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Dressler L, Bortolomeazzi M, Keddar MR, Misetic H, Sartini G, Acha-Sagredo A, Montorsi L, Wijewardhane N, Repana D, Nulsen J, Goldman J, Pollitt M, Davis P, Strange A, Ambrose K, Ciccarelli FD. Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. Genome Biol 2022; 23:35. [PMID: 35078504 PMCID: PMC8790917 DOI: 10.1186/s13059-022-02607-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
Background Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue homeostasis and cancer development. Results Here, we collect a literature-based repertoire of 3355 well-known or predicted drivers of cancer and non-cancer somatic evolution in 122 cancer types and 12 non-cancer tissues. Mapping the alterations of these genes in 7953 pan-cancer samples reveals that, despite the large size, the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. High overlap exists between drivers of cancer and non-cancer somatic evolution, although significant differences emerge in their recurrence. We confirm and expand the unique properties of drivers and identify a core of evolutionarily conserved and essential genes whose germline variation is strongly counter-selected. Somatic alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation. Conclusions Our study offers a comprehensive overview of our current understanding of the genetic events initiating clone expansion and cancer revealing significant gaps and biases that still need to be addressed. The compendium of cancer and non-cancer somatic drivers, their literature support, and properties are accessible in the Network of Cancer Genes and Healthy Drivers resource at http://www.network-cancer-genes.org/. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02607-z.
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Abstract
CRISPR-mediated genome engineering technologies have been adapted to a wide variety of organisms with high efficiency and specificity. The yellow fever mosquito, Aedes aegypti , is one such organism. It is also responsible for transmitting a wide variety of deadly viruses including Dengue, Zika, Yellow fever, and Chikungunya. The key to successful CRISPR-mediated gene editing applications is the delivery of both Cas9 ribonuclease and single-guide RNA (sgRNA ) to the nucleus of desired cells. Various methods have been developed for supplying the Cas9 endonuclease, sgRNA , and donor DNA to Ae. aegypti. In this chapter, we focus on methods of direct embryo delivery of editing components, presenting detailed step-by-step CRISPR/Cas9-based genome-editing protocols for inducing desired heritable edits in mosquitoes as well as insights into successful application of these protocols. We also highlight potential opportunities for customizing these protocols to manipulate the mosquito genome for innovative in vivo gene function studies.
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Affiliation(s)
- Ruichen Sun
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ming Li
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Conor J McMeniman
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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Li DM, Li J, Wang DR, Xu YC, Zhu GF. Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC PLANT BIOLOGY 2021; 21:558. [PMID: 34814832 PMCID: PMC8611967 DOI: 10.1186/s12870-021-03315-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. RESULTS Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda 'Red Leaf', Kaempferia rotunda 'Silver Diamonds' and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630-163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172-88,632 bp), a small single copy (SSC, 15,393-15,917 bp) and a pair of inverted repeats (IRs, 29,673-29,833 bp). The genomes contain 111-113 different genes, including 79 protein coding genes, 28-30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + "the Kaempferia clade" consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. CONCLUSIONS Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dai-Rong Wang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ye-Chun Xu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies. Neural Comput Appl 2021; 33:15669-15692. [PMID: 34155424 PMCID: PMC8208613 DOI: 10.1007/s00521-021-06188-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
During the last (15) years, improved omics sequencing technologies have expanded the scale and resolution of various biological applications, generating high-throughput datasets that require carefully chosen software tools to be processed. Therefore, following the sequencing development, bioinformatics researchers have been challenged to implement alignment algorithms for next-generation sequencing reads. However, nowadays selection of aligners based on genome characteristics is poorly studied, so our benchmarking study extended the “state of art” comparing 17 different aligners. The chosen tools were assessed on empirical human DNA- and RNA-Seq data, as well as on simulated datasets in human and mouse, evaluating a set of parameters previously not considered in such kind of benchmarks. As expected, we found that each tool was the best in specific conditions. For Ion Torrent single-end RNA-Seq samples, the most suitable aligners were CLC and BWA-MEM, which reached the best results in terms of efficiency, accuracy, duplication rate, saturation profile and running time. About Illumina paired-end osteomyelitis transcriptomics data, instead, the best performer algorithm, together with the already cited CLC, resulted Novoalign, which excelled in accuracy and saturation analyses. Segemehl and DNASTAR performed the best on both DNA-Seq data, with Segemehl particularly suitable for exome data. In conclusion, our study could guide users in the selection of a suitable aligner based on genome and transcriptome characteristics. However, several other aspects, emerged from our work, should be considered in the evolution of alignment research area, such as the involvement of artificial intelligence to support cloud computing and mapping to multiple genomes.
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Abstract
The cause of Alzheimer’s disease (AD) is poorly understood. In 1991, the amyloid hypothesis postulated that β-amyloid (Aβ) accumulation is a key element. It follows that clearing the brain of Aβ would be beneficial, which has not been the case. Therefore, Aβ is likely a result, not a cause, of AD and may be protective rather than harmful. The apolipoprotein E4 (apoE4) allele is the strongest genetic risk factor for AD. Klotho (KL), encoded by the KL gene, may be another AD-related protein. FGF21 is a circulating endocrine hormone, mainly secreted by the liver, mostly during fasting. FGF21 acts by binding to its receptor FGFR1 and co-receptor β-klotho. FGF21 is neuroprotective and could delay onset of AD. In the present study, the KL protein structure was examined to determine whether it may interact with Aβ. Protein data bank (pdb) entries for klotho and Aβ were searched on the RCSB Protein Data Bank for β-KL and AD amyloid β-peptide. The protein structures were superimposed and aligned on PYMOL v2.3.4 with the super command, which super aligns two protein selections. To evaluate the conservation and alignment of the Aβ and KL genomes across species, BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser, was used. The amino acid residues phe76-val96 of KL aligned closely with residues asp7-asn27 of Aβ. Cross-species comparison of KL revealed a high degree of alignment and conservation in the chimp and 27 other primates; however, less alignment and conservation were observed in the mouse, dog and elephant, even less in the chicken, western clawed frog (Xenopus tropicalis), zebrafish and lamprey. The current finding of amino acid residues phe76-val96 of klotho aligning closely with residues asp7-asn27 of Aβ suggests that Aβ can enhance the ability of klotho to draw FGF21 to regions of incipient neurodegeneration in AD. The problem arises with age. Older individuals do not heal or repair tissue damage as well as younger individuals. As neurodegeneration advances in an older individual, perhaps caused by neuroinflammation related to herpes simplex virus type 1, increasing amounts of amyloid are produced, forming an adhesive web, as the brain tries to hold the pathologic process in check. Meanwhile, the damage increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.
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Affiliation(s)
- Steven Lehrer
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Lehrer S, Rheinstein PH. Alignment of Alzheimer's Disease Amyloid-β Peptide and Herpes Simplex Virus-1 pUL15 C-Terminal Nuclease Domain. J Alzheimers Dis Rep 2020; 4:373-377. [PMID: 33163898 PMCID: PMC7592838 DOI: 10.3233/adr-200231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: The cause of Alzheimer’s disease (AD) is poorly understood. Neurotropic microbes, particularly herpesviruses, might set off chronic neuroinflammation. Amyloid-β (Aβ) has antimicrobial properties and could represent a brain defense against infection. Objective: We searched for protein sequence alignment between herpes simplex virus type I (HSV-1) HSV-2, and Aβ. Methods: Protein data bank (pdb) structures for Aβ, HSV-1, and HSV-2 were searched on the RCSB Protein Data Bank. The protein structures were superimposed and aligned on PYMOL v 2.3.4. Results: For HSV-1 and Aβ, amino acid residues ser549 – his569 of HSV-1 aligned closely with residues asp7 - asn27 of Aβ. For HSV-2 and Aβ, amino acid residues of HSV-2 aligned less closely than those of HSV-1 with residues of Aβ. Conclusion: Conjugating and binding to the same alpha helix in the HSV-1 protease, Aβ could be marking HSV-1 for attack by the immune system, providing a rapid inherited immune response to a destructive neurotropic virus that would otherwise require the more time-consuming involvement of T-cells, B-cells, and the adaptive immune system. But older people do not respond to viral infections as well as younger individuals. When HSV-1 infection advances in an old person, more and more amyloid is produced, forming an adhesive web. As the brain tries to hold the pathologic process in check, neuroinflammation increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.
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Lehrer S, Rheinstein PH. Human Gene Sequences in SARS-CoV-2 and Other Viruses. In Vivo 2020; 34:1633-1636. [PMID: 32503822 DOI: 10.21873/invivo.11954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
In a previous study, we identified a 117 base severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence in the human genome with 94.6% identity. The sequence was in chromosome 1p within an intronic region of the netrin G1 (NTNG1) gene. The sequence matched a sequence in the SARS-CoV-2 Orf1b gene in non-structural protein 14 (NSP14), which is an exonuclease and NSP15, an endoribonuclease. In the current study we compared the human genome with other viral genomes to determine some of the characteristics of human sequences found in the latter. Most of the viruses had human sequences, but they were short. Hepatitis A and St Louis encephalitis had human sequences that were longer than the 117 base SARS-Cov-2 sequence, but they were in non-coding regions of the human genome. The SARS-Cov-2 sequence was the only long sequence found in a human gene (NTNG1). The related coronaviruses SARS-Cov had a 41 BP human sequence on chromosome 3 that was not part of a human gene, and MERS had no human sequence. The 117 base SARS-CoV-2 human sequence is relatively close to the viral spike sequence, separated only by NSP16, a 904 base sequence. The mechanism for SARS-CoV-2 infection is the binding of the virus spike protein to the membrane-bound form of angiotensin-converting enzyme 2 (ACE2) and internalization of the complex by the host cell. We have no explanation for the NSP14 and NSP15 SARS-Cov-2 sequences we observed here or how they might relate to infectiousness. Further studies are warranted.
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Affiliation(s)
- Steven Lehrer
- Department of Radiation Oncology Icahn School of Medicine at Mount Sinai, New York, NY, U.S.A.
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Xu G, Bian C, Nie Z, Li J, Wang Y, Xu D, You X, Liu H, Gao J, Li H, Liu K, Yang J, Li Q, Shao N, Zhuang Y, Fang D, Jiang T, Lv Y, Huang Y, Gu R, Xu J, Ge W, Shi Q, Xu P. Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. Gigascience 2020; 9:giz157. [PMID: 31895412 PMCID: PMC6939831 DOI: 10.1093/gigascience/giz157] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/28/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). RESULTS In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. CONCLUSIONS We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.
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Affiliation(s)
- Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhijuan Nie
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Yuyu Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dongpo Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Hongbo Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jiancao Gao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Hongxia Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jian Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Nailin Shao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yanbing Zhuang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dian Fang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Tao Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Ruobo Gu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
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Liu XF, Zhu GF, Li DM, Wang XJ. Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'. PLoS One 2019; 14:e0224038. [PMID: 31644545 PMCID: PMC6808432 DOI: 10.1371/journal.pone.0224038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/03/2019] [Indexed: 11/18/2022] Open
Abstract
Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.
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Affiliation(s)
- Xiao-Fei Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xiao-Jing Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, Guangdong, China
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Lehrer S, Rheinstein PH. Mouse mammary tumor viral env sequences are not present in the human genome but are present in breast tumors and normal breast tissues. Virus Res 2019; 266:43-47. [PMID: 30951792 DOI: 10.1016/j.virusres.2019.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 01/28/2023]
Abstract
In 1936, John Joseph Bittner identified mouse mammary tumor virus (MMTV), a milk transmitted beta retrovirus, a form of single-stranded positive-sense RNA virus. A retrovirus inserts a copy of its genome into the DNA of a host cell, thus altering the cell's genome. In the current analysis, we searched for MMTV sequences within the human genome. To compare the MMTV genome to the human genome, we used BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser. BLAT can align a user sequence of 25 bases or more to the genome. 60 MMTV sequences were in the human genome. Of 56 sequences from the MMTV POL gene, 36 POL sequences were from the same part of the gene, beginning at viral nucleotide 4800 but of different lengths. 8 viral sequences began at nucleotide ∼3430 of the POL gene. Four viral sequences were from GAGdUTPase, encoded by the MMTV PRO gene. Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is an enzyme present in several major retroviral families. In MMTV dUTPase may be essential for viral replication. Since BLAT identified no MMTV envelope (env) sequence in the human genome, the env sequences from breast tumors and normal breast tissue found in other studies may have come from an MMTV infection. However, no one is certain how MMTV could enter human cells, since the cells do not have a cellular receptor for MMTV, as do mouse cells.
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Affiliation(s)
- Steven Lehrer
- Department of Radiation Oncolog, Icahn School of Medicine at Mount Sinai, New York, United States.
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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis. Molecules 2019; 24:molecules24030474. [PMID: 30699955 PMCID: PMC6385120 DOI: 10.3390/molecules24030474] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 01/17/2023] Open
Abstract
Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.
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Ma K, Shi W, Xu M, Liu J, Zhang F. Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca 2+ Channel Blocker. FRONTIERS IN PLANT SCIENCE 2018; 9:244. [PMID: 29559983 PMCID: PMC5845709 DOI: 10.3389/fpls.2018.00244] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/12/2018] [Indexed: 05/12/2023]
Abstract
It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.
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Affiliation(s)
- Keshi Ma
- College of Life Sciences, Capital Normal University, Beijing, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Wenshuo Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Mengyue Xu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiaxi Liu
- College of Life Sciences, Capital Normal University, Beijing, China
- *Correspondence: Jiaxi Liu
| | - Feixiong Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
- Feixiong Zhang
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13
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Latteyer S, Tiedje V, König K, Ting S, Heukamp LC, Meder L, Schmid KW, Führer D, Moeller LC. Targeted next-generation sequencing for TP53, RAS, BRAF, ALK and NF1 mutations in anaplastic thyroid cancer. Endocrine 2016; 54:733-741. [PMID: 27696251 DOI: 10.1007/s12020-016-1080-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/04/2016] [Indexed: 12/30/2022]
Abstract
Anaplastic thyroid carcinoma (ATC) is the most aggressive thyroid cancer with a median survival of 4-6 months. Identification of mutations contributing to aberrant activation of signaling cascades in ATC may provide novel opportunities for targeted therapy. Thirty-nine ATC samples were studied by next-generation sequencing (NGS) with an established gene panel. High quality readout was obtained in 30/39 ATC. Twenty-eight ATC harbored a mutation in at least one of the studied genes: TP53 (18/30), NF1 (11/30), ALK (6/30), NRAS (4/30), ATRX (3/30), BRAF (2/30), HRAS (2/30), KRAS (1/30). In 17/30 ATC (54 %) mutations were found in two or more genes. Twenty-one of the identified variants are listed in COSMIC as somatic mutations reported in other cancer entities. In three ATC samples no mutations were detected and none of the ATCs was positive for BRAFV600E. The most frequent mutations were found in TP53 (60 %), followed by NF1 (37 %). ALK mutations were detected in 20 % of ATC and were more frequent than RAS or BRAF mutations. ATRX mutations were identified in 10 % of the ATC samples. These sequencing data from 30 ATC samples demonstrate the accumulation of genetic alterations in ATC because in 90 % of samples mutations were already found in the investigated nine genes alone. Mutations were found with high prevalence in established tumor suppressor and oncogenes in ATC, such as TP53 and H/K/NRAS, but also, although less frequent, in genes that may harbor the potential for targeted treatment in a subset of ATC patients, such as ALK and NF1.
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Affiliation(s)
- Soeren Latteyer
- Department of Endocrinology and Metabolism, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany
| | - Vera Tiedje
- Department of Endocrinology and Metabolism, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany
| | - Katharina König
- Institute of Pathology, University Hospital Cologne, Kerpener Straße 62, Cologne, 50935, Germany
- Labor Dr. Quade und Kollegen GmbH, Medizinisches Versorgungszentrum, Aachener Str. 338, Cologne, 50933, Germany
| | - Saskia Ting
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany
| | - Lukas C Heukamp
- NEO New Oncology AG, Gottfried-Hagen-Str. 20, Cologne, 51105, Germany
- Institute of Hematopathology Hamburg, Fangdieckstraße 75a, Hamburg, 22547, Germany
| | - Lydia Meder
- Institute of Pathology, University Hospital Cologne, Kerpener Straße 62, Cologne, 50935, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany
| | - Dagmar Führer
- Department of Endocrinology and Metabolism, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany
| | - Lars Christian Moeller
- Department of Endocrinology and Metabolism, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, Essen, 45122, Germany.
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Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients. J Thorac Oncol 2016; 10:1049-57. [PMID: 26102443 DOI: 10.1097/jto.0000000000000570] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. METHODS In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. RESULTS We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. CONCLUSION Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.
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15
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Du D, Qi LS. CRISPR Technology for Genome Activation and Repression in Mammalian Cells. Cold Spring Harb Protoc 2016; 2016:pdb.prot090175. [PMID: 26729910 DOI: 10.1101/pdb.prot090175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Targeted modulation of transcription is necessary for understanding complex gene networks and has great potential for medical and industrial applications. CRISPR is emerging as a powerful system for targeted genome activation and repression, in addition to its use in genome editing. This protocol describes how to design, construct, and experimentally validate the function of sequence-specific single guide RNAs (sgRNAs) for sequence-specific repression (CRISPRi) or activation (CRISPRa) of transcription in mammalian cells. In this technology, the CRISPR-associated protein Cas9 is catalytically deactivated (dCas9) to provide a general platform for RNA-guided DNA targeting of any locus in the genome. Fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in mammalian cells. Delivery of multiple sgRNAs further enables activation or repression of multiple genes. By using scaffold RNAs (scRNAs), different effectors can be recruited to different genes for simultaneous activation of some and repression of others. The CRISPRi and CRISPRa methods provide powerful tools for sequence-specific control of gene expression on a genome-wide scale to aid understanding gene functions and for engineering genetic regulatory systems.
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Affiliation(s)
- Dan Du
- Department of Bioengineering, Stanford University, Stanford, California 94305
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305; ChEM-H; Stanford University, Stanford, California 94305
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16
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Campbell MS, Yandell M. An Introduction to Genome Annotation. CURRENT PROTOCOLS IN BIOINFORMATICS 2015; 52:4.1.1-4.1.17. [PMID: 26678385 DOI: 10.1002/0471250953.bi0401s52] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.
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Affiliation(s)
- Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah.,USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah
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Comprehensive Analysis of Disease-Related Genes in Chronic Lymphocytic Leukemia by Multiplex PCR-Based Next Generation Sequencing. PLoS One 2015; 10:e0129544. [PMID: 26053404 PMCID: PMC4459702 DOI: 10.1371/journal.pone.0129544] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/11/2015] [Indexed: 12/31/2022] Open
Abstract
Background High resolution molecular studies have demonstrated that the clonal acquisition of gene mutations is an important mechanism that may promote rapid disease progression and drug resistance in chronic lymphocytic leukemia (CLL). Therefore, the early and sensitive detection of such mutations is an important prerequisite for future predictive CLL diagnostics in the clinical setting. Material & Methods Here, we describe a novel, target-specific next generation sequencing (NGS) approach, which combines multiplex PCR-based target enrichment and library generation with ultra-deep high-throughput parallel sequencing using a MiSeq platform. We designed a CLL specific target panel, covering hotspots or complete coding regions of 15 genes known to be recurrently mutated and/or related to B-cell receptor signaling. Results High-throughput sequencing was performed using as little as 40 ng of peripheral blood B-cell DNA from 136 CLL patients and a dilution series of two ATM- or TP53-mutated cell lines, the latter of which demonstrated a limit of mutation detection below 5%. Using a stringent functional assessment algorithm, 102 mutations in 8 genes were identified in CLL patients, including hotspot regions of TP53, SF3B1, NOTCH1, ATM, XPO1, MYD88, DDX3X and the B-cell receptor signaling regulator PTPN6. The presence of mutations was significantly associated with an advanced disease status und molecular markers of an inferior prognosis, such as an unmutated IGHV mutation status or positivity for ZAP70 by flow cytometry. Conclusion In summary, targeted sequencing using an amplicon based library technology allows a resource-efficient and sensitive mutation analysis for diagnostic or exploratory purposes and facilitates molecular subtyping of patient sets with adverse prognosis.
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Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ, Lu MYJ, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH. Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. Genome Biol Evol 2014; 6:2258-73. [PMID: 25152353 PMCID: PMC4202321 DOI: 10.1093/gbe/evu181] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Feathers are hallmark avian integument appendages, although they were also present on theropods. They are composed of flexible corneous materials made of α- and β-keratins, but their genomic organization and their functional roles in feathers have not been well studied. First, we made an exhaustive search of α- and β-keratin genes in the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, we studied α- and β-keratin gene expression patterns in five types of feather epidermis. The expression patterns of β-keratin genes were different in different feather types, whereas those of α-keratin genes were less variable. In addition, we obtained extensive α- and β-keratin mRNA in situ hybridization data, showing that α-keratins and β-keratins are preferentially expressed in different parts of the feather components. Together, our data suggest that feather morphological and structural diversity can largely be attributed to differential combinations of α- and β-keratin genes in different intrafeather regions and/or feather types from different body parts. The expression profiles provide new insights into the evolutionary origin and diversification of feathers. Finally, functional analysis using mutant chicken keratin forms based on those found in the human α-keratin mutation database led to abnormal phenotypes. This demonstrates that the chicken can be a convenient model for studying the molecular biology of human keratin-based diseases.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jie Yan
- Department of Pathology, Keck School of Medicine, University of Southern California Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Molecular Biology of Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Randall B Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago
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Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, Pardo-Manuel de Villena F, Baric RS, Heise MT, Peng X, Katze MG. Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. RNA Biol 2014; 11:875-90. [PMID: 24922324 PMCID: PMC4179962 DOI: 10.4161/rna.29442] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).
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Affiliation(s)
- Laurence Josset
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Nicolas Tchitchek
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Lisa E Gralinski
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Martin T Ferris
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Amie J Eisfeld
- Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA
| | - Richard R Green
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Matthew J Thomas
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Jennifer Tisoncik-Go
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA
| | | | - Ralph S Baric
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Mark T Heise
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Xinxia Peng
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Michael G Katze
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
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20
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Zhao H, Peng Z, Fei B, Li L, Hu T, Gao Z, Jiang Z. BambooGDB: a bamboo genome database with functional annotation and an analysis platform. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau006. [PMID: 24602877 PMCID: PMC3944406 DOI: 10.1093/database/bau006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein–protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China, State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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21
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Zhao H, Peng Z, Fei B, Li L, Hu T, Gao Z, Jiang Z. BambooGDB: a bamboo genome database with functional annotation and an analysis platform. Database (Oxford) 2014. [PMID: 24602877 DOI: 10.1093/database/bau100636t36t36t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein-protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org.
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China, State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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22
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Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 2013; 8:2180-96. [PMID: 24136345 PMCID: PMC3922765 DOI: 10.1038/nprot.2013.132] [Citation(s) in RCA: 764] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sequence-specific control of gene expression on a genome-wide scale is an important approach for understanding gene functions and for engineering genetic regulatory systems. We have recently described an RNA-based method, CRISPR interference (CRISPRi), for targeted silencing of transcription in bacteria and human cells. The CRISPRi system is derived from the Streptococcus pyogenes CRISPR (clustered regularly interspaced palindromic repeats) pathway, requiring only the coexpression of a catalytically inactive Cas9 protein and a customizable single guide RNA (sgRNA). The Cas9-sgRNA complex binds to DNA elements complementary to the sgRNA and causes a steric block that halts transcript elongation by RNA polymerase, resulting in the repression of the target gene. Here we provide a protocol for the design, construction and expression of customized sgRNAs for transcriptional repression of any gene of interest. We also provide details for testing the repression activity of CRISPRi using quantitative fluorescence assays and native elongating transcript sequencing. CRISPRi provides a simplified approach for rapid gene repression within 1-2 weeks. The method can also be adapted for high-throughput interrogation of genome-wide gene functions and genetic interactions, thus providing a complementary approach to RNA interference, which can be used in a wider variety of organisms.
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Affiliation(s)
- Matthew H Larson
- 1] Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Howard Hughes Medical Institute, UCSF, San Francisco, California, USA. [3] California Institute for Quantitative Biomedical Research, San Francisco, California, USA
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