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Shachar R, Dierks D, Garcia-Campos MA, Uzonyi A, Toth U, Rossmanith W, Schwartz S. Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids. Genome Biol 2024; 25:48. [PMID: 38360609 PMCID: PMC10870504 DOI: 10.1186/s13059-024-03182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms. RESULTS Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression. CONCLUSIONS Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.
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Affiliation(s)
- Ran Shachar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | | | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, 1090, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, 1090, Austria
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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2
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Ijaz J, Harry E, Raine K, Menzies A, Beal K, Quail MA, Zumalave S, Jung H, Coorens THH, Lawson ARJ, Leongamornlert D, Francies HE, Garnett MJ, Ning Z, Campbell PJ. Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas. CELL GENOMICS 2024; 4:100484. [PMID: 38232733 PMCID: PMC10879010 DOI: 10.1016/j.xgen.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling. Complex structural variation and subclonal variants meant that haplotype-aware de novo methods were required to generate contiguous cancer genome assemblies. Chromosomes were assembled separately and scaffolded using haplotype-resolved Hi-C reads, producing accurate assemblies even with up to 900 structural rearrangements. There were widespread differences between the chromothriptic and wild-type copies of chromosomes in topologically associated domains, chromatin accessibility, histone modifications, and gene expression. Differential epigenome peaks were most enriched within 10 kb of chromothriptic structural variants. Alterations in transcriptome and higher-order chromosome organization frequently occurred near differential epigenetic marks. Overall, chromothripsis reshapes gene regulation, causing coordinated changes in epigenetic landscape, transcription, and chromosome conformation.
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Affiliation(s)
- Jannat Ijaz
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | | | - Keiran Raine
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Health Innovation East, Unit C, Magog Court, Shelford Bottom, Cambridge CB22 3AD, UK
| | | | | | | | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Hayley E Francies
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; GSK, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
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3
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Harris SE, Alexis MS, Giri G, Cavazos FF, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577729. [PMID: 38352439 PMCID: PMC10862761 DOI: 10.1101/2024.01.29.577729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
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Affiliation(s)
- Sarah E. Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | - Maria S. Alexis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Remix Therapeutics, Cambridge, MA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
| | | | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA
- Center for RNA Biology and Medicine, Riverside, CA
| | - Maria M. Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
| | | | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC
- RNA Discovery Center, University of North Carolina, Chapel Hill, NC
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4
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Guzman C, Duttke S, Zhu Y, De Arruda Saldanha C, Downes N, Benner C, Heinz S. Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation. Nucleic Acids Res 2023; 51:e80. [PMID: 37403796 PMCID: PMC10450201 DOI: 10.1093/nar/gkad562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Cis-regulatory elements (CREs) can be classified by the shapes of their transcription start site (TSS) profiles, which are indicative of distinct regulatory mechanisms. Massively parallel reporter assays (MPRAs) are increasingly being used to study CRE regulatory mechanisms, yet the degree to which MPRAs replicate individual endogenous TSS profiles has not been determined. Here, we present a new low-input MPRA protocol (TSS-MPRA) that enables measuring TSS profiles of episomal reporters as well as after lentiviral reporter chromatinization. To sensitively compare MPRA and endogenous TSS profiles, we developed a novel dissimilarity scoring algorithm (WIP score) that outperforms the frequently used earth mover's distance on experimental data. Using TSS-MPRA and WIP scoring on 500 unique reporter inserts, we found that short (153 bp) MPRA promoter inserts replicate the endogenous TSS patterns of ∼60% of promoters. Lentiviral reporter chromatinization did not improve fidelity of TSS-MPRA initiation patterns, and increasing insert size frequently led to activation of extraneous TSS in the MPRA that are not active in vivo. We discuss the implications of our findings, which highlight important caveats when using MPRAs to study transcription mechanisms. Finally, we illustrate how TSS-MPRA and WIP scoring can provide novel insights into the impact of transcription factor motif mutations and genetic variants on TSS patterns and transcription levels.
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Affiliation(s)
- Carlos Guzman
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
- Department of Bioengineering, Graduate Program in Bioinformatics & Systems Biology, U.C. San Diego, La Jolla, CA 92093, USA
| | - Sascha Duttke
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Yixin Zhu
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Camila De Arruda Saldanha
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Nicholas L Downes
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
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5
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Zeng P, Ge X, Li Z. Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:2029. [PMID: 37653946 PMCID: PMC10220956 DOI: 10.3390/plants12102029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available Brassica oleracea-nigra MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived B. oleracea plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental B. oleracea, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived B. oleracea plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to B. nigra, in all five MAALs more DEGs were downregulated than upregulated. Trans-effects were likely more prevailing than cis-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that cis- and trans-mechanisms synergistically regulated alien gene transcriptions after distant hybridization.
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Affiliation(s)
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (P.Z.); (Z.L.)
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6
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Brosh R, Coelho C, Ribeiro-Dos-Santos AM, Ellis G, Hogan MS, Ashe HJ, Somogyi N, Ordoñez R, Luther RD, Huang E, Boeke JD, Maurano MT. Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus. Mol Cell 2023; 83:1140-1152.e7. [PMID: 36931273 PMCID: PMC10081970 DOI: 10.1016/j.molcel.2023.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big-IN to scarlessly integrate large DNA payloads incorporating deletions, rearrangements, and inversions affecting single or multiple DHSs, as well as surgical alterations to transcription factor (TF) recognition sequences. Multiple mESC clones were derived for each payload, sequence-verified, and analyzed for Sox2 expression. We found that two DHSs comprising a handful of key TF recognition sequences were each sufficient for long-range activation of Sox2 expression. By contrast, three nearby DHSs were entirely context dependent, showing no activity alone but dramatically augmenting the activity of the autonomous DHSs. Our results highlight the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for the dissection of other genomic loci.
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Affiliation(s)
- Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Nicolette Somogyi
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Raven D Luther
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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7
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Ding SD, Leitão AB, Day JP, Arunkumar R, Phillips M, Zhou SO, Jiggins FM. Trans-regulatory changes underpin the evolution of the Drosophila immune response. PLoS Genet 2022; 18:e1010453. [PMID: 36342922 PMCID: PMC9671443 DOI: 10.1371/journal.pgen.1010453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/17/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
When an animal is infected, the expression of a large suite of genes is changed, resulting in an immune response that can defend the host. Despite much evidence that the sequence of proteins in the immune system can evolve rapidly, the evolution of gene expression is comparatively poorly understood. We therefore investigated the transcriptional response to parasitoid wasp infection in Drosophila simulans and D. sechellia. Although these species are closely related, there has been a large scale divergence in the expression of immune-responsive genes in their two main immune tissues, the fat body and hemocytes. Many genes, including those encoding molecules that directly kill pathogens, have cis regulatory changes, frequently resulting in large differences in their expression in the two species. However, these changes in cis regulation overwhelmingly affected gene expression in immune-challenged and uninfected animals alike. Divergence in the response to infection was controlled in trans. We argue that altering trans-regulatory factors, such as signalling pathways or immune modulators, may allow natural selection to alter the expression of large numbers of immune-responsive genes in a coordinated fashion. A fundamental question in biology is the nature of the genetic changes underlying evolutionary change, and immune systems provide an ideal system to examine this as they tend to evolve fast as animals adapt to an ever-changing array of parasites and pathogens. Comparing two species of the fruit fly Drosophila, we found that the transcriptional response to infection evolves extremely fast. However, changes in cis (where the genetic change is on the same DNA molecule as the gene in question) and trans (where the genetic change can be elsewhere in the genome) are playing different roles. Changes in cis frequently caused large differences in immune gene expression between species, but these differences were seen regardless of whether the animal was infected. In contrast, changes in trans were responsible for altering how gene expression changes in response to infection. Immune responses are complex and multifaceted, requiring the expression of many genes to be altered in a tightly regulated manner when the animal is infected. Natural selection acting on trans regulatory factors may allow the expression of many downstream genes to be altered in a coordinated fashion.
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Affiliation(s)
| | - Alexandre B. Leitão
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Champalimaud Foundation, Lisbon, Portugal
| | - Jonathan P. Day
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ramesh Arunkumar
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Morgan Phillips
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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8
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Krieger G, Lupo O, Wittkopp P, Barkai N. Evolution of transcription factor binding through sequence variations and turnover of binding sites. Genome Res 2022; 32:1099-1111. [PMID: 35618416 DOI: 10.1101/gr.276715.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 01/08/2023]
Abstract
Variations in noncoding regulatory sequences play a central role in evolution. Interpreting such variations, however, remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related genomes are present within the same nucleus. TFs localize preferentially to sites containing their known consensus motifs but occupy only a small fraction of the motif-containing sites available within the genomes. Differential binding of TFs to the orthologous alleles was well explained by variations that alter motif sequence, whereas differences in chromatin accessibility between alleles were of little apparent effect. Motif variations that abolished binding when present in only one allele were still bound when present in both alleles, suggesting evolutionary compensation, with a potential role for sequence conservation at the motif's vicinity. At the level of the full promoter, we identify cases of binding-site turnover, in which binding sites are reciprocally gained and lost, yet most interspecific differences remained uncompensated. Our results show the flexibility of TFs to bind imprecise motifs and the fast evolution of TF binding sites between related species.
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Affiliation(s)
- Gat Krieger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Patricia Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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9
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Abstract
Cell fusions have a long history of supporting biomedical research. These experimental models, historically referred to as 'somatic cell hybrids', involve combining the plasma membranes of two cells and merging their nuclei within a single cytoplasm. Cell fusion studies involving human and chimpanzee pluripotent stem cells, rather than somatic cells, highlight the need for responsible communication and a revised nomenclature. Applying the terms 'hybrid' and 'parental' to the fused and source cell lines, respectively, evokes reproductive relationships that do not exist between humans and other species. These misnomers become more salient in the context of fused pluripotent stem cells derived from different but closely related species. Here, we propose a precise, versatile and generalizable framework to describe these fused cell lines. We recommend the term 'composite cell line', to distinguish cell lines that are experimentally created through fusions from both reproductive hybrids and natural cell fusion events without obscuring the model in overly technical terms. For scientific audiences, we further recommend technical nomenclature that describes the contributing species, ploidy and cell type.
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10
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Efficient human-like antibody repertoire and hybridoma production in trans-chromosomic mice carrying megabase-sized human immunoglobulin loci. Nat Commun 2022; 13:1841. [PMID: 35383174 PMCID: PMC8983744 DOI: 10.1038/s41467-022-29421-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/15/2022] [Indexed: 11/15/2022] Open
Abstract
Trans-chromosomic (Tc) mice carrying mini-chromosomes with megabase-sized human immunoglobulin (Ig) loci have contributed to the development of fully human therapeutic monoclonal antibodies, but mitotic instability of human mini-chromosomes in mice may limit the efficiency of hybridoma production. Here, we establish human antibody-producing Tc mice (TC-mAb mice) that stably maintain a mouse-derived, engineered chromosome containing the entire human Ig heavy and kappa chain loci in a mouse Ig-knockout background. Comprehensive, high-throughput DNA sequencing shows that the human Ig repertoire, including variable gene usage, is well recapitulated in TC-mAb mice. Despite slightly altered B cell development and a delayed immune response, TC-mAb mice have more subsets of antigen-specific plasmablast and plasma cells than wild-type mice, leading to efficient hybridoma production. Our results thus suggest that TC-mAb mice offer a valuable platform for obtaining fully human therapeutic antibodies, and a useful model for elucidating the regulation of human Ig repertoire formation. Trans-chromosomic (Tc) mice have helped the development of therapeutic antibodies, but chromosome instability limits its application. Here the authors develop a new line of Tc mice with full human Ig heavy and kappa loci integrated into the mouse artificial chromosome for stable passage, and confirm efficient generation of B cell responses and specific antibodies.
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11
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Kazuki Y, Gao FJ, Yamakawa M, Hirabayashi M, Kazuki K, Kajitani N, Miyagawa-Tomita S, Abe S, Sanbo M, Hara H, Kuniishi H, Ichisaka S, Hata Y, Koshima M, Takayama H, Takehara S, Nakayama Y, Hiratsuka M, Iida Y, Matsukura S, Noda N, Li Y, Moyer AJ, Cheng B, Singh N, Richtsmeier JT, Oshimura M, Reeves RH. A transchromosomic rat model with human chromosome 21 shows robust Down syndrome features. Am J Hum Genet 2022; 109:328-344. [PMID: 35077668 DOI: 10.1016/j.ajhg.2021.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022] Open
Abstract
Progress in earlier detection and clinical management has increased life expectancy and quality of life in people with Down syndrome (DS). However, no drug has been approved to help individuals with DS live independently and fully. Although rat models could support more robust physiological, behavioral, and toxicology analysis than mouse models during preclinical validation, no DS rat model is available as a result of technical challenges. We developed a transchromosomic rat model of DS, TcHSA21rat, which contains a freely segregating, EGFP-inserted, human chromosome 21 (HSA21) with >93% of its protein-coding genes. RNA-seq of neonatal forebrains demonstrates that TcHSA21rat expresses HSA21 genes and has an imbalance in global gene expression. Using EGFP as a marker for trisomic cells, flow cytometry analyses of peripheral blood cells from 361 adult TcHSA21rat animals show that 81% of animals retain HSA21 in >80% of cells, the criterion for a "Down syndrome karyotype" in people. TcHSA21rat exhibits learning and memory deficits and shows increased anxiety and hyperactivity. TcHSA21rat recapitulates well-characterized DS brain morphology, including smaller brain volume and reduced cerebellar size. In addition, the rat model shows reduced cerebellar foliation, which is not observed in DS mouse models. Moreover, TcHSA21rat exhibits anomalies in craniofacial morphology, heart development, husbandry, and stature. TcHSA21rat is a robust DS animal model that can facilitate DS basic research and provide a unique tool for preclinical validation to accelerate DS drug development.
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12
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Cell division- and DNA replication-free reprogramming of somatic nuclei for embryonic transcription. iScience 2021; 24:103290. [PMID: 34849463 PMCID: PMC8609233 DOI: 10.1016/j.isci.2021.103290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/03/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023] Open
Abstract
Nuclear transfer systems represent the efficient means to reprogram a cell and in theory provide a basis for investigating the development of endangered species. However, conventional nuclear transfer using oocytes of laboratory animals does not allow reprogramming of cross-species nuclei owing to defects in cell divisions and activation of embryonic genes. Here, we show that somatic nuclei transferred into mouse four-cell embryos arrested at the G2/M phase undergo reprogramming toward the embryonic state. Remarkably, genome-wide transcriptional reprogramming is induced within a day, and ZFP281 is important for this replication-free reprogramming. This system further enables transcriptional reprogramming of cells from Oryx dammah, now extinct in the wild. Thus, our findings indicate that arrested mouse embryos are competent to induce intra- and cross-species reprogramming. The direct induction of embryonic transcripts from diverse genomes paves a unique approach for identifying mechanisms of transcriptional reprogramming and genome activation from a diverse range of species.
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13
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Tissue context determines the penetrance of regulatory DNA variation. Nat Commun 2021; 12:2850. [PMID: 33990600 PMCID: PMC8121920 DOI: 10.1038/s41467-021-23139-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
Functional assessment of disease-associated sequence variation at non-coding regulatory elements is complicated by their high degree of context sensitivity to both the local chromatin and nuclear environments. Allelic profiling of DNA accessibility across individuals has shown that only a select minority of sequence variation affects transcription factor (TF) occupancy, yet low sequence diversity in human populations means that no experimental assessment is available for the majority of disease-associated variants. Here we describe high-resolution in vivo maps of allelic DNA accessibility in liver, kidney, lung and B cells from 5 increasingly diverged strains of F1 hybrid mice. The high density of heterozygous sites in these hybrids enables precise quantification of effect size and cell-type specificity for hundreds of thousands of variants throughout the mouse genome. We show that chromatin-altering variants delineate characteristic sensitivity profiles for hundreds of TF motifs. We develop a compendium of TF-specific sensitivity profiles accounting for genomic context effects. Finally, we link maps of allelic accessibility to allelic transcript levels in the same samples. This work provides a foundation for quantitative prediction of cell-type specific effects of non-coding variation on TF activity, which will facilitate both fine-mapping and systems-level analyses of common disease-associated variation in human genomes.
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14
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Akerman I, Maestro MA, De Franco E, Grau V, Flanagan S, García-Hurtado J, Mittler G, Ravassard P, Piemonti L, Ellard S, Hattersley AT, Ferrer J. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene. Cell Rep 2021; 35:108981. [PMID: 33852861 PMCID: PMC8052186 DOI: 10.1016/j.celrep.2021.108981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene.
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Affiliation(s)
- Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR), Medical School, University of Birmingham, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK.
| | - Miguel Angel Maestro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Vanessa Grau
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Sarah Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Javier García-Hurtado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Gerhard Mittler
- Max-Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Philippe Ravassard
- INSERM, CNRS, Paris Brain Institute - Hôpital Pitié-Salpêtrière, Paris, France
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK; Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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15
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Mancera E, Nocedal I, Hammel S, Gulati M, Mitchell KF, Andes DR, Nobile CJ, Butler G, Johnson AD. Evolution of the complex transcription network controlling biofilm formation in Candida species. eLife 2021; 10:e64682. [PMID: 33825680 PMCID: PMC8075579 DOI: 10.7554/elife.64682] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
We examine how a complex transcription network composed of seven 'master' regulators and hundreds of target genes evolved over a span of approximately 70 million years. The network controls biofilm formation in several Candida species, a group of fungi that are present in humans both as constituents of the microbiota and as opportunistic pathogens. Using a variety of approaches, we observed two major types of changes that have occurred in the biofilm network since the four extant species we examined last shared a common ancestor. Master regulator 'substitutions' occurred over relatively long evolutionary times, resulting in different species having overlapping but different sets of master regulators of biofilm formation. Second, massive changes in the connections between the master regulators and their target genes occurred over much shorter timescales. We believe this analysis is the first detailed, empirical description of how a complex transcription network has evolved.
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Affiliation(s)
- Eugenio Mancera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad IrapuatoIrapuatoMexico
| | - Isabel Nocedal
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | - Stephen Hammel
- School of Biomolecular and Biomedical Science, Conway Institute, University College DublinDublinIreland
| | - Megha Gulati
- Department of Molecular and Cell Biology, University of California, MercedMercedUnited States
| | - Kaitlin F Mitchell
- Department of Medical Microbiology and Immunology, University of WisconsinMadisonUnited States
| | - David R Andes
- Department of Medical Microbiology and Immunology, University of WisconsinMadisonUnited States
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, MercedMercedUnited States
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College DublinDublinIreland
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
- Microbiome Initiative, Chan Zuckerberg BiohubSan FranciscoUnited States
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16
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Umans BD, Battle A, Gilad Y. Where Are the Disease-Associated eQTLs? Trends Genet 2021; 37:109-124. [PMID: 32912663 PMCID: PMC8162831 DOI: 10.1016/j.tig.2020.08.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem, mostly from adults. In this review we evaluate recent findings and suggest an alternative strategy, drawing on the dynamic and highly context-specific nature of gene regulation. We discuss new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states.
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Affiliation(s)
- Benjamin D Umans
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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17
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De Toma I, Dierssen M. Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19. Sci Rep 2021; 11:1930. [PMID: 33479353 PMCID: PMC7820501 DOI: 10.1038/s41598-021-81451-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 infection has spread uncontrollably worldwide while it remains unknown how vulnerable populations, such as Down syndrome (DS) individuals are affected by the COVID-19 pandemic. Individuals with DS have more risk of infections with respiratory complications and present signs of auto-inflammation. They also present with multiple comorbidities that are associated with poorer COVID-19 prognosis in the general population. All this might place DS individuals at higher risk of SARS-CoV-2 infection or poorer clinical outcomes. In order to get insight into the interplay between DS genes and SARS-cov2 infection and pathogenesis we identified the genes associated with the molecular pathways involved in COVID-19 and the host proteins interacting with viral proteins from SARS-CoV-2. We then analyzed the overlaps of these genes with HSA21 genes, HSA21 interactors and other genes consistently differentially expressed in DS (using public transcriptomic datasets) and created a DS-SARS-CoV-2 network. We detected COVID-19 protective and risk factors among HSA21 genes and interactors and/or DS deregulated genes that might affect the susceptibility of individuals with DS both at the infection stage and in the progression to acute respiratory distress syndrome. Our analysis suggests that at the infection stage DS individuals might be more susceptible to infection due to triplication of TMPRSS2, that primes the viral S protein for entry in the host cells. However, as the anti-viral interferon I signaling is also upregulated in DS, this might increase the initial anti-viral response, inhibiting viral genome release, viral replication and viral assembly. In the second pro-inflammatory immunopathogenic phase of the infection, the prognosis for DS patients might worsen due to upregulation of inflammatory genes that might favor the typical cytokine storm of COVID-19. We also detected strong downregulation of the NLRP3 gene, critical for maintenance of homeostasis against pathogenic infections, possibly leading to bacterial infection complications.
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Affiliation(s)
- Ilario De Toma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Biomedical Research Networking Center On Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.
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18
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Chen L, Capra JA. Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput Biol 2020; 16:e1008334. [PMID: 33137083 PMCID: PMC7660921 DOI: 10.1371/journal.pcbi.1008334] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 11/12/2020] [Accepted: 09/12/2020] [Indexed: 12/12/2022] Open
Abstract
Deep neural networks (DNNs) have achieved state-of-the-art performance in identifying gene regulatory sequences, but they have provided limited insight into the biology of regulatory elements due to the difficulty of interpreting the complex features they learn. Several models of how combinatorial binding of transcription factors, i.e. the regulatory grammar, drives enhancer activity have been proposed, ranging from the flexible TF billboard model to the stringent enhanceosome model. However, there is limited knowledge of the prevalence of these (or other) sequence architectures across enhancers. Here we perform several hypothesis-driven analyses to explore the ability of DNNs to learn the regulatory grammar of enhancers. We created synthetic datasets based on existing hypotheses about combinatorial transcription factor binding site (TFBS) patterns, including homotypic clusters, heterotypic clusters, and enhanceosomes, from real TF binding motifs from diverse TF families. We then trained deep residual neural networks (ResNets) to model the sequences under a range of scenarios that reflect real-world multi-label regulatory sequence prediction tasks. We developed a gradient-based unsupervised clustering method to extract the patterns learned by the ResNet models. We demonstrated that simulated regulatory grammars are best learned in the penultimate layer of the ResNets, and the proposed method can accurately retrieve the regulatory grammar even when there is heterogeneity in the enhancer categories and a large fraction of TFBS outside of the regulatory grammar. However, we also identify common scenarios where ResNets fail to learn simulated regulatory grammars. Finally, we applied the proposed method to mouse developmental enhancers and were able to identify the components of a known heterotypic TF cluster. Our results provide a framework for interpreting the regulatory rules learned by ResNets, and they demonstrate that the ability and efficiency of ResNets in learning the regulatory grammar depends on the nature of the prediction task.
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Affiliation(s)
- Ling Chen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Genetics Institute and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Computer Science, Vanderbilt University, Nashville, TN, United States of America
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19
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Zeitlinger J. Seven myths of how transcription factors read the cis-regulatory code. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 23:22-31. [PMID: 33134611 PMCID: PMC7592701 DOI: 10.1016/j.coisb.2020.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genomics data are now being generated at large quantities, of exquisite high resolution and from single cells. They offer a unique opportunity to develop powerful machine learning algorithms, including neural networks, to uncover the rules of the cis-regulatory code. However, current modeling assumptions are often not based on state-of-the-art knowledge of the cis-regulatory code from transcription, developmental genetics, imaging and structural studies. Here I aim to fill this gap by giving a brief historical overview of the field, describing common misconceptions and providing knowledge that might help to guide computational approaches. I will describe the principles and mechanisms involved in the combinatorial requirement of transcription factor binding motifs for enhancer activity, including the role of chromatin accessibility, repressors and low-affinity motifs in the cis-regulatory code. Deciphering the cis-regulatory code would unlock an enormous amount of regulatory information in the genome and would allow us to locate cis-regulatory genetic variants involved in development and disease.
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Affiliation(s)
- Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
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20
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Mattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Melé M. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol 2020; 21:210. [PMID: 32819422 PMCID: PMC7439725 DOI: 10.1186/s13059-020-02110-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure cis and trans effects between human and mouse. RESULTS Our approach reveals that cis effects are widespread across transcribed regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that trans effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that cis-trans compensation is common within promoters, we do not see evidence of widespread cis-trans compensation at enhancers. Cis-trans compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers. CONCLUSIONS Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.
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Affiliation(s)
- Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel Andergassen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Philipp G Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - John L Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO, 80301, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain.
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21
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Kelley DR. Cross-species regulatory sequence activity prediction. PLoS Comput Biol 2020; 16:e1008050. [PMID: 32687525 PMCID: PMC7392335 DOI: 10.1371/journal.pcbi.1008050] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 07/30/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022] Open
Abstract
Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, model organisms have been less explored. Model organism genomes offer both additional training sequences and unique annotations describing tissue and cell states unavailable in humans. Here, we develop a strategy to train deep convolutional neural networks simultaneously on multiple genomes and apply it to learn sequence predictors for large compendia of human and mouse data. Training on both genomes improves gene expression prediction accuracy on held out and variant sequences. We further demonstrate a novel and powerful approach to apply mouse regulatory models to analyze human genetic variants associated with molecular phenotypes and disease. Together these techniques unleash thousands of non-human epigenetic and transcriptional profiles toward more effective investigation of how gene regulation affects human disease.
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Affiliation(s)
- David R. Kelley
- Calico Life Sciences, South San Francisco, California, United States of America
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22
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Gallardo-Fuentes L, Santos-Pereira JM, Tena JJ. Functional Conservation of Divergent p63-Bound cis-Regulatory Elements. Front Genet 2020; 11:339. [PMID: 32411176 PMCID: PMC7200997 DOI: 10.3389/fgene.2020.00339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/20/2020] [Indexed: 11/26/2022] Open
Abstract
The transcription factor p63 is an essential regulator of vertebrate ectoderm development, including epidermis, limbs, and craniofacial tissues. Here, we have investigated the evolutionary conservation of p63 binding sites (BSs) between zebrafish and human. First, we have analyzed sequence conservation of p63 BSs by comparing ChIP-seq data from human keratinocytes and zebrafish embryos, observing a very poor conservation. Next, we compared the gene regulatory network orchestrated by p63 in both species and found a high overlap between them, suggesting a high degree of functional conservation during evolution despite sequence divergence and the large evolutionary distance. Finally, we used transgenic reporter assays in zebrafish embryos to functionally validate a set of equivalent p63 BSs from zebrafish and human located close to genes involved in epidermal development. Reporter expression was driven by human and zebrafish BSs to many common tissues related to p63 expression domains. Therefore, we conclude that the gene regulatory network controlled by p63 is highly conserved across vertebrates despite the fact that p63-bound regulatory elements show high divergence.
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Affiliation(s)
- Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M Santos-Pereira
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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23
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Genome-wide impacts of alien chromatin introgression on wheat gene transcriptions. Sci Rep 2020; 10:4801. [PMID: 32179864 PMCID: PMC7076028 DOI: 10.1038/s41598-020-61888-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/04/2020] [Indexed: 01/29/2023] Open
Abstract
Agronomic characteristics and tolerance to biotic and abiotic stresses in hexaploid wheat can be drastically improved through wheat-alien introgression. However, the transcriptional level interactions of introduced alien genes in the wheat genetic background is rarely investigated. In this study, we report the genome-wide impacts of introgressed chromosomes derived from Ae. longissima on gene transcriptions of the wheat landrace Chinese Spring. RNA-seq analyses demonstrated 5.37% and 4.30% of the genes were significantly differentially expressed (DEGs) in CS-Ae. longissima disomic 3Sl#2(3B) substitution line TA3575 and disomic 6Sl#3 addition line TA7548, respectively when compared to CS. In addition, 561 DEGs, including 413 up-regulated and 148 down-regulated or not transcribed genes, were simultaneously impacted by introgressed chromosomes 3Sl#2 and 6Sl#3, which accounts for 41.25% of the DEGs in TA3575 and 38.79% in TA7548. Seventeen DEGs, annotated as R genes, were shared by both introgression lines carrying chromosomes 3Sl#2 and 6Sl#3, which confer resistance to powdery mildew. This study will benefit the understanding of the wheat gene responses as result of alien gene(s) or chromosome intogression and the plant defense response initiated by powdery mildew resistance genes in chromosomes 3Sl#2 and 6Sl#3.
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24
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Martínez de Lagrán M. Mapping behavioral landscapes in Down syndrome animal models. PROGRESS IN BRAIN RESEARCH 2020; 251:145-179. [DOI: 10.1016/bs.pbr.2020.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Cornelissen LM, Henneman L, Drenth AP, Schut E, de Bruijn R, Klarenbeek S, Zwart W, Jonkers J. Exogenous ERα Expression in the Mammary Epithelium Decreases Over Time and Does Not Contribute to p53-Deficient Mammary Tumor Formation in Mice. J Mammary Gland Biol Neoplasia 2019; 24:305-321. [PMID: 31729597 DOI: 10.1007/s10911-019-09437-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/09/2019] [Indexed: 12/09/2022] Open
Abstract
Approximately 75% of all breast cancers express the nuclear hormone receptor estrogen receptor α (ERα). However, the majority of mammary tumors from genetically engineered mouse models (GEMMs) are ERα-negative. To model ERα-positive breast cancer in mice, we exogenously introduced expression of mouse and human ERα in an existing GEMM of p53-deficient breast cancer. After initial ERα expression during mammary gland development, expression was reduced or lost in adult glands and p53-deficient mammary tumors. Chromatin immunoprecipitation (ChIP)-sequencing analysis of primary mouse mammary epithelial cells (MMECs) derived from these models, in which expression of the ERα constructs was induced in vitro, confirmed interaction of ERα with the DNA. In human breast and endometrial cancer, and also in healthy breast tissue, DNA binding of ERα is facilitated by the pioneer factor FOXA1. Surprisingly, the ERα binding sites identified in primary MMECs, but also in mouse mammary gland and uterus, showed an high enrichment of ERE motifs, but were devoid of Forkhead motifs. Furthermore, exogenous introduction of FOXA1 and GATA3 in ERα-expressing MMECs was not sufficient to promote ERα-responsiveness of these cells. Together, this suggests that species-specific differences in pioneer factor usage between mouse and human are dictated by the DNA sequence, resulting in ERα-dependencies in mice that are not FOXA1 driven. These species-specific differences in ERα-biology may limit the utility of mice for in vivo modeling of ERα-positive breast cancer.
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Affiliation(s)
- Lisette M Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Linda Henneman
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
- Mouse Clinic for Cancer and Aging - Transgenic facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands
| | - Anne Paulien Drenth
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Eva Schut
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
- Division of Molecular Carcinogenisis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, Eindhoven, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
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26
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Striedter GF. Variation across Species and Levels: Implications for Model Species Research. BRAIN, BEHAVIOR AND EVOLUTION 2019; 93:57-69. [PMID: 31416083 DOI: 10.1159/000499664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/08/2019] [Indexed: 11/19/2022]
Abstract
The selection of model species tends to involve two typically unstated assumptions, namely: (1) that the similarity between species decreases steadily with phylogenetic distance, and (2) that similarities are greater at lower levels of biological organization. The first assumption holds on average, but species similarities tend to decrease with the square root of divergence time, rather than linearly, and lineages with short generation times (which includes most model species) tend to diverge faster than average, making the decrease in similarity non-monotonic. The second assumption is more difficult to test. Comparative molecular research has traditionally emphasized species similarities over differences, whereas comparative research at higher levels of organization frequently highlights the species differences. However, advances in comparative genomics have brought to light a great variety of species differences, not just in gene regulation but also in protein coding genes. Particularly relevant are cases in which homologous high-level characters are based on non-homologous genes. This phenomenon of non-orthologous gene displacement, or "deep non-homology," indicates that species differences at the molecular level can be surprisingly large. Given these observations, it is not surprising that some findings obtained in model species do not generalize across species as well as researchers had hoped, even if the research is molecular.
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Affiliation(s)
- Georg F Striedter
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA,
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27
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Dong Z, Yu J, Li H, Huang W, Xu L, Zhao Y, Zhang T, Xu W, Jiang J, Su Z, Jin W. Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines. Nucleic Acids Res 2019; 46:5012-5028. [PMID: 29579310 PMCID: PMC6007749 DOI: 10.1093/nar/gky209] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize chromosomes in two oat–maize addition (OMA) lines. We found that the majority of maize genes displayed maize-specific transcription in the oat genomic environment. Nevertheless, a quarter of the expressed genes encoded by the two maize chromosomes were differentially expressed genes (DEGs). Notably, highly conserved orthologs were more severely differentially expressed in OMAs than less conserved orthologs. Additionally, syntenic genes and highly abundant genes were over-represented among DEGs. Gene suppression was more common than activation among the DEGs; however, the genes in the former maize pericentromere, which expanded to become the new centromere in OMAs, were activated. Histone modifications (H3K4me3, H3K9ac and H3K27me3) were consistent with these transcriptome results. We expect that cis regulation is responsible for unchanged expression in OMA versus maize; and trans regulation is the predominant mechanism behind DEGs. The genome interaction identified here reveals the important consequences of interspecific/intergeneric crosses and potential mechanisms of plant evolution when genomic environments interact.
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Affiliation(s)
- Zhaobin Dong
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China.,Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, CA 94710, USA
| | - Juan Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Hui Li
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Wei Huang
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Ling Xu
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China.,Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, CA 94710, USA
| | - Yue Zhao
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 10093, P. R. China
| | - Weiwei Jin
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China
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Nair RR, Corrochano S, Gasco S, Tibbit C, Thompson D, Maduro C, Ali Z, Fratta P, Arozena AA, Cunningham TJ, Fisher EMC. Uses for humanised mouse models in precision medicine for neurodegenerative disease. Mamm Genome 2019; 30:173-191. [PMID: 31203387 PMCID: PMC6759662 DOI: 10.1007/s00335-019-09807-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 05/11/2019] [Indexed: 12/11/2022]
Abstract
Neurodegenerative disease encompasses a wide range of disorders afflicting the central and peripheral nervous systems and is a major unmet biomedical need of our time. There are very limited treatments, and no cures, for most of these diseases, including Alzheimer's Disease, Parkinson's Disease, Huntington Disease, and Motor Neuron Diseases. Mouse and other animal models provide hope by analysing them to understand pathogenic mechanisms, to identify drug targets, and to develop gene therapies and stem cell therapies. However, despite many decades of research, virtually no new treatments have reached the clinic. Increasingly, it is apparent that human heterogeneity within clinically defined neurodegenerative disorders, and between patients with the same genetic mutations, significantly impacts disease presentation and, potentially, therapeutic efficacy. Therefore, stratifying patients according to genetics, lifestyle, disease presentation, ethnicity, and other parameters may hold the key to bringing effective therapies from the bench to the clinic. Here, we discuss genetic and cellular humanised mouse models, and how they help in defining the genetic and environmental parameters associated with neurodegenerative disease, and so help in developing effective precision medicine strategies for future healthcare.
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Affiliation(s)
- Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Silvia Corrochano
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Samanta Gasco
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Charlotte Tibbit
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Cheryl Maduro
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Zeinab Ali
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Abraham Acevedo Arozena
- Unidad de Investigación Hospital Universitario de Canarias, FUNCANIS, Instituto de Tecnologías Biomédicas ULL, and CIBERNED, La Laguna, 38320, Tenerife, Spain
| | | | - Elizabeth M C Fisher
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK.
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK.
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29
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Elevated TREM2 Gene Dosage Reprograms Microglia Responsivity and Ameliorates Pathological Phenotypes in Alzheimer's Disease Models. Neuron 2019. [PMID: 29518357 DOI: 10.1016/j.neuron.2018.02.002] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Variants of TREM2 are associated with Alzheimer's disease (AD). To study whether increasing TREM2 gene dosage could modify the disease pathogenesis, we developed BAC transgenic mice expressing human TREM2 (BAC-TREM2) in microglia. We found that elevated TREM2 expression reduced amyloid burden in the 5xFAD mouse model. Transcriptomic profiling demonstrated that increasing TREM2 levels conferred a rescuing effect, which includes dampening the expression of multiple disease-associated microglial genes and augmenting downregulated neuronal genes. Interestingly, 5xFAD/BAC-TREM2 mice showed further upregulation of several reactive microglial genes linked to phagocytosis and negative regulation of immune cell activation. Moreover, these mice showed enhanced process ramification and phagocytic marker expression in plaque-associated microglia and reduced neuritic dystrophy. Finally, elevated TREM2 gene dosage led to improved memory performance in AD models. In summary, our study shows that a genomic transgene-driven increase in TREM2 expression reprograms microglia responsivity and ameliorates neuropathological and behavioral deficits in AD mouse models.
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30
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Zhu F, Nair RR, Fisher EMC, Cunningham TJ. Humanising the mouse genome piece by piece. Nat Commun 2019; 10:1845. [PMID: 31015419 PMCID: PMC6478830 DOI: 10.1038/s41467-019-09716-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/23/2019] [Indexed: 12/14/2022] Open
Abstract
To better understand human health and disease, researchers create a wide variety of mouse models that carry human DNA. With recent advances in genome engineering, the targeted replacement of mouse genomic regions with orthologous human sequences has become increasingly viable, ranging from finely tuned humanisation of individual nucleotides and amino acids to the incorporation of many megabases of human DNA. Here, we examine emerging technologies for targeted genomic humanisation, we review the spectrum of existing genomically humanised mouse models and the insights such models have provided, and consider the lessons learned for designing such models in the future. Generation of transgenic mice has become routine in studying gene function and disease mechanisms, but often this is not enough to fully understand human biology. Here, the authors review the current state of the art of targeted genomic humanisation strategies and their advantages over classic approaches.
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Affiliation(s)
- Fei Zhu
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK.
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31
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Alexandre CM, Urton JR, Jean-Baptiste K, Huddleston J, Dorrity MW, Cuperus JT, Sullivan AM, Bemm F, Jolic D, Arsovski AA, Thompson A, Nemhauser JL, Fields S, Weigel D, Bubb KL, Queitsch C. Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. Mol Biol Evol 2019; 35:837-854. [PMID: 29272536 DOI: 10.1093/molbev/msx326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.
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Affiliation(s)
| | - James R Urton
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dino Jolic
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | | | - Stan Fields
- Department of Genome Sciences, University of Washington, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Christin Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA
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32
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Laurent JM, Fu X, German S, Maurano MT, Zhang K, Boeke JD. Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype. PRECISION CLINICAL MEDICINE 2019; 2:1-7. [PMID: 30944767 PMCID: PMC6432742 DOI: 10.1093/pcmedi/pby019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/24/2018] [Indexed: 11/13/2022] Open
Abstract
Age-related Macular Degeneration (AMD) is a leading cause of blindness in the developed world, especially in aging populations, and is therefore an important target for new therapeutic development. Recently, there have been several studies demonstrating strong associations between AMD and sites of heritable genetic variation at multiple loci, including a highly significant association at 10q26. The 10q26 risk region contains two genes, HTRA1 and ARMS2, both of which have been separately implicated as causative for the disease, as well as dozens of sites of non-coding variation. To date, no studies have successfully pinpointed which of these variant sites are functional in AMD, nor definitively identified which genes in the region are targets of such regulatory variation. In order to efficiently decipher which sites are functional in AMD phenotypes, we describe a general framework for combinatorial assembly of large ‘synthetic haplotypes’ along with delivery to relevant disease cell types for downstream functional analysis. We demonstrate the successful and highly efficient assembly of a first-draft 119kb wild-type ‘assemblon’ covering the HTRA1/ARMS2 risk region. We further propose the parallelized assembly of a library of combinatorial variant synthetic haplotypes covering the region, delivery and analysis of which will identify functional sites and their effects, leading to an improved understanding of AMD development. We anticipate that the methodology proposed here is highly generalizable towards the difficult problem of identifying truly functional variants from those discovered via GWAS or other genetic association studies.
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Affiliation(s)
- Jon M Laurent
- Institute for Systems Genetics.,Department of Biochemistry and Molecular Pathology
| | - Xin Fu
- Shiley Eye Institute, UCSD School of Medicine
| | - Sergei German
- Institute for Systems Genetics.,Department of Biochemistry and Molecular Pathology
| | - Matthew T Maurano
- Institute for Systems Genetics.,Department of Pathology, NYU Langone Health
| | - Kang Zhang
- Shiley Eye Institute, UCSD School of Medicine
| | - Jef D Boeke
- Institute for Systems Genetics.,Department of Biochemistry and Molecular Pathology
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33
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Chen L, Fish AE, Capra JA. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol 2018; 14:e1006484. [PMID: 30286077 PMCID: PMC6191148 DOI: 10.1371/journal.pcbi.1006484] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 10/16/2018] [Accepted: 09/02/2018] [Indexed: 12/30/2022] Open
Abstract
Genomic regions with gene regulatory enhancer activity turnover rapidly across mammals. In contrast, gene expression patterns and transcription factor binding preferences are largely conserved between mammalian species. Based on this conservation, we hypothesized that enhancers active in different mammals would exhibit conserved sequence patterns in spite of their different genomic locations. To investigate this hypothesis, we evaluated the extent to which sequence patterns that are predictive of enhancers in one species are predictive of enhancers in other mammalian species by training and testing two types of machine learning models. We trained support vector machine (SVM) and convolutional neural network (CNN) classifiers to distinguish enhancers defined by histone marks from the genomic background based on DNA sequence patterns in human, macaque, mouse, dog, cow, and opossum. The classifiers accurately identified many adult liver, developing limb, and developing brain enhancers, and the CNNs outperformed the SVMs. Furthermore, classifiers trained in one species and tested in another performed nearly as well as classifiers trained and tested on the same species. We observed similar cross-species conservation when applying the models to human and mouse enhancers validated in transgenic assays. This indicates that many short sequence patterns predictive of enhancers are largely conserved. The sequence patterns most predictive of enhancers in each species matched the binding motifs for a common set of TFs enriched for expression in relevant tissues, supporting the biological relevance of the learned features. Thus, despite the rapid change of active enhancer locations between mammals, cross-species enhancer prediction is often possible. Our results suggest that short sequence patterns encoding enhancer activity have been maintained across more than 180 million years of mammalian evolution.
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Affiliation(s)
- Ling Chen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - Alexandra E. Fish
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, United States of America
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, United States of America
- Departments of Biomedical Informatics and Computer Science, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
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34
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Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1423. [PMID: 29694718 PMCID: PMC6202284 DOI: 10.1002/wsbm.1423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 03/11/2018] [Indexed: 01/17/2023]
Abstract
Sequence-specific transcription factors (TFs) bind short DNA sequences in the genome to regulate the expression of target genes. In the last decade, numerous technical advances have enabled the determination of the DNA-binding specificities of many of these factors. Large-scale screens of many TFs enabled the creation of databases of TF DNA-binding specificities, typically represented as position weight matrices (PWMs). Although great progress has been made in determining and predicting binding specificities systematically, there are still many surprises to be found when studying a particular TF's interactions with DNA in detail. Paralogous TFs' binding specificities can differ in subtle ways, in a manner that is not immediately apparent from looking at their PWMs. These differences affect gene regulatory outputs and enable TFs to rewire transcriptional networks over evolutionary time. This review discusses recent observations made in the study of TF-DNA interactions that highlight the importance of continued in-depth analysis of TF-DNA interactions and their inherent complexity. This article is categorized under: Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Julia M. Rogers
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA,Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
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35
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Fish A, Chen L, Capra JA. Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity. Genome Biol Evol 2018; 9:2615-2625. [PMID: 28985297 PMCID: PMC5737616 DOI: 10.1093/gbe/evx194] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2017] [Indexed: 12/31/2022] Open
Abstract
Studies of regulatory activity and gene expression have revealed an intriguing dichotomy: There is substantial turnover in the regulatory activity of orthologous sequences between species; however, the expression level of orthologous genes is largely conserved. Understanding how distal regulatory elements, for example, enhancers, evolve and function is critical, as alterations in gene expression levels can drive the development of both complex disease and functional divergence between species. In this study, we investigated determinants of the conservation of regulatory enhancer activity for orthologous sequences across mammalian evolution. Using liver enhancers identified from genome-wide histone modification profiles in ten diverse mammalian species, we compared orthologous sequences that exhibited regulatory activity in all species (conserved-activity enhancers) to shared sequences active only in a single species (species-specific-activity enhancers). Conserved-activity enhancers have greater regulatory potential than species-specific-activity enhancers, as quantified by both the density and diversity of transcription factor binding motifs. Consistent with their greater regulatory potential, conserved-activity enhancers have greater regulatory activity in humans than species-specific-activity enhancers: They are active across more cellular contexts, and they regulate more genes than species-specific-activity enhancers. Furthermore, the genes regulated by conserved-activity enhancers are expressed in more tissues and are less tolerant of loss-of-function mutations than those targeted by species-specific-activity enhancers. These consistent results across various stages of gene regulation demonstrate that conserved-activity enhancers are more pleiotropic than their species-specific-activity counterparts. This suggests that pleiotropy is associated with the conservation of regulatory across mammalian evolution.
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Affiliation(s)
- Alexandra Fish
- Vanderbilt Genetics Institute, Vanderbilt University.,Department of Biological Sciences, Vanderbilt Genetics Institute, Vanderbilt University
| | - Ling Chen
- Department of Biological Sciences, Vanderbilt Genetics Institute, Vanderbilt University
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University.,Department of Biological Sciences, Vanderbilt Genetics Institute, Vanderbilt University.,Departments of Biomedical Informatics and Computer Science, Center for Structural Biology, Vanderbilt University
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36
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Production of a Human Cell Line with a Plant Chromosome. Methods Mol Biol 2018. [PMID: 29754235 DOI: 10.1007/978-1-4939-7795-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
It is a major challenge in biology to know whether chromosome functions of replication, segregation, gene expression, inheritance, etc. are conserved among evolutionary distant organisms where common structural features are maintained. Establishment of hybrid cell lines between evolutionary distant organisms, such as humans and plants, would be one of the promising synthetic approaches to study the evolutionary conservation of chromosome functions. In this chapter, we describe the protocol for successful establishment of human cell lines with a functional plant chromosome. Systematic analyses of hybrid cells will facilitate the evolutionary study of organisms with respect to chromosome functions. It will also provide a basic platform for genome writing and construction of chromosomal shuttle vectors .
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37
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Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. eLife 2018; 7:33084. [PMID: 29648536 PMCID: PMC5943035 DOI: 10.7554/elife.33084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from 10 human and 7 chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across 6 million years of primate evolution.
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Affiliation(s)
- Michelle C Ward
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
| | - Siming Zhao
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Mohammad M Karimi
- MRC London Institute of Medical Sciences, Imperial College, London, United Kingdom
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
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38
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Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
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Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
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39
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Lowe R, Barton C, Jenkins CA, Ernst C, Forman O, Fernandez-Twinn DS, Bock C, Rossiter SJ, Faulkes CG, Ozanne SE, Walter L, Odom DT, Mellersh C, Rakyan VK. Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species. Genome Biol 2018; 19:22. [PMID: 29452591 PMCID: PMC5815211 DOI: 10.1186/s13059-018-1397-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/19/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ageing-associated differentially methylated positions (aDMPs) in human and mouse. These are CpG sites at which DNA methylation dynamics show significant correlations with age. We hypothesise that aDMPs are pan-mammalian and are a dynamic molecular readout of lifespan variation among different mammalian species. RESULTS A large-scale integrated analysis of aDMPs in six different mammals reveals a strong negative relationship between rate of change of methylation levels at aDMPs and lifespan. This relationship also holds when comparing two different dog breeds with known differences in lifespans. In an ageing cohort of aneuploid mice carrying a complete copy of human chromosome 21, aDMPs accumulate far more rapidly than is seen in human tissues, revealing that DNA methylation at aDMP sites is largely shaped by the nuclear trans-environment and represents a robust molecular readout of the ageing cellular milieu. CONCLUSIONS Overall, we define the first dynamic molecular readout of lifespan differences among mammalian species and propose that aDMPs will be an invaluable molecular tool for future evolutionary and mechanistic studies aimed at understanding the biological factors that determine lifespan in mammals.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - Carl Barton
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | | | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Oliver Forman
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - Denise S Fernandez-Twinn
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Susan E Ozanne
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Lutz Walter
- Primate Genetics Laboratory, Leibniz Institute for Primate Research, German Primate Center, Göttingen, Germany
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Cathryn Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
- Centre for Genomic Health, Queen Mary University of London, EC1M 6BQ, London, UK.
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40
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Sokhi UK, Liber MP, Frye L, Park S, Kang K, Pannellini T, Zhao B, Norinsky R, Ivashkiv LB, Gong S. Dissection and function of autoimmunity-associated TNFAIP3 (A20) gene enhancers in humanized mouse models. Nat Commun 2018; 9:658. [PMID: 29440643 PMCID: PMC5811492 DOI: 10.1038/s41467-018-03081-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 01/18/2018] [Indexed: 12/18/2022] Open
Abstract
Enhancers regulate gene expression and have been linked with disease pathogenesis. Little is known about enhancers that regulate human disease-associated genes in primary cells relevant for pathogenesis. Here we use BAC transgenics and genome editing to dissect, in vivo and in primary immune cells, enhancers that regulate human TNFAIP3, which encodes A20 and is linked with autoimmune diseases. A20 expression is dependent on a topologically associating subdomain (sub-TAD) that harbors four enhancers, while another >20 enhancers in the A20 locus are redundant. This sub-TAD contains cell- and activation-specific enhancers, including an enhancer (termed TT>A) harboring a proposed causal SLE-associated SNV. Deletion of the sub-TAD or the TT>A enhancer results in enhanced inflammatory responses, autoantibody production, and inflammatory arthritis, thus establishing functional importance in vivo and linking enhancers with a specific disease phenotype. These findings provide insights into enhancers that regulate human A20 expression to prevent inflammatory pathology and autoimmunity. The human TNFAIP3 gene, which encodes for A20, is associated with autoimmune diseases. Here, the authors use BAC transgenics combined with CRISPR- and recombineering-mediated genome editing to dissect in vivo and in primary immune cells, the role of enhancers regulating TNFAIP3.
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Affiliation(s)
- Upneet K Sokhi
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Mark P Liber
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Laura Frye
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Sungho Park
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Kyuho Kang
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Tania Pannellini
- Research Division and Department of Pathology, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA
| | | | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA. .,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Medicine, New York, NY, 10065, USA. .,Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Shiaoching Gong
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Center for Genomic Research, Hospital for Special Surgery, New York, NY, 10021, USA. .,Rockefeller University, New York, NY, 10065, USA.
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41
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Deveson IW, Brunck ME, Blackburn J, Tseng E, Hon T, Clark TA, Clark MB, Crawford J, Dinger ME, Nielsen LK, Mattick JS, Mercer TR. Universal Alternative Splicing of Noncoding Exons. Cell Syst 2018; 6:245-255.e5. [DOI: 10.1016/j.cels.2017.12.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 10/18/2017] [Accepted: 12/08/2017] [Indexed: 01/31/2023]
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42
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Dynamic evolution of regulatory element ensembles in primate CD4 + T cells. Nat Ecol Evol 2018; 2:537-548. [PMID: 29379187 DOI: 10.1038/s41559-017-0447-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
How evolutionary changes at enhancers affect the transcription of target genes remains an important open question. Previous comparative studies of gene expression have largely measured the abundance of messenger RNA, which is affected by post-transcriptional regulatory processes, hence limiting inferences about the mechanisms underlying expression differences. Here, we directly measured nascent transcription in primate species, allowing us to separate transcription from post-transcriptional regulation. We used precision run-on and sequencing to map RNA polymerases in resting and activated CD4+ T cells in multiple human, chimpanzee and rhesus macaque individuals, with rodents as outgroups. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Genes regulated by larger numbers of enhancers are more frequently transcribed at evolutionarily stable levels, despite reduced conservation at individual enhancers. Adaptive nucleotide substitutions are associated with lineage-specific transcription and at one locus, SGPP2, we predict and experimentally validate that multiple substitutions contribute to human-specific transcription. Collectively, our findings suggest a pervasive role for evolutionary compensation across ensembles of enhancers that jointly regulate target genes.
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43
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Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny. PLoS One 2017; 12:e0188357. [PMID: 29200426 PMCID: PMC5714339 DOI: 10.1371/journal.pone.0188357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/06/2017] [Indexed: 01/01/2023] Open
Abstract
The insulin/TOR signal transduction pathway plays a critical role in determining such important traits as body and organ size, metabolic homeostasis and life span. Although this pathway is highly conserved across the animal kingdom, the affected traits can exhibit important differences even between closely related species. Evolutionary studies of regulatory regions require the reliable identification of transcription factor binding sites. Here we have focused on the Insulin Receptor (InR) expression from its P2 promoter in the Drosophila genus, which in D. melanogaster is up-regulated by hypophosphorylated Drosophila FOXO (dFOXO). We have finely characterized this transcription factor binding sites in vitro along the 1.3 kb region upstream of the InR P2 promoter in five Drosophila species. Moreover, we have tested the effect of mutations in the characterized dFOXO sites of D. melanogaster in transgenic flies. The number of experimentally established binding sites varies across the 1.3 kb region of any particular species, and their distribution also differs among species. In D. melanogaster, InR expression from P2 is differentially affected by dFOXO binding sites at the proximal and distal halves of the species 1.3 kb fragment. The observed uneven distribution of binding sites across this fragment might underlie their differential contribution to regulate InR transcription.
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44
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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species. Proc Natl Acad Sci U S A 2017; 114:E11037-E11046. [PMID: 29203652 PMCID: PMC5754749 DOI: 10.1073/pnas.1618075114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1 Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
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45
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Simonti CN, Pavličev M, Capra JA. Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints. Mol Biol Evol 2017; 34:2856-2869. [PMID: 28961735 PMCID: PMC5850124 DOI: 10.1093/molbev/msx219] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transposable element (TE)-derived sequences make up approximately half of most mammalian genomes, and many TEs have been co-opted into gene regulatory elements. However, we lack a comprehensive tissue- and genome-wide understanding of how and when TEs gain regulatory activity in their hosts. We evaluated the prevalence of TE-derived DNA in enhancers and promoters across hundreds of human and mouse cell lines and primary tissues. Promoters are significantly depleted of TEs in all tissues compared with their overall prevalence in the genome (P < 0.001); enhancers are also depleted of TEs, though not as strongly as promoters. The degree of enhancer depletion also varies across contexts (1.5-3×), with reproductive and immune cells showing the highest levels of TE regulatory activity in humans. Overall, in spite of the regulatory potential of many TE sequences, they are significantly less active in gene regulation than expected from their prevalence. TE age is predictive of the likelihood of enhancer activity; TEs originating before the divergence of amniotes are 9.2 times more likely to have enhancer activity than TEs that integrated in great apes. Context-specific enhancers are more likely to be TE-derived than enhancers active in multiple tissues, and young TEs are more likely to overlap context-specific enhancers than old TEs (86% vs. 47%). Once TEs obtain enhancer activity in the host, they have similar functional dynamics to one another and non-TE-derived enhancers, likely driven by pleiotropic constraints. However, a few TE families, most notably endogenous retroviruses, have greater regulatory potential. Our observations suggest a model of regulatory co-option in which TE-derived sequences are initially repressed, after which a small fraction obtains context-specific enhancer activity, with further gains subject to pleiotropic constraints.
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Affiliation(s)
| | - Mihaela Pavličev
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - John A. Capra
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
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46
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Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution. Nat Commun 2017; 8:1092. [PMID: 29061983 PMCID: PMC5653656 DOI: 10.1038/s41467-017-01037-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/09/2017] [Indexed: 12/23/2022] Open
Abstract
Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.
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Affiliation(s)
- Emily S Wong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Bianca M Schmitt
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | | | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aisling Redmond
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Frances Connor
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Tim F Rayner
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Christine Feig
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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47
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Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR. Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biol 2017; 18:167. [PMID: 28877740 PMCID: PMC5588721 DOI: 10.1186/s13059-017-1287-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/14/2017] [Indexed: 02/07/2023] Open
Abstract
Background The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. Results Here, we show that the C2H2-ZF expansion in metazoans is facilitated by contribution of non-base-contacting residues to DNA binding energy, allowing base-contacting specificity residues to mutate without catastrophic loss of DNA binding. In contrast, C2H2-ZF DNA binding in fungi, plants, and other lineages is constrained by reliance on base-contacting residues for DNA-binding functionality. Reconstructions indicate that virtually every DNA triplet was recognized by at least one C2H2-ZF domain in the common progenitor of placental mammals, but that extant C2H2-ZF domains typically bind different sequences from these ancestral domains, with changes facilitated by non-base-contacting residues. Conclusions Our results suggest that the evolution of C2H2-ZFs in metazoans was expedited by the interaction of non-base-contacting residues with the DNA backbone. We term this phenomenon “kaleidoscopic evolution,” to reflect the diversity of both binding motifs and binding motif transitions and the facilitation of their diversification. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1287-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Sanie Mnaimneh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. .,Canadian Institute for Advanced Research, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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48
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Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. eLife 2017; 6. [PMID: 28792889 PMCID: PMC5550276 DOI: 10.7554/elife.28440] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022] Open
Abstract
Sequence variation within enhancers plays a major role in both evolution and disease, yet its functional impact on transcription factor (TF) occupancy and enhancer activity remains poorly understood. Here, we assayed the binding of five essential TFs over multiple stages of embryogenesis in two distant Drosophila species (with 1.4 substitutions per neutral site), identifying thousands of orthologous enhancers with conserved or diverged combinatorial occupancy. We used these binding signatures to dissect two properties of developmental enhancers: (1) potential TF cooperativity, using signatures of co-associations and co-divergence in TF occupancy. This revealed conserved combinatorial binding despite sequence divergence, suggesting protein-protein interactions sustain conserved collective occupancy. (2) Enhancer in-vivo activity, revealing orthologous enhancers with conserved activity despite divergence in TF occupancy. Taken together, we identify enhancers with diverged motifs yet conserved occupancy and others with diverged occupancy yet conserved activity, emphasising the need to functionally measure the effect of divergence on enhancer activity.
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Affiliation(s)
- Pierre Khoueiry
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lucia Ciglar
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Pei-Chen Peng
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - E Hilary Gustafson
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Saurabh Sinha
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - Eileen Em Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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49
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He BZ, Zhou X, O'Shea EK. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway. eLife 2017; 6:25157. [PMID: 28485712 PMCID: PMC5446240 DOI: 10.7554/elife.25157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/29/2017] [Indexed: 01/23/2023] Open
Abstract
Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network’s targets, possibly extending its physiological functions. The diversity of life on Earth has intrigued generations of scientists and nature lovers alike. Research over recent decades has revealed that much of the diversity we can see did not require the invention of new genes. Instead, living forms diversified mostly by using old genes in new ways – for example, by changing when or where an existing gene became active. This kind of change is referred to as “regulatory evolution”. A class of proteins called transcription factors are hot spots in regulatory evolution. These proteins recognize specific sequences of DNA to control the activity of other genes, and so represent the “readers” of the genetic information. Small changes to how a transcription factor is regulated, or the genes it targets, can lead to dramatic changes in an organism. Before we can understand how life on Earth evolved to be so diverse, scientists must first answer how transcription factors evolve and what consequences this has on their target genes. So far, most studies of regulatory evolution have focused on networks of transcription factors and genes that control how an organism develops. He et al. have now studied a regulatory network that is behind a different process, namely how an organism responds to stress or starvation. These two types of regulatory networks are structured differently and work in different ways. These differences made He et al. wonder if the networks evolved differently too. The chemical phosphate is an essential nutrient for all living things, and He et al. compared how two different species of yeast responded to a lack of phosphate. The key difference was how much a major transcription factor known as Pho4 depended on a so-called co-activator protein named Pho2 to carry out its role. Baker’s yeast (Saccharomyces cerevisiae), which is commonly used in laboratory experiments, requires both Pho4 and Pho2 to activate about 20 genes when inorganic phosphate is not available in its environment. However, in a related yeast species called Candida glabrata, Pho4 has evolved to depend less on Pho2. He et al. went on to show that, as well as being less dependent on Pho2, Pho4 in C. glabrata activates more than three times as many genes as Pho4 in S. cerevisiae does in the absence of phosphate. These additional gene targets for Pho4 in C. glabrata are predicted to extend the network’s activities, and allow it to regulate new process including the yeast’s responses to other types of stress and the building of the yeast’s cell wall. Together these findings show a new way that regulatory networks can evolve, that is, by reducing its dependence on the co-activator, a transcription factor can expand the number of genes it targets. This has not been seen for regulatory networks related to development, suggesting that different networks can indeed evolve in different ways. Lastly, because disease-causing microbes are often stressed inside their hosts and C. glabrata sometimes infects humans, understanding how this yeast’s response to stress has evolved may lead to new ways to prevent and treat this infection.
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Affiliation(s)
- Bin Z He
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Xu Zhou
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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50
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van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. Small chromosomal regions position themselves autonomously according to their chromatin class. Genome Res 2017; 27:922-933. [PMID: 28341771 PMCID: PMC5453326 DOI: 10.1101/gr.213751.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/22/2017] [Indexed: 11/24/2022]
Abstract
The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
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Affiliation(s)
- Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute & Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.,Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josien C Haan
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Dominika Bijos
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - An Weuts
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Koen Theunis
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Sjoerd J B Holwerda
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Parveen Kumar
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Boris Joffe
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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