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Encyclopedia > Chimpanzee genome project

The Chimpanzee Genome Project is an effort to determine the DNA sequence of the genome of the closest living human relatives. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species. The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life, and most viruses. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ...

Chimp-human chromosome differences. The major structural difference is that human chromosome 2 (green color code) was derived from two smaller chromosomes that are found in other great apes (now called 2A and 2B, see: Entrez PubMed 15218271). Parts of human chromosome 2 are scattered among parts of several cat and rat chromosomes in these species that are more distantly related to humans (more ancient common ancestors; about 85 million years since the human/rodent common ancestor: Entrez PubMed 12552136)
Chimp-human chromosome differences. The major structural difference is that human chromosome 2 (green color code) was derived from two smaller chromosomes that are found in other great apes (now called 2A and 2B, see: Entrez PubMed 15218271). Parts of human chromosome 2 are scattered among parts of several cat and rat chromosomes in these species that are more distantly related to humans (more ancient common ancestors; about 85 million years since the human/rodent common ancestor: Entrez PubMed 12552136)

Contents

Changes in chromosomes during evolution. ... Changes in chromosomes during evolution. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ...


Starting the chimpanzee genome project

Human and common chimpanzee fuckchromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres producing human chromosome two. There are only nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, 18. After the completion of the Human genome project, a Common Chimpanzee genome project was initiated. In December of 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as the forkhead-box P2 transcription factor, which is involved in speech development, have undergone rapid evolution in the human lineage. Several genes involved in hearing were also found to have changed rapidly during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and Common Chimpanzees are about 10 times the typical difference between pairs of humans. Figure 1: Chromosome. ... Genera Subfamily Ponginae Pongo - Orangutans Gigantopithecus (extinct) Sivapithecus (extinct) Subfamily Homininae Gorilla - Gorillas Pan - Chimpanzees Homo - Humans Paranthropus (extinct) Australopithecus (extinct) Sahelanthropus (extinct) Ardipithecus (extinct) Kenyanthropus (extinct) Pierolapithecus (extinct) (tentative) The Hominids (Hominidae) are a biological family which includes humans, extinct species of humanlike creatures and the other great apes... A telomere is a region of highly repetitive DNA at the end of a chromosome that functions as a disposable buffer. ... The Human Genome Project (HGP) endeavoured to map the human genome down to the nucleotide (or base pair) level and to identify all the genes present in it. ... December 2003: January - February - March - April - May - June - July - August - September - October - November - December - → Events December 31, 2003 In Taiwan, President Chen Shui-bian signs a law that allows referendums to be held. ... 2003 (MMIII) was a common year starting on Wednesday of the Gregorian calendar. ... In molecular biology, a transcription factor is a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. ...


Draft genome sequence of the common chimpanzee

Analysis of the genome was published in Nature on September 1, 2005, in an article produced by the Chimpanzee Sequencing and Analysis Consortium, a group of scientists which is supported in part by the National Human Genome Research Institute, one of the National Institutes of Health. The article marked the completion of the draft genome sequence[1]. A database[2] now exists containing the genetic differences between human and chimpanzee genes, with about thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. Gene duplications account for most of the sequence differences between humans and chimps. Single-base-pair substitutions account for about half as much genetic change as does gene duplication. Nature is one of the oldest and most reputable scientific journals, first published on 4 November 1869. ... September 1 is the 244th day of the year (245th in leap years). ... 2005 (MMV) was a common year starting on Saturday of the Gregorian calendar. ... The Chimpanzee Sequencing and Analysis Consortium is the international team of researchers who have been attempting to sequence the chimpanzee genome. ... The National Human Genome Research Institute (NHGRI) is a division of the National Institutes of Health, located in Bethesda, Maryland. ... The National Institutes of Health (NIH) is the primary agency of the United States government responsible for medical research. ... A point mutation, or substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide. ... In biology, mutations are changes to the genetic material (usually DNA or RNA). ... Figure 1: Chromosome. ... Chromosomal translocation of the 4th and 20th chromosome. ... Schematic of a region of a chromosome before and after a duplication event Gene duplication occurs when an error in DNA replication leads to the duplication of a region of DNA containing a (generally functional) gene. ...


Typical human and chimp homologs of proteins differ in only an average of two amino acids. About 30 percent of all human proteins are identical in sequence to the corresponding chimp protein. As mentioned above, gene duplications are a major source of differences between human and chimp genetic material, with about 2.7 percent of the genome now representing differences having been produced by gene duplications or deletions during approximately 6 million years since humans and chimps diverged from their common evolutionary ancestor. The term homologue or homolog has several meanings: In biology, homologues are structures that are alike because of shared ancestry. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ...


About 600 genes have been identified that may have been undergoing strong positive selection in the human and chimp lineages; many of these genes are involved in immune system defense against microbial disease (example: granulysin is protective against Mycobacterium tuberculosis, see: Entrez PubMed 9756476) or are targeted receptors of pathogenic microorganisms (example: Glycophorin C and Plasmodium falciparum). By comparing human and chimp genes to the genes of other mammals, it has been found that genes coding for transcription factors (such as forkhead-box P2 (FOXP2), mentioned above) have often evolved faster in the human relative to chimp; relatively small changes in these genes may account for the morphological differences between humans and chimps. A set of 348 transcription factor genes code for proteins with an average of about 50 percent more amino acid changes in the human lineage than in the chimp lineage. The immune system is the system of specialized cells and organs that protect an organism from outside biological influences. ... Binomial name Mycobacterium tuberculosis Zopf, 1883 Mycobacterium tuberculosis is the bacterium that causes most cases of tuberculosis. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Glycophorin C (GYPC; CD236/CD236R; glycoprotein beta; glycoconnectin; PAS-2) is an integral membrane protein of the erythrocyte and acts as the receptor for the Plasmodium falciparum protein PfEBP-2 (erythrocyte binding protein 2; baebl; EBA-140). ... Binomial name Plasmodium falciparum Welch, 1897 Plasmodium falciparum is a protozoan parasite, one of the species of Plasmodium that cause malaria in humans. ... In the context of genetics, a transcription factor is a regulatory protein that initiates the transcription of certain genes upon binding with DNA. The binding of a transcription factor to a specific DNA sequence can result in either an increased rate of transcription of the gene, known as activated transcription...


Six human chromosomal regions were found that may have been under particularly strong and coordinated selection during the past 250,000 years. These regions contain at least one marker allele that seems unique to the human lineage while the entire chromosomal region shows lower than normal genetic variation. This pattern suggests that one or a few strongly selected genes in the chromosome region may have been preventing the random accumulation of neutral changes in other nearby genes. One such region on chromosome 7 contains the FOXP2 gene (mentioned above) and this region also includes the Cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is important for ion transport in tissues such as the salt-secreting epithelium of sweat glands. Human mutations in the CFTR gene might be selected for as a way to survive cholera (see: Entrez PubMed 15905150). An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. ... FOXP2 (forkhead box P2) is a gene that is implicated in the development of language skills, including grammatical competence. ... Cystic fibrosis transmembrane conductance regulator (CFTR) is an ABC (ATP-binding cassette) transporter-class protein that functions in transporting chloride ions across epithelial cells found in the lung, liver, pancreas, digestive tract, reproductive tract, and skin. ... Cholera (also called Asiatic cholera) is an infectious disease, caused by bacteria that are typically ingested by drinking water that is contaminated by improper sanitation, or by eating improperly cooked fish, especially shellfish. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ...


Another such region on chromosome 4 may contain elements regulating the expression of a nearby protocadherin[3] gene that may be important for brain development and function[4]. Although changes in expression of genes that are expressed in the brain tend to be less than for other organs (such as liver) on average, gene expression changes in the brain have been more dramatic in the human lineage than in the chimp lineage[5]. This is consistent with the dramatic divergence of the unique pattern of human brain development seen in the human lineage compared to the ancestral great ape pattern. The protocadherin-beta gene cluster on chromosome 5 also shows evidence of possible positive selection (see: Entrez PubMed 15777644). Comparative brain sizes In animals, the brain, or encephalon (Greek for in the head), is the control center of the central nervous system. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ...


Results from the human and chimp genome analyses should help in understanding some human diseases. Humans appear to have lost a functional caspase-12 gene, which in other primates codes for an enzyme that may protect against Alzheimer's disease. Caspases are a group of cysteine proteases, enzymes with a crucial cysteine residue that can cleave other proteins, after an aspartic acid residue, a specificity which is unusual among proteases. ...


Image:Humanchimpchromosomes.png Image File history File links Download high resolution version (980x262, 14 KB) Summary I made this diagram using PhotoShop and ClarisDraw. ...


Genes of the Chromosome 2 fusion site

Diagramatic representation of the location of the fusion site of chromosomes 2A and 2B and the genes inserted at this location.
Diagramatic representation of the location of the fusion site of chromosomes 2A and 2B and the genes inserted at this location.

The results of the chimpanzee genome project suggest that when ancestral chromosomes 2A and 2B fused to produce human chromosome 2, no genes were lost from the fused ends of 2A and 2B. At the site of fusion, there is approximately 150,000 base pairs of sequence not found in chimpanzee chromosomes 2A and 2B. Additional linked copies of the PGML/FOXD/CBWD genes exist elsewhere in the human genome, particularly near the p end of chromosome 9. This suggests that a copy of these genes may have been added to the end of the ancestral 2A or 2B prior to the fusion event. It remains to be determined if these inserted genes confer a selective advantage. Image File history File links Download high resolution version (454x611, 48 KB) Summary I made this diagram using PhotoShop and ClarisDraw. ... Image File history File links Download high resolution version (454x611, 48 KB) Summary I made this diagram using PhotoShop and ClarisDraw. ... Chromosome 2 is one of the 23 pairs of chromosomes in humans. ...

  • PGML. The phosphoglucomutase-like gene of human chromosome 2. This gene is incomplete and may not produce a functional transcript [6].
  • FOXD. The forkhead box D4-like gene is an example of an intronless gene. The function of this gene is not known, but it may code for a transcription control protein.
  • CBWD. Cobalamin synthetase is a bacterial enzyme that makes vitamin B12. In the distant past, a common ancestor to mice and apes incorporated a copy of a cobalamin synthetase gene. Humans are unusual in that they have several copies of cobalamin synthetase-like genes, including the one on chromosome 2. It remains to be determined what the function of these human cobalamin synthetase-like genes is. If these genes are involved in vitamin B12 metabolism, this could be relevant to human evolution. A major change in human development is greater post-natal brain growth than is observed in other apes. Vitamin B12 is important for brain gevelopment, and vitamin B12 deficiency during brain development results in severe neurological defects in human children.
  • CXYorf1-like protein. Several transcripts of unknown function corresponding to this region have been isolated. This region is also present in the closely related chromosome 9p terminal region that contains copies of the PGML/FOXD/CBWD genes.
  • Many ribosomal protein L23a pseudogenes are scattered through the human genome.

Phosphoglucomutase (EC 5. ... Chemical structure of Vitamin B12 The name vitamin B12 (or B12 for short) is used in two different ways. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... A pseudogene is a nucleotide sequences that is similar to a normal gene, but is not expressed as a functional protein. ...

References

  1. ^  Chimpanzee Sequencing and Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human genome". Nature 437: 69-87. (September 1) Entrez PubMed 16136131; Cheng Z, Ventura M et al. (2005). "A genome-wide comparison of recent chimpanzee and human segmental duplications". Nature 437: 88-93. (September 1) Entrez PubMed 16136132
  2. ^  Chimp genome statistics and chromosomes. Chimp mitochondrial DNA sequence.
  3. ^  Discussion of Protocadherins in Geoffrey M. Cooper (2000). The Cell - A Molecular Approach, Sinauer Associates, Inc. Sunderland (MA). ISBN 0-87893-106-6. Online textbook.
  4. ^  "New Genome Comparison Finds Chimps, Humans Very Similar at the DNA Level" National Human Genome Research Institute
  5. ^  Khaitovich et al. (2005). "Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees". Science. DOI:10.1126/science.1108296. (September 1)
  6. ^  Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions by Y. Fan, T. Newman, E. Linardopoulou and B. J. Trask in Genome Research (2002) Volume 12 pages 1663-1672. Entrez PubMed 12421752

Nature is one of the oldest and most reputable scientific journals, first published on 4 November 1869. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Nature is one of the oldest and most reputable scientific journals, first published on 4 November 1869. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Science is the journal of the American Association for the Advancement of Science (AAAS). ... A digital object identifier (or DOI) is a permanent identifier (permalink) given to a World Wide Web file or other Internet document so that if its Internet address changes, users will be redirected to its new address. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ...

See also


  Results from FactBites:
 
Harvard Gazette: Chimpanzee genome effort shines light on human evolution (979 words)
DNA for the chimpanzee genome project was taken from the blood of a male chimpanzee at the Yerkes National Primate Research Center in Atlanta.
The sequencing and assembly of the chimpanzee genome was done at the Broad Institute and at the Washington University School of Medicine in St. Louis.
Though completing the chimpanzee genome is an achievement in itself, it is the ability to now compare chimpanzee and human DNA side-by-side that has researchers excited.
CHIMPS AND CHIMPANZEES (2431 words)
Chimpanzees rarely live past the age of 40 in the wild, but have been known to reach the age of 60 in captivity, although Tarzan star Cheeta is still alive as of 2006 at the age of 74.
The first of these early trans-continental chimpanzees came from Angola and were presented as a gift to the Prince of Orange in 1640, and were followed by a few of its brethren over the next several years.
It is thought that humans shared a common ancestor with chimpanzees and gorillas as recently as four to seven million years ago, and that they have about 95 to 99.4 percent of their DNA in common with humans, with at least some of the difference occurring in 'junk' DNA.
  More results at FactBites »

 
 

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