Release date: 2016-12-23
The human genome work sketch has been published for 15 years, and the whole genome of each species has also been released. Second-generation sequencing (NGS) makes genome sequencing a breeze. Can you still send CNS articles in the order? Is it whimsical? Looking back at the 2016 CNS article, the results are positive. Now sequencing can not only be done by measuring genomes and transcriptomes, but the genome data can even be analyzed together with the proteome. In this article, we take a look at this year's article published on the CNS through large-scale sequencing to see what the latest research trends are.
1 genome
Genomic sequencing
The research that can be published on the CNS is of great scientific value. What is the measurement of the genome? Why? How to measure it. There are 7 CNS articles in this year's pure genome-wide sequencing, three of which are cover articles. These 7 articles have certain characteristics:
Rare sample: icewood is more than 5,000 years ago;
Unique evolutionary status: valerian from the ocean to the land and back to the ocean; hippocampus with special body type and male parenting;
Technology milestones: Long sequencing completes the gorilla genome; third generation sequencing publishes the most continuous human genome.
Special environment: whole genome sequencing of nearly 400 Atlantic salmon in polluted waters;
A large number of samples: 10 different types of habitats, more than 125,000 viral sequences in 3,042 samples from around the world.
Science: Pathogen genome 5,300 years ago
Science and Nature have reported that researchers have extracted the oldest pathogen genome from icewood that was more than 5,000 years ago. The study was published on the January 7th issue of Science. An important question addressed by this study is when the hybrid H. pylori strains carried by modern Europeans occur.
Special evolutionary status allows the psyllium genome to be placed on the cover of Nature
The sequencing and research of the marine flowering plant Zostera marina genome illustrates how marine algae evolved into terrestrial plants and then returned to the sea. On February 18th, Nature reported the results of the whole genome sequencing of Valerian by cover story, research report and news outlook. The study marks the results of eight years of work by 35 scientists from around the world, not only helping botanists analyze the evolution of alfalfa, but also promote understanding of the evolution of flowering plants in general.
The results of Chinese scientists are on the cover of Nature: Deciphering the hippocampal genome
Researcher Lin Qiang, a researcher at the South China Sea Institute of Oceanology, Chinese Academy of Sciences, led a research paper jointly completed by laboratories such as Germany, Singapore, and Huada Gene as cover story and long paper (Article) published on Nature on December 15, 2016. Lin Qiang's research team carried out genome sequencing and analysis of the tiger-tailed hippocampus, and found that hippocampus is currently the fastest-growing species in whole-genome fish. Analysis shows that the loss of hippocampal gene is related to the loss of teeth and pelvic fins. The gene is copied and the newly generated gene makes male pregnancy possible. The regulation of the original disappears and changes the skeleton, and the body is protected by bone plate.
Science cover: breakthrough in genome long sequencing
Gordon et al. used long-length sequencing technology to improve the genome data of our close relatives, and the article was published on the April 1st issue of Science. The assembled fragments are reduced from a single individual and the previously missed genes and non-coding gene loci are restored. The long read length sequencing technology has become very practical, making it possible for individual laboratories to produce high quality complex mammalian genetic components.
Nature: Publishing the most continuous human genome with third-generation sequencing in Korea
Researchers at the National Seoul National University School of Medicine and the US company known as "Sequencing Dark Horse" - 10x Genomics uses the newly released GemCodeTM sequencing platform and the third-generation sequencing PacBio single-molecule real-time sequencing platform on October 13th in Nature A new study was published on the de novo assembly and haplotype phasing information analysis of a Korean genome (AK1). This is the most continuous human genome assembly ever published. The authors filled in gaps in the reference genome of specific populations and identified structural variations.
Science: Genomic sequencing shows rapid evolution of fish to adapt to pollution
An article published in the December 9 issue of Science reported full-genome sequencing of nearly 400 Atlantic salmon that lived in four contaminated East Coast regions of the United States. The results of the study showed that the genetic analysis of the team showed Atlantic salmon. The genetic diversity allows them to adapt particularly well and survive in completely altered habitats. At the genetic level, tolerant populations evolved in a highly similar manner. This suggests that these fish have carried genetic variations that allow them to adapt to contaminating sites and may have evolved some solutions to pollution.
Nature's major achievements: revealing 125,000 viral genomes
In a study published in Nature on August 17, the DOE JGI researchers analyzed data from the DOE JGI Integrated Microbial Genomes with Microbiome Samples. The management and analysis system obtained more than 5 trillion bases (Tb) of sequences from 10 different types of habitats, 3,042 samples from around the world. They worked hard to screen large piles of data sets and generated more than 125,000 viral sequences containing 2.79 million proteins. The number of viral sequences was increased by 50-fold, and 99% of the identified virus families were not closely related to previously sequenced viruses, and the first global virus distribution map was constructed.
Genomic analysis
The innovation of sequencing technology has brought convenience in sequencing. When a large amount of genomic data emerges, how to analyze these data becomes the first problem. There are also three articles on the CNS this year that provide examples of how to analyze the promoters of genomic mutations and the evolutionary origins of cis-regulatory elements:
2 Nature: Cancer Genome Analysis Reveals Significant Increases in Promoter Mutations
Recent cancer genome-wide analysis has identified numerous somatic point mutation hotspots within gene promoters. Just positive selection may not adequately explain the frequency of promoter point mutations in the cancer genome. Two papers on Nature on April 14 explored this relationship and found evidence of a mechanism linking transcription initiation to DNA repair. Over a thousand cancer genome analyses have found that an increase in the density of mutations on the gene promoter is associated with transcriptional initiation activities and damage to nucleotide excision repair.
Cell: Dynamic regulation of the Capsaspora genome and multicellular animal origin
It is unclear whether the genomic regulatory elements originated in animals or are already present in the single-cell ancestors of metazoans. So an article published on Cell on May 19 performed a multifunctional genomic analysis of the parasitic single-celled organism Capsaspora owczarzaki. Analysis has shown that the emergence of multicellular organisms in animals is associated with a major shift in the complexity of cis-regulatory elements in the genome, especially the emergence of distal enhancer regulation.
Genome-based evolutionary problem
Too many bacteria will be sequenced, but the big coffee style is to interpret esoteric evolution with a simple E. coli genome. In his previous report, Richard E. Lenski was called "the person who put evolutionary history into the bottle", and his experimental study of chemistry has an extraordinary influence in this field. Lenski's work has always been a surprise, and the development of whole-genome sequencing has also been incorporated into his chemistry experiments.
Nature: Evolutionary coffee uses 25 years of bacterial analysis to analyze how the genome evolved
Richard E. Lenski began cultivating bacteria and passing it in 1988, and he used these bacteria to complete a number of remarkable chemical experiments. In an article published online in Nature on August 1st, he and his team analyzed 264 complete genomes from 12 E. coli populations to confirm their genomic evolution rates and patterns over 50,000 generations. Using a new approach combining experimental evolution with genome sequencing, 264 whole-genome sequencing supports the benefit of most fixed mutations.
2 transcriptome
In terms of the transcriptome, many new technologies and concepts have emerged this year. As published on the CNS: a new method called PARIS can perform transcriptome RNA structure analysis on living cells; another method called transient transcriptome sequencing (TT-seq) can map human transient transcriptome sequencing. The ImmGen program is precisely the study of the gene expression group and its regulation of the mouse immune system. The preliminary results have been published on Cell. The researchers also completed the first large-scale evaluation of different single brain neuron transcriptomes by analyzing individual neuronal nuclei from the human brain. Scientists also used exome sequencing and transcriptome sequencing differences to reveal the different causes of chemosensitivity in testicular cancer.
Transcriptome new technology
Cell: A new method for transcriptome RNA structure analysis of living cells
In an article published on May 19th by Cell, researchers at Stanford in the United States have developed a new method called PARIS. This is a method of mapping RNA double-stranded maps in a living cell with reversible psoralen cross-linking, near base pair resolution. This new method directly recognizes base pair pairing interactions of living cells and determines RNA structure and RNA-RNA interactions. The advantage of PARIS and its associated methods is the ability to facilitate the discovery of higher order lncRNA structures.
Science: New Technology Mapping Human Transient Transcriptome Sequencing
A highly sensitive method called transient transcriptome sequencing (TT-seq) can be used to capture and identify even very short-lived RNA molecules. The results of this study were published in Science on June 3. RNA molecules captured using the TT-seq technique provide a snapshot of all active DNA regions in the cell for a certain period of time, including regulatory DNA sequences located between genes that were previously difficult to find. TT-seq gives you a tool to understand how different types of cells in the genome are regulated and how gene regulatory programs work.
Transcriptome new plan
Cell: Immunogene transcriptome technology for global analysis of interferon-induced networks
The purpose of the ImmGen program is to provide an in-depth analysis of gene expression and regulation of the mouse immune system, including systematic analysis of cytokine-triggered responses. In this article, published on January 28th in Cell, the researchers performed detailed and dynamic B-lymphocyte analysis of interferon-induced transcriptional responses in many hematopoietic cell types.
Science: The first large-scale transcriptome completion of different brain neurons
The Scripps Institute, the University of California, San Diego, and the Illumina team have completed the first large-scale assessment of different single brain neuron transcriptomes. Their research shows the amazing diversity of molecules used by human brain cells to transcribe genetic information from DNA to RNA and produce proteins. The researchers accomplished this feat by analyzing individual neuronal nuclei from the human brain. This allows for the classification of 16 gray subtypes in the cerebral cortex that participate in the "grey matter" of thought, cognition, and many other functions. The study was published in the June issue of Science.
Transcriptome-based pathology
Nature Cover: The genomics reveal the difference in chemosensitivity of testicular cancer
Researchers at the Dana-Farber Cancer Institute in the United States reported on November 30 that they have been able to identify unique genomic changes necessary for testicular cancer proliferation, explaining why some of them are not like most solid tumors. Can be cured with chemotherapy. The malignant germ cells that have lost heterozygosity as shown on the cover of this issue are undergoing an apoptotic process. To explore the underlying and clinical resistance of germ cell cancer chemotherapy sensitivity, they revealed differences in sensitivity using whole exome/transcriptome sequencing and cytology studies.
3 protein genome
Today's proteomic analysis means more than just two-dimensional electrophoresis, not just mass spectrometry. The latest trend in proteomic analysis is to work with the data of the genome, called the "proteogenomic". There are two large-scale studies of protein genomes published in CNS in 2016, targeting breast cancer and ovarian cancer.
Nature: The first large-scale proteome-genomic research results for breast cancer
Based on data from the Cancer Genome Atlas (TCGA) program, a joint US team of scientists has completed the first large-scale "proteogenomic" study of breast cancer, linking DNA mutations to protein signals and helping to identify cancer-driven genes. This research work focuses on proteins and their modifications to better understand cancer. A related article published in Nature on June 2 shows that integrating genomic and proteomic data to obtain a more complete picture of cancer biology is more comprehensive than any single analysis.
Cell: Large-scale protein genomics analysis of the United States for ovarian cancer
Aggregate detection of tumor proteins in 169 ovarian cancer patients identified key proteins present in their tumors, which is considered to be the largest of its kind. By integrating their findings in the proteome and known tumor genome data, the researchers' report shows potential new insights into ovarian cancer. Related work was published online on June 29th. This development shows the power of combining genomic and proteomic data. This method, called protein genomics, gives people a more complete understanding of the biology of ovarian cancer.
Source: Bio-Exploration
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