approximately what percentage of the human genome consists of repetitive dna or transposable elements?

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Transposons

Transposable elements, also known as “jumping genes,” are DNA sequences that move from one location on the genome to another. These elements were first identified more than 50 years ago by American geneticist Barbara McClintock. Although biologists were initially skeptical of McClintock’s discovery, they now recognize that transposable elements make up a significant portion of most eukaryotic genomes. However, scientists are only just beginning to understand the function of jumping genes.

Transposable elements (TEs), also known as "jumping genes," are DNA sequences that move from one location on the genome to another. These elements were first identified more than 50 years ago by geneticist Barbara McClintock of Cold Spring Harbor Laboratory in New York. Biologists were initially skeptical of McClintock's discovery. Over the next several decades, however, it became apparent that not only do TEs "jump," but they are also found in almost all organisms (both prokaryotes and eukaryotes) and typically in large numbers. For example, TEs make up approximately 50% of the human genome and up to 90% of the maize genome (SanMiguel, 1996).

Types of Transposons

Today, scientists know that there are many different types of TEs, as well as a number of ways to categorize them. One of the more common divisions is between those TEs that require reverse transcription (i.e., the transcription of RNA into DNA) in order to transpose and those that do not. The former elements are known as retrotransposons or class 1 TEs, whereas the latter are known as DNA transposons or class 2 TEs. The Ac/Ds system that McClintock discovered falls in the latter category. Different classes of transposable elements are found in the genomes of different eukaryotic organisms (Figure 1).

Figure 1: The relative amount of retrotransposons and DNA transposons in diverse eukaryotic genomes

This graph shows the contribution of DNA transposons and retrotransposons in percentage relative to the total number of transposable elements in each species. (Sc: Saccharomyces cerevisiae; Sp: Schizosaccharomyces pombe; Hs: Homo sapiens; Mm: Mus musculus; Os: Oryza sativa; Ce: Caenorhabditis elegans; Dm: Drosophila melanogaster; Ag: Anopheles gambiae, malaria mosquito; Aa: Aedes aegypti, yellow fever mosquito; Eh: Entamoeba histolytica; Ei: Entamoeba invadens; Tv: Trichomonas vaginalis.)

DNA Transposons

All complete or "autonomous" class 2 TEs encode the protein transposase, which they require for insertion and excision (Figure 2). Some of these TEs also encode other proteins. Note that DNA transposons never use RNA intermediaries—they always move on their own, inserting or excising themselves from the genome by means of a so-called "cut and paste" mechanism.

Figure 2: Classes of mobile elements.

DNA transposons (e.g., Tc-1-mariner) have inverted terminal inverted repeats (ITRs) and a single open reading frame (ORF) that encodes a transposase. They are flanked by short direct repeats (DRs). Retrotransposons are divided into autonomous and nonautonomous classes depending on whether they have ORFs that encode proteins required for retrotransposition. Common autonomous retrotransposons are (i) LTRs or (ii) non-LTRs. Examples of LTR retrotransposons are human endogenous retroviruses (HERV) (shown) and various Ty elements of S. cerevisiae (not shown). These elements have terminal LTRs and slightly overlapping ORFs for their group-specific antigen (gag), protease (prt), polymerase (pol), and envelope (env) genes. They produce target site duplications (TSDs) upon insertion. Also shown are the reverse transcriptase (RT) and endonuclease (EN) domains. Other LTR retrotransposons that are responsible for most mobile-element insertions in mice are the intracisternal A-particles (IAPs), early transposons (Etns), and mammalian LTR-retrotransposons (MaLRs). These elements are not present in humans, and essentially all are defective, so the source of their RT in trans remains unknown. L1 is an example of a non-LTR retrotransposon. L1s consist of a 5'-untranslated region (5' UTR) containing an internal promoter, two ORFs, a 3' UTR, and a poly(A) signal followed by a poly(A) tail (An). L1s are usually flanked by 7- to 20-bp target site duplications (TSDs). The RT, EN, and a conserved cysteine-rich domain (C) are shown. An Alu element is an example of a nonautonomous retrotransposon. Alus contain two similar monomers, the left (L) and the right (R), and end in a poly(A) tail. Approximate full-length element sizes are given in parentheses.

Class 2 TEs are characterized by the presence of terminal inverted repeats, about 9 to 40 base pairs long, on both of their ends (Figure 3). As the name suggests and as Figure 3 shows, terminal inverted repeats are inverted complements of each other; for instance, the complement of ACGCTA (the inverted repeat on the right side of the TE in the figure) is TGCGAT (which is the reverse order of the terminal inverted repeat on the left side of the TE in the figure). One of the roles of terminal inverted repeats is to be recognized by transposase.

Figure 3: The structure of a DNA transposon.

DNA transposons, also known as class 2 transposable elements, are flanked at both ends by terminal inverted repeats. The inverted repeats are complements of each other (the repeat at one end is a mirror image of, and composed of complementary nucleotides to, the repeat at the opposing end).

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Human genome

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For a non-technical introduction to the topic, see Introduction to genetics.

Genomic information

Graphical representation of the idealized human diploid karyotype, showing the organization of the genome into chromosomes. This drawing shows both the male (XY) and female (XX) versions of the 23rd chromosome pair. Chromosomes are shown aligned at their centromeres. The mitochondrial DNA is not shown.

NCBI genome ID 51 Ploidy diploid

Genome size 3,100 Mbp[1] (mega-basepairs) per haploid genome

6,200 Mbp total (diploid).

Number of chromosomes 23 pairs

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome.[2] Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1% due to single-nucleotide variants[3] and 0.6% when considering indels),[4] these are considerably smaller than the differences between humans and their closest living relatives, the bonobos and chimpanzees (~1.1% fixed single-nucleotide variants [5] and 4% when including indels).[6]

Although the sequence of the human genome has been (almost) completely determined by DNA sequencing, it is not yet fully understood. Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, and signals controlling epigenetic inheritance.

Prior to the acquisition of the full genome sequence, estimates of the number of human genes ranged from 50,000 to 140,000 (with occasional vagueness about whether these estimates included non-protein coding genes).[7] As genome sequence quality and the methods for identifying protein-coding genes improved,[8] the count of recognized protein-coding genes dropped to 19,000-20,000.[9] However, a fuller understanding of the role played by sequences that do not encode proteins, but instead express regulatory RNA, has raised the total number of genes to at least 46,831,[10] plus another 2300 micro-RNA genes.[11] By 2012, functional DNA elements that encode neither RNA nor proteins have been noted.[12] A 2018 population survey found another 300 million bases of human genome that was not in the reference sequence.[13]

Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA genes, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined.[14]

1 Sequencing 2 Completeness

3 Molecular organization and gene content

3.1 Information content

4 Coding vs. noncoding DNA

5 Coding sequences (protein-coding genes)

6 Noncoding DNA (ncDNA)

6.1 Pseudogenes

6.2 Genes for noncoding RNA (ncRNA)

6.3 Introns and untranslated regions of mRNA

6.4 Regulatory DNA sequences

6.5 Repetitive DNA sequences

6.6 Mobile genetic elements (transposons) and their relics

7 Genomic variation in humans

7.1 Human reference genome

7.2 Measuring human genetic variation

7.2.1 Mapping human genomic variation

7.3 Structural variation

7.4 SNP frequency across the human genome

7.5 Personal genomes

7.6 Human knockouts

8 Human genetic disorders

9 Evolution

10 Mitochondrial DNA

11 Epigenome 12 See also 13 References 14 External links

Sequencing[edit]

The first human genome sequences were published in nearly complete draft form in February 2001 by the Human Genome Project[15] and Celera Corporation.[16] Completion of the Human Genome Project's sequencing effort was announced in 2004 with the publication of a draft genome sequence, leaving just 341 gaps in the sequence, representing highly-repetitive and other DNA that could not be sequenced with the technology available at the time.[8] The human genome was the first of all vertebrates to be sequenced to such near-completion, and as of 2018, the diploid genomes of over a million individual humans had been determined using next-generation sequencing.[17] In 2021 it was reported that the T2T consortium had filled in all of the gaps in the X chromosome.[18]

These data are used worldwide in biomedical science, anthropology, forensics and other branches of science. Such genomic studies have led to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution.

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Source : en.wikipedia.org

LS 7A Week 9

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LS 7A Week 9--PCR & Genome Variation, Mutation & DNA repair

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The estimated number of genes in the human genome is:

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25,000

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The C-value paradox states that genome size:

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is uncorrelated with complexity.

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Terms in this set (35)

The estimated number of genes in the human genome is:

25,000

The C-value paradox states that genome size:

is uncorrelated with complexity.

The complexity of an organism is proportional to the number of genes in its genome.

False

Only 2.5% of the human genome actually codes for proteins. The other 97.5% includes:

Introns, noncoding RNA, repetitive DNA

Complex organisms can be characterized as having a:

large genome with few protein-coding genes.

small genome with few protein-coding genes.

small genome with many protein-coding genes.

large genome with many protein-coding genes.

None of the options are correct