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Saber MM, Adeyemi Babarinde I, Hettiarachchi N, Saitou N. Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. Genome Biol Evol 2016; 8:2076-92. [PMID: 27289096 PMCID: PMC4987104 DOI: 10.1093/gbe/evw132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.
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Affiliation(s)
- Morteza Mahmoudi Saber
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Isaac Adeyemi Babarinde
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Nilmini Hettiarachchi
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Naruya Saitou
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res 2015; 25:1703-14. [PMID: 26335633 PMCID: PMC4617966 DOI: 10.1101/gr.192542.115] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/20/2015] [Indexed: 11/25/2022]
Abstract
The Drosophila genome activator Vielfaltig (Vfl), also known as Zelda (Zld), is thought to prime enhancers for activation by patterning transcription factors (TFs). Such priming is accompanied by increased chromatin accessibility, but the mechanisms by which this occurs are poorly understood. Here, we analyze the effect of Zld on genome-wide nucleosome occupancy and binding of the patterning TF Dorsal (Dl). Our results show that early enhancers are characterized by an intrinsically high nucleosome barrier. Zld tackles this nucleosome barrier through local depletion of nucleosomes with the effect being dependent on the number and position of Zld motifs. Without Zld, Dl binding decreases at enhancers and redistributes to open regions devoid of enhancer activity. We propose that Zld primes enhancers by lowering the high nucleosome barrier just enough to assist TFs in accessing their binding motifs and promoting spatially controlled enhancer activation if the right patterning TFs are present. We envision that genome activators in general will utilize this mechanism to activate the zygotic genome in a robust and precise manner.
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Blazie SM, Babb C, Wilky H, Rawls A, Park JG, Mangone M. Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. BMC Biol 2015; 13:4. [PMID: 25601023 PMCID: PMC4343181 DOI: 10.1186/s12915-015-0116-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/12/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Here we developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from Caenorhabditis elegans intestine, pharynx and body muscle tissues and study changes in their tissue-specific transcriptomes and 3'UTRomes. RESULTS We have identified thousands of novel genes and isoforms differentially expressed between these three tissues. The intestine transcriptome is expansive, expressing over 30% of C. elegans mRNAs, while muscle transcriptomes are smaller but contain characteristic unique gene signatures. Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation. We have precisely mapped approximately 20,000 tissue-specific polyadenylation sites and discovered that about 30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3'UTR isoforms significantly enriched with microRNA targets. CONCLUSIONS For the first time, PAT-Seq allowed us to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.
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Affiliation(s)
- Stephen M Blazie
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Cody Babb
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Henry Wilky
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
| | - Alan Rawls
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
| | - Jin G Park
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
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Seridi L, Ryu T, Ravasi T. Dynamic epigenetic control of highly conserved noncoding elements. PLoS One 2014; 9:e109326. [PMID: 25289637 PMCID: PMC4188601 DOI: 10.1371/journal.pone.0109326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022] Open
Abstract
Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.
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Affiliation(s)
- Loqmane Seridi
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Taewoo Ryu
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail: (T. Ryu); (T. Ravasi)
| | - Timothy Ravasi
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (T. Ryu); (T. Ravasi)
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Schuettengruber B, Oded Elkayam N, Sexton T, Entrevan M, Stern S, Thomas A, Yaffe E, Parrinello H, Tanay A, Cavalli G. Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila. Cell Rep 2014; 9:219-233. [PMID: 25284790 DOI: 10.1016/j.celrep.2014.08.072] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/08/2014] [Accepted: 08/27/2014] [Indexed: 12/21/2022] Open
Abstract
Metazoan genomes are partitioned into modular chromosomal domains containing active or repressive chromatin. In flies, Polycomb group (PcG) response elements (PREs) recruit PHO and other DNA-binding factors and act as nucleation sites for the formation of Polycomb repressive domains. The sequence specificity of PREs is not well understood. Here, we use comparative epigenomics and transgenic assays to show that Drosophila domain organization and PRE specification are evolutionarily conserved despite significant cis-element divergence within Polycomb domains, whereas cis-element evolution is strongly correlated with transcription factor binding divergence outside of Polycomb domains. Cooperative interactions of PcG complexes and their recruiting factor PHO stabilize PHO recruitment to low-specificity sequences. Consistently, PHO recruitment to sites within Polycomb domains is stabilized by PRC1. These data suggest that cooperative rather than hierarchical interactions among low-affinity sequences, DNA-binding factors, and the Polycomb machinery are giving rise to specific and strongly conserved 3D structures in Drosophila.
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Affiliation(s)
- Bernd Schuettengruber
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Noa Oded Elkayam
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Sexton
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Marianne Entrevan
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Shani Stern
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aubin Thomas
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Eitan Yaffe
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hugues Parrinello
- Montpellier GenomiX IBiSA, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Giacomo Cavalli
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Abstract
Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
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Babbitt GA, Alawad MA, Schulze KV, Hudson AO. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res 2014; 42:10915-26. [PMID: 25200075 PMCID: PMC4176184 DOI: 10.1093/nar/gku811] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Mohammed A Alawad
- B. Thomas Golisano College of Computing and Information Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, USA 77030
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
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Robinson MC, Stone EA, Singh ND. Population genomic analysis reveals no evidence for GC-biased gene conversion in Drosophila melanogaster. Mol Biol Evol 2013; 31:425-33. [PMID: 24214536 DOI: 10.1093/molbev/mst220] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene conversion is the nonreciprocal exchange of genetic material between homologous chromosomes. Multiple lines of evidence from a variety of taxa strongly suggest that gene conversion events are biased toward GC-bearing alleles. However, in Drosophila, the data have largely been indirect and unclear, with some studies supporting the predictions of a GC-biased gene conversion model and other data showing contradictory findings. Here, we test whether gene conversion events are GC-biased in Drosophila melanogaster using whole-genome polymorphism and divergence data. Our results provide no support for GC-biased gene conversion and thus suggest that this process is unlikely to significantly contribute to patterns of polymorphism and divergence in this system.
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Affiliation(s)
- Matthew C Robinson
- Department of Biological Sciences, Program in Genetics, North Carolina State University
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Affiliation(s)
- James G. D. Prendergast
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- * E-mail:
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