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80-556: GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants”. The result will be

160-430: A big potential to modify the genetic control in a host organism. The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations. Retrotransposons are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form

240-506: A defined structure that are able to change their location in the genome. TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have

320-483: A digital quantification of the RNA transcript abundances in biological samples. Using a reference genome, a researcher can usually determine, with some confidence, the original mRNA (and therefore which gene ) the tag was extracted from. Unlike a similar technique serial analysis of gene expression (SAGE) in which tags come from other parts of transcripts, CAGE is primarily used to locate exact transcription start sites in

400-659: A high or low level of support based on a new method developed to score the quality of transcripts. The current GENCODE Human gene set version (GENCODE Release 20) includes annotation files (in GTF and GFF3 formats), FASTA files and METADATA files associated with the GENCODE annotation on all genomic regions (reference-chromosomes/patches/scaffolds/haplotypes). The annotation data is referred on reference chromosomes and stored in separated files which include: Gene annotation, PolyA features annotated by HAVANA, (Retrotransposed) pseudogenes predicted by

480-485: A large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an RNA intermediate. Retrotransposons are composed of DNA , but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack

560-405: A main driving role to generate genetic novelty and natural genome editing. Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel Jurassic Park and the subsequent film tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from

640-526: A major paper discussing the results from a major release – GENCODE Release 7, which was frozen in December 2011. 2018 In 2018, one of the latest additions to the GENCODE project was the CRISPR/Cas9 track on human and model organism assemblies. CRISPR is a genome editing technique that uses sequences of RNA that successfully bind to the region edited with high specificity. The new track was designed to assist in

720-413: A major role in shaping the genome. Duplication may range from extension of short tandem repeats , to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes . Such duplications are probably fundamental to the creation of genetic novelty. Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of

800-467: A major theme of the book. The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of

880-561: A mounting challenge for the GENCODE project to come up with an updated notion of a gene. The Human Genome Project was an international research effort to determine the sequence of the human genome and identify the genes that it contains. The Project was coordinated by the National Institutes of Health and the U.S. Department of Energy. Additional contributors included universities across the United States and international partners in

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960-474: A new site. This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans . Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome size varies widely across species. Invertebrates have small genomes, this

1040-415: A reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications. DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and

1120-487: A reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs). Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of

1200-450: A set of annotation covers the complete genome rather than just the regions that have been manually annotated, a merged data set is created using manual annotations from HAVANA, together with automatic annotations from the Ensembl automatically annotated gene set. This process also adds unique full-length CDS predictions from the Ensembl protein coding set into manually annotated genes, to provide

1280-551: A set of annotations including all protein-coding loci with alternatively transcribed variants , non-coding loci with transcript evidence, and pseudogenes . GENCODE is currently progressing towards its goals in Phase 2 of the project. The most recent release of the Human geneset annotations is Gencode 36, with a freeze date of December 2020. This release utilises the latest GRCh38 human reference genome assembly. The latest release for

1360-404: A single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular chromosome , however, some bacterial species have linear or multiple chromosomes. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if

1440-424: A vocabulary into which genome fits systematically. It is very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is difficult to decide which molecules to include in the definition; for example, bacteria usually have one or two large DNA molecules ( chromosomes ) that contain all of

1520-485: Is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight.  Before this loss, DNA methylation allows the adequate expansion of the genome. In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules,

1600-421: Is an important new source of evidence, but generating complete gene models from it is a difficult problem. As part of GENCODE, a competition was run to assess the quality of predictions produced by various RNAseq prediction pipelines (Refer to RGASP below). To confirm uncertain models, GENCODE also has an experimental validation pipeline using RNA sequencing and RACE. For GENCODE 7, transcript models are assigned

1680-432: Is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes. Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome. Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on

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1760-444: Is carried in plasmids . For this, the word genome should not be used as a synonym of chromosome . Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode , which each have only one pair, to a fern species that has 720 pairs. It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount

1840-564: Is even more than what is necessary for DNA protein-coding and noncoding genes due to the fact that eukaryotic genomes show as much as 64,000-fold variation in their sizes. However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical human cell has two copies of each of 22 autosomes , one inherited from each parent, plus two sex chromosomes , making it diploid. Gametes , such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to

1920-492: Is facilitated by active DNA demethylation , a process that entails the DNA base excision repair pathway. This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to 5-hydroxymethylcytosine (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2 . Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to

2000-440: Is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice , a mouse , the plant Arabidopsis thaliana , the puffer fish , and the bacteria E. coli . In December 2013, scientists first sequenced the entire genome of a Neanderthal , an extinct species of humans . The genome

2080-401: Is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA. High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to

2160-456: Is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish

2240-421: Is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see developmental biology ). The work is both in vivo and in silico . There are many enormous differences in size in genomes, specially mentioned before in

2320-582: The Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity. The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center , an example both of

2400-406: The economies of scale and of citizen science . Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA , and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of

2480-455: The mitochondria . In addition, algae and plants have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and the organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus. This is the most common use of 'genome' in the scientific literature. Most eukaryotes are diploid , meaning that there are two of each chromosome in

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2560-541: The nAnTi-CAGE protocol, where capped 5′ ends are sequenced on the Illumina platform with no PCR amplification and no tag cleavage. In 2017, Poulain et al. updated the nanoCAGE protocol to use the tagmentation method (based on Tn5 transposition ) for multiplexing. In 2018, Cvetesic et al. increased the sensitivity of CAP-trapped CAGE by introducing selectively degradable carrier RNA (SLIC-CAGE, "Super-Low Input Carrier-CAGE"). In 2021, Takahashi et al. simplified

2640-636: The pilot project were published in June 2007. The findings highlighted the success of the pilot project to create a feasible platform and new technologies to characterise functional elements in the human genome, which paves the way for opening research into genome-wide studies. 2007 October New funding was part of NHGRI's endeavour to scale-up the ENCODE Project to a production phase on the entire genome along with additional pilot-scale studies. 2012 September In September 2012, The GENCODE consortium published

2720-460: The type III restriction enzyme EcoP15I and directly sequenced on the Solexa (then Illumina) platform without concatenation. The CAGEscan methodology (Plessy et al. , 2010), where the enzymatic tag cleavage is skipped, and the 5′ cDNAs sequenced paired-end , was introduced in the same article to connect novel promoters to known annotations. With HeliScopeCAGE (Kanamori-Katayama et al. , 2011),

2800-423: The 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon , Methanococcus jannaschii , was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences

2880-716: The 44 ENCODE regions was frozen on 29 April 2005 and was used in the first ENCODE Genome Annotation Assessment Project (E-GASP) workshop. GENCODE Release 1 contained 416 known loci, 26 novel (coding DNA sequence) CDS loci, 82 novel transcript loci, 78 putative loci, 104 processed pseudogenes and 66 unprocessed pseudogenes. 2005 October A second version (release 02) was frozen on 14 October 2005, containing updates following discoveries from experimental validations using RACE and RT-PCR techniques. GENCODE Release 2 contained 411 known loci, 30 novel CDS loci, 81 novel transcript loci, 83 putative loci, 104 processed pseudogenes and 66 unprocessed pseudogenes. 2007 June The conclusions from

2960-795: The CAP-trapped CAGE protocol was changed to skip the enzymatic tag cleavage and sequence directly the capped 5′ ends on the HeliScope platform, without PCR amplification. It was then automated by Itoh et al. in 2012. In 2012, the standard CAGE protocol was updated by Takahashi et al. to cleave tags with EcoP15I and sequence them on the Illumina-Solexa platform. In 2013, Batut et al. combined CAP trapper, template switching, and 5′-phosphate-dependent exonuclease digestion in RAMPAGE to maximize promoter specificity. In 2014, Murata et al. published

3040-543: The COVID-19 pandemic during 2020, there has been an urge to support research responding to the situation, so GENCODE has reviewed and improved the annotation for a set of protein-coding genes associated with SARSCoV-2 infection. The key participants of the GENCODE project have remained relatively consistent throughout its various phases, with the Wellcome Trust Sanger Institute now leading the overall efforts of

3120-568: The GENCODE consortium that run pipelines that aid the manual annotators in producing models in unannotated regions, and to identify potential missed or incorrect manual annotation, including completely missing loci, missing alternative isoforms, incorrect splice sites and incorrect biotypes. These are fed back to the manual annotators using the AnnoTrack tracking system. Some of these pipelines use data from other ENCODE subgroups including RNASeq data, histone modification and CAGE and Ditag data. RNAseq data

3200-458: The GENCODE website contains a Genome Browser for human and mouse where you can reach any genomic region by giving the chromosome number and start-end position (e.g. 22:30,700,000..30,900,000), as well as by ENS transcript id (with/without version), ENS gene id (with/without version) and gene name. The browser is powered by Biodalliance. The definition of a "gene" has never been a trivial issue, with numerous definitions and notions proposed throughout

3280-513: The United Kingdom, France, Germany, Japan, and China. The Human Genome Project formally began in 1990 and was completed in 2003, 2 years ahead of its original schedule. Ensembl is part of the GENCODE project. A key research area of the GENCODE project was to investigate the biological significance of long non-coding RNAs (lncRNA). To better understand the lncRNA expression in Humans, a sub project

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3360-531: The Yale & UCSC pipelines, but not by HAVANA, long non-coding RNAs, and tRNA structures predicted by tRNA-Scan. Some examples of the lines in the GTF format are shown below: The columns within the GENCODE GTF file formats are described below. Format description of GENCODE GTF file. TAB-separated standard GTF columns Description of key-value pairs in 9th column of the GENCODE GTF file (format: key "value") Also,

3440-669: The accuracy and completeness of GENCODE annotations have been continuously refined through its iteration of releases. A comparison of key statistics from 3 major GENCODE releases until 2014 is shown below. It is evident that although the coverage, in terms of total number of genes discovered, is steady increasing, the number of protein-coding genes has actually decreased. This is mostly attributed to new experimental evidence obtained using Cap Analysis Gene Expression (CAGE) clusters, annotated PolyA sites, and peptide hits. Putative loci can be verified by wet-lab experiments and computational predictions are analysed manually. Currently, to ensure

3520-507: The advent of the ENCODE/GENCODE project, even more problematic aspects of the definition have been uncovered, including alternative splicing (where a series of exons are separated by introns), intergenic transcriptions, and the complex patterns of dispersed regulation, together with non-genic conservation and the abundance of noncoding RNA genes. As GENCODE endeavours to build an encyclopaedia of genes and gene variants, these problems presented

3600-412: The blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are

3680-549: The cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes. However, some symbiotic bacteria (e.g. Serratia symbiotica ) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. Some bacteria have auxiliary genetic material, also part of their genome, which

3760-478: The chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the " mitochondrial genome ". The DNA found within the chloroplast may be referred to as the " plastome ". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome. Unlike prokaryotes where exon-intron organization of protein coding genes exists but

3840-455: The co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome . A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at

3920-415: The complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174 , of 5386 base pairs. The first bacterial genome to be sequenced was that of Haemophilus influenzae , completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of

4000-445: The details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size , gene order, codon usage bias , and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005). Duplications play

4080-441: The essential genetic material but they also contain smaller extrachromosomal plasmid molecules that carry important genetic information. The definition of 'genome' that is commonly used in the scientific literature is usually restricted to the large chromosomal DNA molecules in bacteria. Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in

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4160-481: The feasibility of automated genome annotations based on transcriptome sequencing. RGASP is organised in a consortium framework modelled after the EGASP (ENCODE Genome Annotation Assessment Project) gene prediction workshop, and two rounds of workshops have been conducted to address different aspects of RNA-seq analysis as well as changing sequencing technologies and formats. One of the main discoveries from rounds 1 & 2 of

4240-523: The film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator. The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and cannot afford genetically engineered children. Cap analysis gene expression The output of CAGE is a set of short nucleotide sequences (often called tags in analogy to expressed sequence tags ) with their observed counts. Copy numbers of CAGE tags provide

4320-584: The first end-to-end human genome sequence in March 2022. The term genome was created in 1920 by Hans Winkler , professor of botany at the University of Hamburg , Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest the name is a blend of the words gene and chromosome . However, see omics for a more thorough discussion. A few related -ome words already existed, such as biome and rhizome , forming

4400-458: The genome such as regulatory sequences (see non-coding DNA ), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome . Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics . The genomes of many organisms have been sequenced and various regions have been annotated. The Human Genome Project

4480-468: The genome. This knowledge in turn allows a researcher to investigate promoter structure necessary for gene expression. CAGE tags tend to start with an extra guanine (G) that is not encoded in the genome, which is attributed to the template-free 5′-extension during the first-strand cDNA synthesis or reverse-transcription of the cap itself. When not corrected, this can induce erroneous mapping of CAGE tags, for instance to nontranscribed pseudogenes. On

4560-406: The genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes . Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent

4640-455: The human genome All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. In certain lymphocytes in

4720-425: The human genome and 9% of the fruit fly genome. Tandem repeats can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome. In other cases, expansions in the number of tandem repeats in exons or introns can cause disease . For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of

4800-416: The human genome. As part of this stage, the GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. It was envisaged that the results of the first two phases will be used to determine the best path forward for analysing the remaining 99% of the human genome in a cost-effective and comprehensive production phase. 2005 April The first release of the annotation of

4880-517: The human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors. During meiosis , diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome. Genome-wide reprogramming in mouse primordial germ cells involves epigenetic imprint erasure leading to totipotency . Reprogramming

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4960-461: The most complete and up-to-date annotation of the genome possible. Ensembl transcripts are products of the Ensembl automatic gene annotation system (a collection of gene annotation pipelines), termed the Ensembl gene build. All Ensembl transcripts are based on experimental evidence and thus the automated pipeline relies on the mRNAs and protein sequences deposited into public databases from the scientific community. There are several analysis groups in

5040-587: The mouse geneset annotations is Gencode M25, also with a freeze date December 2020. Since September 2009, GENCODE has been the human gene set used by the Ensembl project and each new GENCODE release corresponds to an Ensembl release. 2003 September The project was designed with three phases - Pilot, Technology development and Production phase. The pilot stage of the ENCODE project aimed to investigate in great depth, computationally and experimentally, 44 regions totaling 30 Mb of sequence representing approximately 1% of

5120-476: The multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes. Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective. Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes. Initial sequencing and analysis of

5200-549: The non-polyadenylated RNAs. In DeepCAGE (Valen et al. , 2008), the tag concatemers were sequenced at a higher throughput on the 454 “ next-generation ” sequencing platform. In 2008, barcode multiplexing was added to the DeepCAGE protocol (Maeda et al. , 2008). In nanoCAGE (Plessy et al. , 2010), the 5′ ends or RNAs were captured with the template-switching method instead of CAP Trapper, in order to analyze smaller starting amounts of total RNA. Longer tags were cleaved with

5280-789: The nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in Huntington's disease , a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression. Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion. Transposable elements (TEs) are sequences of DNA with

5360-426: The nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as the X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome. A genome sequence

5440-409: The off-target and the guide. 2020 Among other achievements, it has been completed the first pass manual annotation of the mouse reference genome, it has started a cooperation with RefSeq and Uniprot reference annotation databases toward achieving annotation convergence, and the annotation of lncRNAs has been improved via the discovery of novel loci and novel transcripts at existing loci. Also, given

5520-505: The other hand, this addition of Gs was also utilised as a signal to filter more reliable TSS peaks. The original CAGE method (Shiraki et al. , 2003) was using CAP Trapper for capturing the 5′ ends, oligo-dT primers for synthesizing the cDNAs, the type IIs restriction enzyme MmeI for cleaving the tags, and the Sanger method for sequencing them. Random reverse-transcription primers were introduced in 2006 by Kodzius et al. to better detect

5600-572: The project was the importance of read alignment on the quality of gene predictions produced. Hence, a third round of RGASP workshop is currently being conducted (in 2014) to focus primarily on read mapping to the genome. Genome In the fields of molecular biology and genetics , a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses ). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of

5680-550: The project. A summary of key participating institutions of each phase is listed below: Source: Since its inception, GENCODE has released 36 versions of the Human gene set annotations (excluding minor updates). The key summary statistics of the most recent GENCODE Human gene set annotation ( Release 36, December 2020 freeze ) is shown below: Through advancements in sequencing technologies (such as RT-PCR-seq), increased coverage from manual annotations (HAVANA group), and improvements to automatic annotation algorithms using Ensembl,

5760-590: The proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes. Noncoding sequences include introns , sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats. Short, non-coding sequences that are repeated head-to-tail are called tandem repeats . Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of

5840-439: The proteins encoded by LINEs for transposition. The Alu element is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies. DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in

5920-428: The search for appropriate guide sentences by listing potential binding sites for the CRISPR/Cas9 complex that are next to transcribed regions, or within 200 bp of one. For each site, the track provides possible guide sequences along with a collection of predicted efficiency and specificity scores for those guide sequences. It also provides information about potential off-targets, grouped by the number of missmatches between

6000-423: The shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome. There is no clear and consistent correlation between morphological complexity and genome size in either prokaryotes or lower eukaryotes . Genome size is largely a function of the expansion and contraction of repetitive DNA elements. Since genomes are very complex, one research strategy

6080-541: The virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size. Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs). In Dictyostelium discoideum , there

6160-435: The years since the discovery of the human genome. First, genes were conceived in the 1900s as discrete units of heredity, then it was thought as the blueprint for protein synthesis, and in more recent times, it was being defined as genetic code that is transcribed into RNA. Although the definition of a gene has evolved greatly over the last century, it has remained a challenging and controversial subject for many researchers. With

6240-726: Was created by GENCODE to develop custom microarray platforms capable of quantifying the transcripts in the GENCODE lncRNA annotation. A number of designs have been created using the Agilent Technologies eArray system, and these designs are available in a standard custom Agilent format. The RNA-seq Genome Annotation Assessment Project (RGASP) project is designed to assess the effectiveness of various computational methods for high quality RNA-sequence data analysis. The primary goals of RGASP are to provide an unbiased evaluation for RNA-seq alignment, transcript characterisation (discovery, reconstruction and quantification) software, and to determine

6320-405: Was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave . New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine . A major step toward that goal was the completion in 2007 of the full genome of James D. Watson , one of

6400-518: Was started in October 1990, and then reported the sequence of the human genome in April 2003, although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequencing of the many repetitive sequences found in human DNA that were not fully uncovered by the original Human Genome Project study, scientists reported

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