scholarly journals Genome-Wide Characterization of Zebrafish Endogenous Retroviruses Reveals Unexpected Diversity in Genetic Organizations and Functional Potentials

2021 ◽  
Author(s):  
Jun Bai ◽  
Zuo-zhen Yang ◽  
Hao Li ◽  
Yun Hong ◽  
Dong-dong Fan ◽  
...  
Keyword(s):  
Human Genome ◽  
Endogenous Retroviruses ◽  
Genetic Evolution ◽  
Past Infection ◽  
Genome Wide ◽  
New Frontier

Endogenous retroviruses (ERVs) are relics of past infection that constitute up to 8% of the human genome. Understanding the genetic evolution of the ERV family and the interplay of ERVs and encoded RNAs and proteins with host function has become a new frontier in biology.

scholarly journals Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences

2005 ◽  
Vol 79 (5) ◽  
pp. 2941-2949 ◽  
Author(s):  
Aline Flockerzi ◽  
Stefan Burkhardt ◽  
Werner Schempp ◽  
Eckart Meese ◽  
Jens Mayer
Keyword(s):  
Human Genome ◽  
Germ Line ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retrovirus ◽  
Long Terminal Repeats ◽  
Essential Information ◽  
Human Endogenous Retroviruses ◽  
Consensus Sequences

ABSTRACT The human genome harbors many distinct families of human endogenous retroviruses (HERVs) that stem from exogenous retroviruses that infected the germ line millions of years ago. Many HERV families remain to be investigated. We report in the present study the detailed characterization of the HERV-K14I and HERV-K14CI families as they are represented in the human genome. Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line ∼39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock. Proviruses of both families were formed during a brief period. A majority of HERV-K14CI proviruses on the Y chromosome mimic a higher evolutionary age, showing that LTR-LTR divergence data can indicate false ages. Fully translatable consensus sequences encoding major retroviral proteins were generated. Most HERV-K14I loci lack an env gene and are structurally reminiscent of LTR retrotransposons. A minority of HERV-K14I variants display an env gene. HERV-K14I proviruses are associated with three distinct LTR families, while HERV-K14CI is associated with a single LTR family. Hybrid proviruses consisting of HERV-K14I and HERV-W sequences that appear to have produced provirus progeny in the genome were detected. Several HERV-K14I proviruses harbor TRPC6 mRNA portions, exemplifying mobilization of cellular transcripts by HERVs. Our analysis contributes essential information on two more HERV families and on the biology of HERV sequences in general.

scholarly journals Genome-Wide Detection and Characterization of Endogenous Retroviruses in Bos taurus

2010 ◽  
Vol 84 (20) ◽  
pp. 10852-10862 ◽  
Author(s):  
Koldo Garcia-Etxebarria ◽  
Begoña Marina Jugo
Keyword(s):  
Phylogenetic Relationship ◽  
Germ Line ◽  
Bos Taurus ◽  
Gc Content ◽  
Endogenous Retroviruses ◽  
Long Terminal Repeats ◽  
Multiple Methods ◽  
Bioinformatic Tools ◽  
Genome Wide

ABSTRACT Endogenous retroviruses (ERVs) are the proviral phase of exogenous retroviruses that become integrated into a host germ line. They can play an important role in the host genome. Bioinformatic tools have been used to detect ERVs in several vertebrates, primarily primates and rodents. Less information is available regarding ERVs in other mammalian groups, and the source of this information is basically experimental. We analyzed the genome of the cow (Bos taurus) using three different methods. A BLAST-based method detected 928 possible ERVs, LTR_STRUC detected 4,487 elements flanked by long terminal repeats (LTRs), and Retrotector detected 9,698 ERVs. The ERVs were not homogeneously distributed across chromosomes; the number of ERVs was positively correlated with chromosomal size and negatively correlated with chromosomal GC content. The bovine ERVs (BoERVs) were classified into 24 putative families, with 20 of them not previously described. One of these new families, BoERV1, was the most abundant family and appeared to be specific to ruminants. An analysis of representatives of ERV families from rodents, primates, and ruminants showed a phylogenetic relationship following their hosts' relationships. This study demonstrates the importance of using multiple methods when trying to identify new ERVs and shows that the number of bovine ERV families is not as limited as previously thought.

scholarly journals Genome-wide approaches and technologies to assess human variation

2013 ◽  
Author(s):  
Claudia Gonzaga-Jauregui
Keyword(s):  
Human Genome ◽  
Genetic Disorders ◽  
Copy Number Variants ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Genomic Technologies ◽  
Genome Wide ◽  
Genome Analyses ◽  
Next Generation Sequencing Ngs

Current genome-wide technologies allow interrogation and exploration of the human genome as never before. Next-generation sequencing (NGS) technologies, along with high resolution Single Nucleotide Polymorphisms (SNP) arrays and array Comparative Genomic Hybrization (aCGH) enable assessment of human genome variation at the finest resolution from base pair changes such as simple nucleotide variants (SNVs) to large copy-number variants (CNVs). The application of these genomic technologies in the clinical setting has also enabled the molecular characterization of genetic disorders and the understanding of the biological functions of more genes in human development, disease, and health. In this review, the current approaches and platforms available for high-throughput human genome analyses, the steps involved in these different methodologies from sample preparation to data analysis, their applications, and limitations are summarized and discussed.

scholarly journals Genome-Wide Characterization of Endogenous Retroviruses in Bombyx mori Reveals the Relatives and Activity of env Genes

2018 ◽  
Vol 9 ◽  
Author(s):  
Min Feng ◽  
Xiong Wang ◽  
Feifei Ren ◽  
Nan Zhang ◽  
Yaohong Zhou ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Endogenous Retroviruses ◽  
Genome Wide

scholarly journals Genome-wide approaches and technologies to assess human variation

2013 ◽  
Author(s):  
Claudia Gonzaga-Jauregui
Keyword(s):  
Human Genome ◽  
Genetic Disorders ◽  
Copy Number Variants ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Genomic Technologies ◽  
Genome Wide ◽  
Genome Analyses ◽  
Next Generation Sequencing Ngs

Current genome-wide technologies allow interrogation and exploration of the human genome as never before. Next-generation sequencing (NGS) technologies, along with high resolution Single Nucleotide Polymorphisms (SNP) arrays and array Comparative Genomic Hybrization (aCGH) enable assessment of human genome variation at the finest resolution from base pair changes such as simple nucleotide variants (SNVs) to large copy-number variants (CNVs). The application of these genomic technologies in the clinical setting has also enabled the molecular characterization of genetic disorders and the understanding of the biological functions of more genes in human development, disease, and health. In this review, the current approaches and platforms available for high-throughput human genome analyses, the steps involved in these different methodologies from sample preparation to data analysis, their applications, and limitations are summarized and discussed.

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