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Processed pseudogene insertions in somatic cells.

Kazazian HH - Mob DNA (2014)

Bottom Line: Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements.Until recently, very few polymorphic processed pseudogenes had been discovered in mammalian genomes.Now several studies have found a number of polymorphic processed pseudogenes in humans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

ABSTRACT
Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements. Processed pseudogenes generally lack introns, end in a 3' poly A, and are flanked by target site duplications. Until recently, very few polymorphic processed pseudogenes had been discovered in mammalian genomes. Now several studies have found a number of polymorphic processed pseudogenes in humans. Moreover, processed pseudogenes can occur in somatic cells, including in various cancers and in early fetal development. One recent somatic insertion of a processed pseudogene has caused a Mendelian X-linked disease, chronic granulomatous disease.

No MeSH data available.


Related in: MedlinePlus

Locations of 48 non-reference gene processed pseudogene insertions sites in the human genome based on reads mapped to source genes. Discordant read mappings are represented by links colored based on chromosome of the source gene. Insertion sites are represented by black circles and the gene labels are based on the position of the source gene. Republished with permission from Nature Communications.
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Figure 1: Locations of 48 non-reference gene processed pseudogene insertions sites in the human genome based on reads mapped to source genes. Discordant read mappings are represented by links colored based on chromosome of the source gene. Insertion sites are represented by black circles and the gene labels are based on the position of the source gene. Republished with permission from Nature Communications.

Mentions: About one year ago, a comprehensive paper on polymorphism among PPs in human beings appeared. Ewing et al. devised a bioinformatic pipeline to detect polymorphic PPs. Using discordant reads not present in reference genomes, they found 48 novel PP insertion sites among 939 low pass genomes from the 1,000 genomes project [22]. These PPs came from a wide variety of source genes, and were spread throughout the human chromosomes (FigureĀ 1). All 48 of these polymorphic PPs were confirmed by locating the precise genomic insertion site. This group also studied the genome sequences of 85 human cancer-normal tissue pairs representing a variety of cancers. Among these cancers they found the first instances of somatic insertion of PPs; three PPs were predicted to occur in lung cancers that were absent from paired normal tissue. The authors also estimated the rate of PP insertion in human beings at one insertion in every approximately 5,200 individuals/generation [22].


Processed pseudogene insertions in somatic cells.

Kazazian HH - Mob DNA (2014)

Locations of 48 non-reference gene processed pseudogene insertions sites in the human genome based on reads mapped to source genes. Discordant read mappings are represented by links colored based on chromosome of the source gene. Insertion sites are represented by black circles and the gene labels are based on the position of the source gene. Republished with permission from Nature Communications.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4151081&req=5

Figure 1: Locations of 48 non-reference gene processed pseudogene insertions sites in the human genome based on reads mapped to source genes. Discordant read mappings are represented by links colored based on chromosome of the source gene. Insertion sites are represented by black circles and the gene labels are based on the position of the source gene. Republished with permission from Nature Communications.
Mentions: About one year ago, a comprehensive paper on polymorphism among PPs in human beings appeared. Ewing et al. devised a bioinformatic pipeline to detect polymorphic PPs. Using discordant reads not present in reference genomes, they found 48 novel PP insertion sites among 939 low pass genomes from the 1,000 genomes project [22]. These PPs came from a wide variety of source genes, and were spread throughout the human chromosomes (FigureĀ 1). All 48 of these polymorphic PPs were confirmed by locating the precise genomic insertion site. This group also studied the genome sequences of 85 human cancer-normal tissue pairs representing a variety of cancers. Among these cancers they found the first instances of somatic insertion of PPs; three PPs were predicted to occur in lung cancers that were absent from paired normal tissue. The authors also estimated the rate of PP insertion in human beings at one insertion in every approximately 5,200 individuals/generation [22].

Bottom Line: Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements.Until recently, very few polymorphic processed pseudogenes had been discovered in mammalian genomes.Now several studies have found a number of polymorphic processed pseudogenes in humans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

ABSTRACT
Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements. Processed pseudogenes generally lack introns, end in a 3' poly A, and are flanked by target site duplications. Until recently, very few polymorphic processed pseudogenes had been discovered in mammalian genomes. Now several studies have found a number of polymorphic processed pseudogenes in humans. Moreover, processed pseudogenes can occur in somatic cells, including in various cancers and in early fetal development. One recent somatic insertion of a processed pseudogene has caused a Mendelian X-linked disease, chronic granulomatous disease.

No MeSH data available.


Related in: MedlinePlus