiu GH, Yang X, Zheng X, Huang C. The eukaryotic genome is structurally and functionally more like a social insect colony than a book. Epigenomics 2017; 9:1469-1483. [PMID: 28972397 DOI: 10.2217/epi-2017-0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.
Collapse
Affiliation(s)
- Guo-Hua Qiu
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xiaoyan Yang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xintian Zheng
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Cuiqin Huang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| |
Collapse
|
17
|
Abstract
Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
Collapse
|
18
|
Abstract
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.
Collapse
|
19
|
Qiu GH. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:31-41. [DOI: 10.1016/j.mrrev.2016.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/22/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
|
20
|
Forsdyke DR. Self/Not-Self? Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
21
|
Davies NJ, Krusche P, Tauber E, Ott S. Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. BMC Evol Biol 2015; 15:227. [PMID: 26482678 PMCID: PMC4613772 DOI: 10.1186/s12862-015-0499-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/28/2015] [Indexed: 01/20/2023] Open
Abstract
Background Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences. Successful comparisons of distantly related species will thus yield highly important sequence elements likely to serve fundamental biological roles. RNA regulatory elements are less well understood than those in DNA. In this study we use the emerging model organism Nasonia vitripennis, a parasitic wasp, in a comparative analysis against 12 insect genomes to identify deeply conserved non-coding elements (CNEs) conserved in large groups of insects, with a focus on 5’ UTRs and promoter sequences. Results We report the identification of 322 CNEs conserved across a broad range of insect orders. The identified regions are associated with regulatory and developmental genes, and contain short footprints revealing aspects of their likely function in translational regulation. The most ancient regions identified in our analysis were all found to overlap transcribed regions of genes, reflecting stronger conservation of translational regulatory elements than transcriptional elements. Further expanding sequence analyses to non-insect species we also report the discovery of, to our knowledge, the two oldest and most ubiquitous CNE’s yet described in the animal kingdom (700 MYA). These ancient conserved non-coding elements are associated with the two ribosomal stalk genes, RPLP1 and RPLP2, and were very likely functional in some of the earliest animals. Conclusions We report the identification of the most deeply conserved CNE’s found to date, and several other deeply conserved elements which are without exception, part of 5’ untranslated regions of transcripts, and occur in a number of key translational regulatory genes, highlighting translational regulation of translational regulators as a conserved feature of insect genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0499-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Peter Krusche
- Warwick Systems Biology Centre, University of Warwick, Coventry, UK.
| | - Eran Tauber
- Department of Genetics, University of Leicester, Leicester, UK.
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry, UK.
| |
Collapse
|
22
|
Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PLoS One 2015; 10:e0139656. [PMID: 26437450 PMCID: PMC4593641 DOI: 10.1371/journal.pone.0139656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
It is becoming increasingly necessary to develop computerized methods for identifying the few disease-causing variants from hundreds discovered in each individual patient. This problem is especially relevant for Copy Number Variants (CNVs), which can be cheaply interrogated via low-cost hybridization arrays commonly used in clinical practice. We present a method to predict the disease relevance of CNVs that combines functional context and clinical phenotype to discover clinically harmful CNVs (and likely causative genes) in patients with a variety of phenotypes. We compare several feature and gene weighing systems for classifying both genes and CNVs. We combined the best performing methodologies and parameters on over 2,500 Agilent CGH 180k Microarray CNVs derived from 140 patients. Our method achieved an F-score of 91.59%, with 87.08% precision and 97.00% recall. Our methods are freely available at https://github.com/compbio-UofT/cnv-prioritization. Our dataset is included with the supplementary information.
Collapse
|
23
|
Ea V, Sexton T, Gostan T, Herviou L, Baudement MO, Zhang Y, Berlivet S, Le Lay-Taha MN, Cathala G, Lesne A, Victor JM, Fan Y, Cavalli G, Forné T. Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains. BMC Genomics 2015; 16:607. [PMID: 26271925 PMCID: PMC4536789 DOI: 10.1186/s12864-015-1786-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Results Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Conclusions Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1786-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vuthy Ea
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Tom Sexton
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France.
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Laurie Herviou
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Marie-Odile Baudement
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Yunzhe Zhang
- School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Soizik Berlivet
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Marie-Noëlle Le Lay-Taha
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Guy Cathala
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
| | - Annick Lesne
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France. .,Laboratoire de Physique de la Matière Condensée, CNRS UMR 7600, UPMC, Sorbonne universités, Paris, France.
| | - Jean-Marc Victor
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France. .,Laboratoire de Physique de la Matière Condensée, CNRS UMR 7600, UPMC, Sorbonne universités, Paris, France.
| | - Yuhong Fan
- School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Giacomo Cavalli
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
| |
Collapse
|
24
|
Raabe CA, Brosius J. Does every transcript originate from a gene? Ann N Y Acad Sci 2015; 1341:136-48. [PMID: 25847549 DOI: 10.1111/nyas.12741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 12/20/2022]
Abstract
Outdated gene definitions favored regions corresponding to mature messenger RNAs, in particular, the open reading frame. In eukaryotes, the intergenic space was widely regarded nonfunctional and devoid of RNA transcription. Original concepts were based on the assumption that RNA expression was restricted to known protein-coding genes and a few so-called structural RNA genes, such as ribosomal RNAs or transfer RNAs. With the discovery of introns and, more recently, sensitive techniques for monitoring genome-wide transcription, this view had to be substantially modified. Tiling microarrays and RNA deep sequencing revealed myriads of transcripts, which cover almost entire genomes. The tremendous complexity of non-protein-coding RNA transcription has to be integrated into novel gene definitions. Despite an ever-growing list of functional RNAs, questions concerning the mass of identified transcripts are under dispute. Here, we examined genome-wide transcription from various angles, including evolutionary considerations, and suggest, in analogy to novel alternative splice variants that do not persist, that the vast majority of transcripts represent raw material for potential, albeit rare, exaptation events.
Collapse
Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | | |
Collapse
|
25
|
Qiu GH. Protection of the genome and central protein-coding sequences by non-coding DNA against DNA damage from radiation. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:108-17. [DOI: 10.1016/j.mrrev.2015.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/11/2015] [Accepted: 04/22/2015] [Indexed: 01/08/2023]
|
26
|
Graur D, Zheng Y, Azevedo RBR. An evolutionary classification of genomic function. Genome Biol Evol 2015; 7:642-5. [PMID: 25635041 PMCID: PMC5322545 DOI: 10.1093/gbe/evv021] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2015] [Indexed: 02/06/2023] Open
Abstract
The pronouncements of the ENCODE Project Consortium regarding "junk DNA" exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into "functional DNA," that is, DNA sequences that have a selected-effect function, and "rubbish DNA," that is, sequences that do not. Functional DNA is further subdivided into "literal DNA" and "indifferent DNA." In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into "junk DNA" and "garbage DNA." Junk DNA neither contributes to nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be 1) transcribed and translated, 2) transcribed but not translated, or 3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: Functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on; however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided into pseudogenes, Lazarus DNA, zombie DNA, and Jekyll-to-Hyde DNA.
Collapse
Affiliation(s)
- Dan Graur
- Department of Biology and Biochemistry, University of Houston
| | - Yichen Zheng
- Department of Biology and Biochemistry, University of Houston
| | | |
Collapse
|
27
|
Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015; 2015:pdb.top083642. [PMID: 25561628 PMCID: PMC5885252 DOI: 10.1101/pdb.top083642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
Collapse
Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany
| | - Leelavati Narlikar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| |
Collapse
|
28
|
Davies KTJ, Tsagkogeorga G, Rossiter SJ. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals. BMC Evol Biol 2014; 14:261. [PMID: 25523630 PMCID: PMC4302572 DOI: 10.1186/s12862-014-0261-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/08/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. RESULTS Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. CONCLUSIONS Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.
Collapse
Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Georgia Tsagkogeorga
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| |
Collapse
|
29
|
Hill AE, Plyler ZE, Tiwari H, Patki A, Tully JP, McAtee CW, Moseley LA, Sorscher EJ. Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA. PLoS One 2014; 9:e109186. [PMID: 25350658 PMCID: PMC4211684 DOI: 10.1371/journal.pone.0109186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/09/2014] [Indexed: 12/03/2022] Open
Abstract
Like many other ancient genes, the cystic fibrosis transmembrane conductance regulator (CFTR) has survived for hundreds of millions of years. In this report, we consider whether such prodigious longevity of an individual gene – as opposed to an entire genome or species – should be considered surprising in the face of eons of relentless DNA replication errors, mutagenesis, and other causes of sequence polymorphism. The conventions that modern human SNP patterns result either from purifying selection or random (neutral) drift were not well supported, since extant models account rather poorly for the known plasticity and function (or the established SNP distributions) found in a multitude of genes such as CFTR. Instead, our analysis can be taken as a polemic indicating that SNPs in CFTR and many other mammalian genes may have been generated—and continue to accrue—in a fundamentally more organized manner than would otherwise have been expected. The resulting viewpoint contradicts earlier claims of ‘directional’ or ‘intelligent design-type’ SNP formation, and has important implications regarding the pace of DNA adaptation, the genesis of conserved non-coding DNA, and the extent to which eukaryotic SNP formation should be viewed as adaptive.
Collapse
Affiliation(s)
- Aubrey E. Hill
- Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zackery E. Plyler
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joel P. Tully
- Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christopher W. McAtee
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Leah A. Moseley
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric J. Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
30
|
Oliver PL, Chodroff RA, Gosal A, Edwards B, Cheung AFP, Gomez-Rodriguez J, Elliot G, Garrett LJ, Lickiss T, Szele F, Green ED, Molnár Z, Ponting CP. Disruption of Visc-2, a Brain-Expressed Conserved Long Noncoding RNA, Does Not Elicit an Overt Anatomical or Behavioral Phenotype. Cereb Cortex 2014; 25:3572-85. [PMID: 25209608 PMCID: PMC4585502 DOI: 10.1093/cercor/bhu196] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Although long noncoding RNAs (lncRNAs) are proposed to play essential roles in mammalian neurodevelopment, we know little of their functions from their disruption in vivo. Combining evidence for evolutionary constraint and conserved expression data, we previously identified candidate lncRNAs that might play important and conserved roles in brain function. Here, we demonstrate that the sequence and neuronal transcription of lncRNAs transcribed from the previously uncharacterized Visc locus are conserved across diverse mammals. Consequently, one of these lncRNAs, Visc-2, was selected for targeted deletion in the mouse, and knockout animals were subjected to an extremely detailed anatomical and behavioral characterization. Despite a neurodevelopmental expression pattern of Visc-2 that is highly localized to the cortex and sites of neurogenesis, anomalies in neither cytoarchitecture nor neuroproliferation were identified in knockout mice. In addition, no abnormal motor, sensory, anxiety, or cognitive behavioral phenotypes were observed. These results are important because they contribute to a growing body of evidence that lncRNA loci contribute on average far less to brain and biological functions than protein-coding loci. A high-throughput knockout program focussing on lncRNAs, similar to that currently underway for protein-coding genes, will be required to establish the distribution of their organismal functions.
Collapse
Affiliation(s)
- Peter L Oliver
- MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Rebecca A Chodroff
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK Genome Technology Branch
| | - Amrit Gosal
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | | | - Amanda F P Cheung
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Julio Gomez-Rodriguez
- Embryonic Stem Cells and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Gene Elliot
- Embryonic Stem Cells and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Lisa J Garrett
- Embryonic Stem Cells and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Tom Lickiss
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Francis Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | | | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Chris P Ponting
- MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| |
Collapse
|
31
|
Babarinde IA, Saitou N. Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol 2014; 5:2330-43. [PMID: 24259317 PMCID: PMC3879966 DOI: 10.1093/gbe/evt177] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages, with primates and rodents having highest and lowest number of CNSs, respectively, whereas carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3-5.5% of the mammalian genomes and have signatures of selective constraints that are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared with carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggest that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.
Collapse
Affiliation(s)
- Isaac Adeyemi Babarinde
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima Japan
| | | |
Collapse
|
32
|
Affiliation(s)
- J. Rich
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
| | - V. V. Ogryzko
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
| | | |
Collapse
|
33
|
Mehta SL, Dharap A, Vemuganti R. Expression of transcribed ultraconserved regions of genome in rat cerebral cortex. Neurochem Int 2014; 77:86-93. [PMID: 24953281 DOI: 10.1016/j.neuint.2014.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022]
Abstract
Emerging evidence indicates that 481 regions of the genome (>200 bp) that actively transcribe noncoding RNAs shows 100% homology between humans, rats and mice. These transcribed ultraconserved regions (T-UCRs) are thought to control the essential regulatory functions basic for life in rodents and mammals. Using microarray analysis, we presently show that 107 T-UCRs are actively expressed in adult rat cerebral cortex. They are grouped into intragenic (61) and intergenic (46) based on their genic location. Interestingly, 10 T-UCRs are expressed at unusually high levels in cerebral cortex. Additionally, many T-UCRs also showed cogenic expression. We further analyzed the correlation of intragenic T-UCRs with their host protein coding genes. Surprisingly, most of the expressed intragenic T-UCRs (54 out of 61) displayed a negative correlation with their host gene expression. T-UCRs are thought to control the splicing and transcription of the protein-coding genes that host them and flank them. Bioinformatics analysis indicated that the protein products of majority of these genes are nuclear in localization, share protein domains and are involved in the regulation of diverse biological and molecular functions including metabolism, development, cell cycle, binding and transcription factor regulation. In conclusion, this is the first study to shows that many T-UCRs are expressed in rodent brain and they might play a role in physiological brain functions.
Collapse
Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Ashutosh Dharap
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
| |
Collapse
|
34
|
Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
|
35
|
A genetic program theory of aging using an RNA population model. Ageing Res Rev 2014; 13:46-54. [PMID: 24263168 DOI: 10.1016/j.arr.2013.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/08/2013] [Indexed: 12/11/2022]
Abstract
Aging is a common characteristic of multicellular eukaryotes. Copious hypotheses have been proposed to explain the mechanisms of aging, but no single theory is generally acceptable. In this article, we refine the RNA population gene activating model (Lv et al., 2003) based on existing reports as well as on our own latest findings. We propose the RNA population model as a genetic theory of aging. The new model can also be applied to differentiation and tumorigenesis and could explain the biological significance of non-coding DNA, RNA, and repetitive sequence DNA. We provide evidence from the literature as well as from our own findings for the roles of repetitive sequences in gene activation. In addition, we predict several phenomena related to aging and differentiation based on this model.
Collapse
|
36
|
Mason CE, Porter SG, Smith TM. Characterizing multi-omic data in systems biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 799:15-38. [PMID: 24292960 DOI: 10.1007/978-1-4614-8778-4_2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In today's biology, studies have shifted to analyzing systems over discrete biochemical reactions and pathways. These studies depend on combining the results from scores of experimental methods that analyze DNA; mRNA; noncoding RNAs, DNA, RNA, and protein interactions; and the nucleotide modifications that form the epigenome into global datasets that represent a diverse array of "omics" data (transcriptional, epigenetic, proteomic, metabolomic). The methods used to collect these data consist of high-throughput data generation platforms that include high-content screening, imaging, flow cytometry, mass spectrometry, and nucleic acid sequencing. Of these, the next-generation DNA sequencing platforms predominate because they provide an inexpensive and scalable way to quickly interrogate the molecular changes at the genetic, epigenetic, and transcriptional level. Furthermore, existing and developing single-molecule sequencing platforms will likely make direct RNA and protein measurements possible, thus increasing the specificity of current assays and making it possible to better characterize "epi-alterations" that occur in the epigenome and epitranscriptome. These diverse data types present us with the largest challenge: how do we develop software systems and algorithms that can integrate these datasets and begin to support a more democratic model where individuals can capture and track their own medical information through biometric devices and personal genome sequencing? Such systems will need to provide the necessary user interactions to work with the trillions of data points needed to make scientific discoveries. Here, we describe novel approaches in the genesis and processing of such data, models to integrate these data, and the increasing ubiquity of self-reporting and self-measured genomics and health data.
Collapse
Affiliation(s)
- Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA,
| | | | | |
Collapse
|
37
|
Gavrilov AA, Chetverina HV, Chermnykh ES, Razin SV, Chetverin AB. Quantitative analysis of genomic element interactions by molecular colony technique. Nucleic Acids Res 2013; 42:e36. [PMID: 24369423 PMCID: PMC3950710 DOI: 10.1093/nar/gkt1322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.
Collapse
Affiliation(s)
- Alexey A Gavrilov
- Group of Genome Spatial Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Viral RNA Biochemistry, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia, Laboratory of Cell Proliferation Problems, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia and Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | | | | | | | | |
Collapse
|
38
|
Makunin IV, Shloma VV, Stephen SJ, Pheasant M, Belyakin SN. Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One 2013; 8:e82362. [PMID: 24349264 PMCID: PMC3862641 DOI: 10.1371/journal.pone.0082362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022] Open
Abstract
Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
Collapse
Affiliation(s)
- Igor V. Makunin
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
- * E-mail:
| | - Viktor V. Shloma
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
| | - Stuart J. Stephen
- Computational Biology Group, CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Michael Pheasant
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
| | | |
Collapse
|
39
|
Bhatia S, Bengani H, Fish M, Brown A, Divizia M, de Marco R, Damante G, Grainger R, van Heyningen V, Kleinjan D. Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia. Am J Hum Genet 2013; 93:1126-34. [PMID: 24290376 DOI: 10.1016/j.ajhg.2013.10.028] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/19/2013] [Accepted: 10/30/2013] [Indexed: 02/07/2023] Open
Abstract
The strictly regulated expression of most pleiotropic developmental control genes is critically dependent on the activity of long-range cis-regulatory elements. This was revealed by the identification of individuals with a genetic condition lacking coding-region mutations in the gene commonly associated with the disease but having a variety of nearby chromosomal abnormalities, collectively described as cis-ruption disease cases. The congenital eye malformation aniridia is caused by haploinsufficiency of the developmental regulator PAX6. We discovered a de novo point mutation in an ultraconserved cis-element located 150 kb downstream from PAX6 in an affected individual with intact coding region and chromosomal locus. The element SIMO acts as a strong enhancer in developing ocular structures. The mutation disrupts an autoregulatory PAX6 binding site, causing loss of enhancer activity, resulting in defective maintenance of PAX6 expression. These findings reveal a distinct regulatory mechanism for genetic disease by disruption of an autoregulatory feedback loop critical for maintenance of gene expression through development.
Collapse
|
40
|
Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression. Proc Natl Acad Sci U S A 2013; 110:19848-53. [PMID: 24248373 DOI: 10.1073/pnas.1310427110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
When brought into captivity, wild animals can adapt to domestication within 10 generations. Such adaptations may decrease fitness in natural conditions. Many selective pressures are disrupted in captivity, including social behavioral networks. Although lack of sociality in captivity appears to mediate domestication, the underlying mechanisms are not well understood. Additionally, determining the contribution of genetic inheritance vs. transgenerational effects during relaxed selection may provide insight into the flexibility of adaptation. When wild-derived mice kept under laboratory conditions for eight generations were reintroduced to sociality and promiscuity (free mate choice), they adapted within two generations. Fitness assessments between this promiscuous lineage and a monogamous laboratory lineage revealed male-specific effects. Promiscuous-line males had deficits in viability, but a striking advantage in attracting mates, and their scent marks were also more attractive to females. Here, we investigate mechanistic details underlying this olfactory signal and identify a role of major urinary protein (MUP) pheromones. Promiscuous-line males inherit higher MUP expression than monogamous-line males through transgenerational inheritance. Sociality-driven maternal and paternal effects reveal intriguing conflicts among parents and offspring over pheromone expression. MUP up-regulation is not driven by hormone-driven transduction pathways, but rather is associated with reduction in DNA methylation of a CpG dinucleotide in the promoter. This reduction in methylation could enhance transcription by promoting the binding of transcription factor USF1 (upstream stimulatory factor 1). Finally, we experimentally demonstrate that increased MUP expression is a female attractant. These results identify molecular mechanisms guiding domestication and adaptive responses to fluctuating sociality.
Collapse
|
41
|
Weischenfeldt J, Symmons O, Spitz F, Korbel JO. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 2013; 14:125-38. [PMID: 23329113 DOI: 10.1038/nrg3373] [Citation(s) in RCA: 374] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genomic structural variants have long been implicated in phenotypic diversity and human disease, but dissecting the mechanisms by which they exert their functional impact has proven elusive. Recently however, developments in high-throughput DNA sequencing and chromosomal engineering technology have facilitated the analysis of structural variants in human populations and model systems in unprecedented detail. In this Review, we describe how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease. We further present advances in delineating disease-causing elements that are affected by structural variants, and we discuss future directions for research on the functional consequences of structural variants.
Collapse
Affiliation(s)
- Joachim Weischenfeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | | | | | | |
Collapse
|
42
|
Appels R, Barrero R, Bellgard M. Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals. Funct Integr Genomics 2013; 13:1-9. [PMID: 23494190 PMCID: PMC3605488 DOI: 10.1007/s10142-013-0319-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/02/2013] [Accepted: 03/03/2013] [Indexed: 11/27/2022]
Abstract
Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
Collapse
Affiliation(s)
- R. Appels
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - R. Barrero
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - M. Bellgard
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| |
Collapse
|
43
|
Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, Bessa J. Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics 2012; 13:713. [PMID: 23253453 PMCID: PMC3541358 DOI: 10.1186/1471-2164-13-713] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 12/14/2012] [Indexed: 01/18/2023] Open
Abstract
Background Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis-regulatory elements (cis-changes) or from changes in the expression pattern or function of transcription factors (trans-changes). While isolated examples of trans-changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear. Results Here, we attempt to examine the prevalence of trans-effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for trans-changes in the evolution of gene expression. Conclusions In total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the trans environment may play a significant role in the evolution of gene expression in vertebrates.
Collapse
Affiliation(s)
- Ana Ariza-Cosano
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, Seville 41013, Spain
| | | | | | | | | | | | | |
Collapse
|
44
|
Díaz-Castillo C, Ranz JM. Recent progress on the identity and characterization of factors that shape gene organization during eukaryotic evolution. Fly (Austin) 2012; 6:158-61. [PMID: 22722673 DOI: 10.4161/fly.20861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Comparative genomics has identified regions of chromosomes susceptible to participate in rearrangements that modify gene order and genome architecture. Additionally, despite the high levels of genome rearrangement, unusually large regions that remain unaffected have also been uncovered. Functional constraints, such as long-range enhancers or local coregulation of neighboring genes, are thought to explain the maintenance of gene order (i.e., collinearity conservation) among distantly related species since the disruption of these protected regions would cause detrimental misregulation of gene expression. Local enrichment of certain genetic elements in regions of conserved collinearity has been used to support the existence of regulatory-based constraints, although the evidence is largely circumstantial. Indeed, a mechanism of chromosome evolution based only on the existence of fragile regions (i.e., those more susceptible to breaks) can also give rise to extended collinearity conservation, making it difficult to determine whether conserved gene organization is actually caused by functional constraints. Chromosome engineering coupled with genome wide expression profiling and phenotypic assays can provide unambiguous evidence for the presence of functional constraints acting on particular genomic regions. We have recently used this integrated approach to evaluate the presence and nature of putative constraints acting on one of the largest chromosomal regions conserved across nine species of Drosophila. We propose that regulatory-based constraints might not suffice to explain the maintenance of gene organization of some chromosome domains over evolutionary time.
Collapse
Affiliation(s)
- Carlos Díaz-Castillo
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA.
| | | |
Collapse
|
45
|
Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, O'Shaughnessy A, Mosaku O, Signolet J, Brennecke P, Kalkan T, Costello I, Humphreys P, Mansfield W, Nakagawa K, Strouboulis J, Behrens A, Bertone P, Hendrich B. NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment. Cell Stem Cell 2012; 10:583-94. [PMID: 22560079 PMCID: PMC3402183 DOI: 10.1016/j.stem.2012.02.020] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 12/14/2011] [Accepted: 02/23/2012] [Indexed: 12/17/2022]
Abstract
Transcriptional heterogeneity within embryonic stem cell (ESC) populations has been suggested as a mechanism by which a seemingly homogeneous cell population can initiate differentiation into an array of different cell types. Chromatin remodeling proteins have been shown to control transcriptional variability in yeast and to be important for mammalian ESC lineage commitment. Here we show that the Nucleosome Remodeling and Deacetylation (NuRD) complex, which is required for ESC lineage commitment, modulates both transcriptional heterogeneity and the dynamic range of a set of pluripotency genes in ESCs. In self-renewing conditions, the influence of NuRD at these genes is balanced by the opposing action of self-renewal factors. Upon loss of self-renewal factors, the action of NuRD is sufficient to silence transcription of these pluripotency genes, allowing cells to exit self-renewal. We propose that modulation of transcription levels by NuRD is key to maintaining the differentiation responsiveness of pluripotent cells.
Collapse
Affiliation(s)
- Nicola Reynolds
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Paulina Latos
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Antony Hynes-Allen
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Remco Loos
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Donna Leaford
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Aoife O'Shaughnessy
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Olukunbi Mosaku
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jason Signolet
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Philip Brennecke
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Tüzer Kalkan
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ita Costello
- Institute for Stem Cell Research and MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH9 3JQ, UK
| | - Peter Humphreys
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - William Mansfield
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kentaro Nakagawa
- London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, UK
| | - John Strouboulis
- Institute of Molecular Oncology, BSRC “Alexander Fleming,” P.O. Box 74145, Varkiza, Greece
| | - Axel Behrens
- London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, UK
| | - Paul Bertone
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Brian Hendrich
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| |
Collapse
|
46
|
Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs. RNA (NEW YORK, N.Y.) 2012; 18:825-43. [PMID: 22361292 PMCID: PMC3312569 DOI: 10.1261/rna.029520.111] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent transcriptome analyses have indicated that a large part of mammalian genomes are transcribed into long non-protein-coding RNAs (lncRNAs). However, only a very small fraction of them have been individually studied, and whether the majority of lncRNAs found in large-scale studies have a cellular role is debated. To gain insight into the sequence features and genomic architecture of the subset of lncRNAs that have been proven to be functional, we created a database containing studied lncRNAs manually culled from the literature along with a parallel database containing all annotated protein-coding human RNAs. The Functional lncRNA Database, which contains 204 lncRNAs and their splicing variants, is available at valadkhanlab.org/database. Analysis of the lncRNAs and their comparison to protein-coding transcripts revealed sequence features including paucity of introns and low GC content in lncRNAs, which could explain several biological characteristics of these transcripts, such as their nuclear localization and low expression level. The predicted ORFs in lncRNAs have poor start codon and ORF contexts, which would lead to activation of the nonsense-mediated decay pathways and thus make it unlikely for most lncRNAs to code for even short peptides. Interestingly, our analyses revealed significant similarities between the lncRNAs and the 3' untranslated regions (3' UTRs) in protein-coding RNAs in structural features and sequence composition. The presence of these intriguing parallels between the lncRNAs and 3' UTRs, which constitute the two main components of the RNA-mediated cellular regulatory system, indicates that highly similar evolutionary constraints govern the function of regulatory RNA sequences in the cell.
Collapse
Affiliation(s)
- Farshad Niazi
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Corresponding authors.E-mail .E-mail .
| | - Saba Valadkhan
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Corresponding authors.E-mail .E-mail .
| |
Collapse
|
47
|
Pauls S, Smith SF, Elgar G. Lens development depends on a pair of highly conserved Sox21 regulatory elements. Dev Biol 2012; 365:310-8. [PMID: 22387845 PMCID: PMC3480646 DOI: 10.1016/j.ydbio.2012.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/16/2012] [Accepted: 02/18/2012] [Indexed: 02/03/2023]
Abstract
Highly conserved non-coding elements (CNEs) linked to genes involved in embryonic development have been hypothesised to correspond to cis-regulatory modules due to their ability to induce tissue-specific expression patterns. However, attempts to prove their requirement for normal development or for the correct expression of the genes they are associated with have yielded conflicting results. Here, we show that CNEs at the vertebrate Sox21 locus are crucial for Sox21 expression in the embryonic lens and that loss of Sox21 function interferes with normal lens development. Using different expression assays in zebrafish we find that two CNEs linked to Sox21 in all vertebrates contain lens enhancers and that their removal from a reporter BAC abolishes lens expression. Furthermore inhibition of Sox21 function after the injection of a sox21b morpholino into zebrafish leads to defects in lens development. These findings identify a direct link between sequence conservation and genomic function of regulatory sequences. In addition to this we provide evidence that putative Sox binding sites in one of the CNEs are essential for induction of lens expression as well as enhancer function in the CNS. Our results show that CNEs identified in pufferfish-mammal whole-genome comparisons are crucial developmental enhancers and hence essential components of gene regulatory networks underlying vertebrate embryogenesis.
Collapse
|
48
|
Haring R, Wallaschofski H. Diving through the "-omics": the case for deep phenotyping and systems epidemiology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:231-4. [PMID: 22320900 DOI: 10.1089/omi.2011.0108] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Enabled by diverse high-throughput technologies, the rapidly evolving field of "-omics sciences" offers the potential to study health and disease in breadth and depth at the human population level. We have recently linked genomics and metabolomics to present the first genome-wide association study of metabolic traits in human urine providing new insights into the functional background of chronic kidney disease. We propose systems epidemiology as a novel approach to study the complexities of human pathophysiology by integrating various population-level omic-metrics and to identify new trans-omic biomarkers.
Collapse
Affiliation(s)
- Robin Haring
- Preventive Medicine & Epidemiology Section, Boston University School of Medicine, Boston, Massachusetts, USA.
| | | |
Collapse
|
49
|
Homozygous deletion of a gene-free region of 4p15 in a child with multiple anomalies: could biallelic loss of conserved, non-coding elements lead to a phenotype? Eur J Med Genet 2011; 55:63-6. [PMID: 22080113 DOI: 10.1016/j.ejmg.2011.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 11/02/2011] [Indexed: 11/21/2022]
Abstract
We report a male patient, offspring of a consanguineous marriage between first cousins, with cognitive impairment, autistic-like behavior, deafness, postaxial polydactyly, and mild dysmorphic features. aCGH revealed a 600 kb homozygous deletion of 4p15.1 (from 33.553 to 34.159 Mb in NCBI36 hg18) encoding several transcripts of unknown function. Both parents are heterozygous for the deletion and the non-affected brother is homozygous for the normal alleles. We hypothesize that this deletion is likely to contribute to the phenotype of the patient. This case underlines the contribution of aCGH in discovering potentially pathogenic CNVs in consanguineous matings.
Collapse
|
50
|
Liu J, Guzman MA, Pezanowski D, Patel D, Hauptman J, Keisling M, Hou SJ, Papenhausen PR, Pascasio JM, Punnett HH, Halligan GE, de Chadarévian JP. FOXO1-FGFR1 fusion and amplification in a solid variant of alveolar rhabdomyosarcoma. Mod Pathol 2011; 24:1327-35. [PMID: 21666686 DOI: 10.1038/modpathol.2011.98] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rhabdomyosarcoma is the most common pediatric soft tissue malignancy. Two major subtypes, alveolar rhabdomyosarcoma and embryonal rhabdomyosarcoma, constitute 20 and 60% of all cases, respectively. Approximately 80% of alveolar rhabdomyosarcoma carry two signature chromosomal translocations, t(2;13)(q35;q14) resulting in PAX3-FOXO1 fusion, and t(1;13)(p36;q14) resulting in PAX7-FOXO1 fusion. Whether the remaining cases are truly negative for gene fusion has been questioned. We are reporting the case of a 9-month-old girl with a metastatic neck mass diagnosed histologically as solid variant alveolar rhabdomyosarcoma. Chromosome analysis showed a t(8;13;9)(p11.2;q14;9q32) three-way translocation as the sole clonal aberration. Fluorescent in situ hybridization (FISH) demonstrated a rearrangement at the FOXO1 locus and an amplification of its centromeric region. Single-nucleotide polymorphism-based microarray analysis illustrated a co-amplification of the FOXO1 gene at 13q14 and the FGFR1 gene at 8p12p11.2, suggesting formation and amplification of a chimerical FOXO1-FGFR1 gene. This is the first report to identify a novel fusion partner FGFR1 for the known anchor gene FOXO1 in alveolar rhabdomyosarcoma.
Collapse
Affiliation(s)
- Jinglan Liu
- Department of Pathology and Laboratory Medicine, St Christopher's Hospital for Children, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|