Human LINE retrotransposons generate processed pseudogenes

10.1038/74184 ◽  
2000 ◽  
Vol 24 (4) ◽  
pp. 363-367 ◽  
Author(s):  
Cécile Esnault ◽  
Joël Maestre ◽  
Thierry Heidmann
Keyword(s):  
Processed Pseudogenes ◽  
Human Line

scholarly journals Evolutionary direction of processed pseudogenes

2016 ◽  
Vol 59 (8) ◽  
pp. 839-849 ◽  
Author(s):  
Guoqing Liu ◽  
Xiangjun Cui ◽  
Hong Li ◽  
Lu Cai
Keyword(s):  
Processed Pseudogenes

scholarly journals A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes

1989 ◽  
Vol 86 (17) ◽  
pp. 6691-6695 ◽  
Author(s):  
B Davies ◽  
S Feo ◽  
E Heard ◽  
M Fried
Keyword(s):  
Ribosomal Protein ◽  
Recombinant Dna ◽  
Single Gene ◽  
Ribosomal Protein Gene ◽  
Pcr Primers ◽  
Pcr Product ◽  
Dna Libraries ◽  
Processed Pseudogenes ◽  
Polymerase Chain ◽  
Genomic Dna Sequence

We have devised a strategy that utilizes the polymerase chain reaction (PCR) for the detection and isolation of intron-containing genes in the presence of an abundance of processed pseudogenes. The method depends on the genomic DNA sequence between the PCR primers spanning at least one intron in the gene of interest, resulting in the generation of a larger intron-containing PCR product in addition to the smaller PCR product amplified from the intronless pseudogenes. A unique intron probe isolated from the larger PCR product is used for the detection of intron-containing clones from recombinant DNA libraries that also contain pseudogene clones. This method has been used successfully for the selective isolation of an intron-containing rat L19 ribosomal protein gene in the presence of multiple pseudogenes. Analysis of a number of mammalian ribosomal protein multigene families by PCR indicates that they all contain only a single gene with introns.

scholarly journals One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

1988 ◽  
Vol 8 (9) ◽  
pp. 3898-3905 ◽  
Author(s):  
C Huxley ◽  
T Williams ◽  
M Fried
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
The Other ◽  
Base Pairs ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Processed Pseudogenes ◽  
Dna Fragment ◽  
Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

Quantification of expression of linked cloned genes in a simian virus 40-transformed xeroderma pigmentosum cell line

1985 ◽  
Vol 5 (7) ◽  
pp. 1685-1693
Author(s):  
M Protić-Sabljić ◽  
D Whyte ◽  
J Fagan ◽  
B H Howard ◽  
C M Gorman ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Cell Lines ◽  
Xeroderma Pigmentosum ◽  
Phenotypic Expression ◽  
Simian Virus 40 ◽  
Fibroblast Cell ◽  
Simian Virus ◽  
Selective Medium ◽  
Normal Human ◽  
Human Line

We wished to determine whether simian virus 40 (SV40)-transformed xeroderma pigmentosum cells, despite their defective DNA repair, were suitable for DNA-mediated gene transfer experiments with linked genes. Expression of a nonselectable gene (cat, coding for chloramphenicol acetyltransferase [CAT]) linked to a selectable gene (gpt, coding for xanthine-guanine phosphoribosyltransferase [XPRT]) in the plasmid pSV2catSVgpt was quantified after transfection of SV40-transformed xeroderma pigmentosum [XP20s(SV40)] and normal human [GM0637(SV40)] fibroblast cell lines. A novel autoradiographic assay with [3H]xanthine incorporation showed 0.5 to 0.7% phenotypic expression of XPRT in both cell lines. Without selection, transient CAT activity was 20 times greater in the GM0637(SV40) than in the XP20s(SV40) cells, and transient XPRT activity was 5 times greater. Both of these transient activities were increased and equalized in both cell lines by transfection with pRSVcat or pRSVgpt. Genotypic transformation to gpt+ occurred at a frequency of 2 X 10(-4) to 4 X 10(-4) in both cell lines with pSV2catSVgpt. After 2 to 3 months in selective medium, stable expression of the (nonselected) cat gene was found in 11 (92%) of 12 gpt-containing clones derived from GM0637(SV40) cells and in 13 (81%) of 16 gpt-containing clones from XP20s(SV40) cells. However, the levels of CAT activity did not correlate with those of XPRT activity, and both of these activities varied more than 100-fold among different clones. Copies (1 to 4) of the gpt gene were integrated in four clones of the GM0637(SV40) cells having an XPRT activity of 1 to 5 nmol/min per mg, but 5 to 80 copies were integrated in four XP20s(SV40) clones with an XPRT activity of 0.8 to 1.8 nmol/min per mg. This study shows that XP20s(SV40) is as suitable for gene transfer experiments as the normal human line GM0637(SV40).

scholarly journals PCR analysis of the H ferritin multigene family reveals the existence of two classes of processed pseudogenes.

1994 ◽  
Vol 4 (2) ◽  
pp. 85-88 ◽  
Author(s):  
B Quaresima ◽  
M T Tiano ◽  
A Porcellini ◽  
P D'Agostino ◽  
M C Faniello ◽  
...  
Keyword(s):  
Multigene Family ◽  
Pcr Analysis ◽  
Processed Pseudogenes

Genes for intermediate filament proteins and the draft sequence of the human genome

2001 ◽  
Vol 114 (14) ◽  
pp. 2569-2575 ◽  
Author(s):  
Michael Hesse ◽  
Thomas M. Magin ◽  
Klaus Weber
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Intermediate Filament ◽  
Muscle Protein ◽  
Gene Families ◽  
Type I ◽  
Type Ii ◽  
Draft Sequence ◽  
Intermediate Filament Proteins ◽  
Processed Pseudogenes

We screened the draft sequence of the human genome for genes that encode intermediate filament (IF) proteins in general, and keratins in particular. The draft covers nearly all previously established IF genes including the recent cDNA and gene additions, such as pancreatic keratin 23, synemin and the novel muscle protein syncoilin. In the draft, seven novel type II keratins were identified, presumably expressed in the hair follicle/epidermal appendages. In summary, 65 IF genes were detected, placing IF among the 100 largest gene families in humans. All functional keratin genes map to the two known keratin clusters on chromosomes 12 (type II plus keratin 18) and 17 (type I), whereas other IF genes are not clustered. Of the 208 keratin-related DNA sequences, only 49 reflect true keratin genes, whereas the majority describe inactive gene fragments and processed pseudogenes. Surprisingly, nearly 90% of these inactive genes relate specifically to the genes of keratins 8 and 18. Other keratin genes, as well as those that encode non-keratin IF proteins, lack either gene fragments/pseudogenes or have only a few derivatives. As parasitic derivatives of mature mRNAs, the processed pseudogenes of keratins 8 and 18 have invaded most chromosomes, often at several positions. We describe the limits of our analysis and discuss the striking unevenness of pseudogene derivation in the IF multigene family. Finally, we propose to extend the nomenclature of Moll and colleagues to any novel keratin.

scholarly journals Brain cell somatic gene recombination and its phylogenetic foundations

2020 ◽  
Vol 295 (36) ◽  
pp. 12786-12795 ◽  
Author(s):  
Gwendolyn Kaeser ◽  
Jerold Chun
Keyword(s):  
Brain Cell ◽  
Gene Recombination ◽  
Evolutionary Origins ◽  
Gene Optimization ◽  
Somatic Gene ◽  
Multiple Copies ◽  
Processed Pseudogenes ◽  
Near Term ◽  
Rt Inhibitors ◽  
Enzymatic Machinery

A new form of somatic gene recombination (SGR) has been identified in the human brain that affects the Alzheimer's disease gene, amyloid precursor protein (APP). SGR occurs when a gene sequence is cut and recombined within a single cell's genomic DNA, generally independent of DNA replication and the cell cycle. The newly identified brain SGR produces genomic complementary DNAs (gencDNAs) lacking introns, which integrate into locations distinct from germline loci. This brief review will present an overview of likely related recombination mechanisms and genomic cDNA-like sequences that implicate evolutionary origins for brain SGR. Similarities and differences exist between brain SGR and VDJ recombination in the immune system, the first identified SGR form that now has a well-defined enzymatic machinery. Both require gene transcription, but brain SGR uses an RNA intermediate and reverse transcriptase (RT) activity, which are characteristics shared with endogenous retrotransposons. The identified gencDNAs have similarities to other cDNA-like sequences existing throughout phylogeny, including intron-less genes and inactive germline processed pseudogenes, with likely overlapping biosynthetic processes. gencDNAs arise somatically in an individual to produce multiple copies; can be functional; appear most frequently within postmitotic cells; have diverse sequences; change with age; and can change with disease state. Normally occurring brain SGR may represent a mechanism for gene optimization and long-term cellular memory, whereas its dysregulation could underlie multiple brain disorders and, potentially, other diseases like cancer. The involvement of RT activity implicates already Food and Drug Administration–approved RT inhibitors as possible near-term interventions for managing SGR-associated diseases and suggest next-generation therapeutics targeting SGR elements.

scholarly journals The Female Line in the Bible. Ratzinger’s Deepening of the Church’s Understanding of Tradition and Mary

Religions ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 310
Author(s):  
Mary Frances McKenna
Keyword(s):  
Holy Spirit ◽  
Full Potential ◽  
Human Being ◽  
Salvation History ◽  
Adam And Eve ◽  
The Bible ◽  
Female Line ◽  
Dei Verbum ◽  
Male Line ◽  
Human Line

This paper explores the female line in the Bible that Joseph Ratzinger identifies as running in parallel to, and being indispensable for, the male line in the Bible. This female line expands the understanding of Salvation History as described by Dei Verbum so that it runs not just from Adam through to Jesus, but also from Adam and Eve to Mary and Jesus, the final Adam. Ratzinger’s female line demonstrates that women are at the heart of God’s plan for humanity. I illustrate that this line is evident when Ratzinger’s method of biblical interpretation is applied to the women of Scripture. Its full potential comes into view through Ratzinger’s development of the Christian notion of person: Person as revealed by Jesus Christ is relatedness without reserve with God and is fully applicable to the human being through Christ. I argue that together, the male and female lines in the Bible form the human line in the Bible, in which the male line represents “the humanity”, every human being, while the female line represents the communal aspect of humanity. Moreover, I contend that Christianity’s notion of mother in relation to God (as Father, Son and Holy Spirit) should be understood through Mary’s response at the Annunciation. Mother in relation to God is to be understood through the Incarnation when Mary, as person, lived her life wholly in relation with and for God.

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