The Experts below are selected from a list of 252 Experts worldwide ranked by ideXlab platform

Mark A Batzer - One of the best experts on this subject based on the ideXlab platform.

  • Tracking Alu evolution in New World primates
    BMC Evolutionary Biology, 2005
    Co-Authors: David A Ray, Mark A Batzer
    Abstract:

    Background Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu Sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu Sequences for loci specific to platyrrhine (New World) primates. Results Branching patterns along an Alu Sequence phylogeny indicate three major classes of platyrrhine-specific Alu Sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; Alu Ta7, Alu Ta10, and Alu Ta15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of Alu Sc- and Alu Sp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu Sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

  • Tracking Alu evolution in New World primates
    BMC evolutionary biology, 2005
    Co-Authors: David A Ray, Mark A Batzer
    Abstract:

    Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu Sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu Sequences for loci specific to platyrrhine (New World) primates. Branching patterns along an Alu Sequence phylogeny indicate three major classes of platyrrhine-specific Alu Sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; Alu Ta7, Alu Ta10, and Alu Ta15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of Alu Sc- and Alu Sp-type elements. This is a novel mode of origin for new Alu subfamilies. The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu Sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

David A Ray - One of the best experts on this subject based on the ideXlab platform.

  • Tracking Alu evolution in New World primates
    BMC Evolutionary Biology, 2005
    Co-Authors: David A Ray, Mark A Batzer
    Abstract:

    Background Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu Sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu Sequences for loci specific to platyrrhine (New World) primates. Results Branching patterns along an Alu Sequence phylogeny indicate three major classes of platyrrhine-specific Alu Sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; Alu Ta7, Alu Ta10, and Alu Ta15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of Alu Sc- and Alu Sp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu Sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

  • Tracking Alu evolution in New World primates
    BMC evolutionary biology, 2005
    Co-Authors: David A Ray, Mark A Batzer
    Abstract:

    Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu Sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu Sequences for loci specific to platyrrhine (New World) primates. Branching patterns along an Alu Sequence phylogeny indicate three major classes of platyrrhine-specific Alu Sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; Alu Ta7, Alu Ta10, and Alu Ta15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of Alu Sc- and Alu Sp-type elements. This is a novel mode of origin for new Alu subfamilies. The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu Sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

Ramit Mehr - One of the best experts on this subject based on the ideXlab platform.

  • Evidence for large diversity in the human transcriptome created by Alu RNA editing
    Nucleic acids research, 2009
    Co-Authors: Michal Barak, Erez Y. Levanon, Eli Eisenberg, Nurit Paz, Gideon Rechavi, George M. Church, Ramit Mehr
    Abstract:

    Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is abundant in the human genome, with many thousands of expressed Alu Sequences undergoing editing. Little is known so far about the contribution of Alu editing to transcriptome complexity. Transcripts derived from a single edited Alu Sequence can be edited in multiple sites, and thus could theoretically generate a large number of different transcripts. Here we explored whether the combinatorial potential nature of edited Alu Sequences is actually fulfilled in the human transcriptome. We analyzed datasets of editing sites and performed an analysis of a detailed transcript set of one edited Alu Sequence. We found that editing appears at many more sites than detected by earlier genomic screens. To a large extent, editing of different sites within the same transcript is only weakly correlated. Thus, rather than finding a few versions of each transcript, a large number of edited variants arise, resulting in immense transcript diversity that eclipses alternative splicing as mechanism of transcriptome diversity, although with less impact on the proteome.

H M Fried - One of the best experts on this subject based on the ideXlab platform.

  • Nuclear export of signal recognition particle RNA is a facilitated process that involves the Alu Sequence domain.
    Journal of cell science, 1994
    Co-Authors: N Bataillé, H M Fried
    Abstract:

    The signal recognition particle is a cytoplasmic RNA-protein complex that mediates translocation of secretory polypeptides into the endoplasmic reticulum. We have used a Xenopus oocyte microinjection assay to determine how signal recognition particle (SRP) RNA is exported from the nucleus. Following nuclear injection, SRP RNA accumulated in the cytoplasm while cytoplasmically injected SRP RNA did not enter the nucleus. Cytoplasmic accumulation of SRP RNA was an apparently facilitated process dependent on limiting trans-acting factors, since nuclear export exhibited saturation kinetics and was completely blocked either at low temperature or by wheat germ agglutinin, a known inhibitor of nuclear pore-mediated transport. At least one target for trans-acting factors that promote nuclear export of SRP RNA appears to be the Alu element of the molecule, since a transcript consisting of only the Alu Sequence was exported from the nucleus in a temperature-dependent manner and the Alu transcript competed in the nucleus for transport with intact SRP RNA. Although the identities of trans-acting factors responsible for SRP RNA transport are at present unknown, we suggest that proteins contained within the cytoplasmic form of SRP are candidates. Consistent with this idea were the effects of a mutation in SRP RNA that prevented binding of two known SRP proteins to the Alu Sequence.

Richard J Maraia - One of the best experts on this subject based on the ideXlab platform.

  • human signal recognition particle srp Alu associated protein also binds Alu interspersed repeat Sequence rnas characterization of human srp9
    Journal of Biological Chemistry, 1995
    Co-Authors: Karl Hsu, Dauyin Chang, Richard J Maraia
    Abstract:

    Nearly 1 million interspersed Alu elements reside in the human genome. Alu retrotransposition is presumably mediated by full-length Alu transcripts synthesized by RNA polymerase III, while some polymerase III-synthesized Alu transcripts undergo 3'-processing and accumulate as small cytoplasmic (sc) RNAs of unknown function. Interspersed Alu Sequences also reside in the untranslated regions of some mRNAs. The Alu Sequence is related to a portion of the 7SL RNA component of signal recognition particle (SRP). This region of 7SL RNA together with 9- and 14-kDa polypeptides (SRP9/14) regulates translational elongation of ribosomes engaged by SRP. Here we characterize human (h) SRP9 and show that it, together with hSRP14 (SRP9/14), forms the activity previously identified as Alu RNA-binding protein (RBP). The primate-specific C-terminal tail of hSRP14 does not appreciably affect binding to scAlu RNA. Kd vAlues for three Alu-homologous scRNAs were determined using Alu RBP (SRP9/14) purified from HeLa cells. The Alu region of 7SL, scAlu, and scB1 RNAs exhibited Kd vAlues of 203 pM, 318 pM, and 1.8 nM, respectively. Finally, Alu RBP can bind with high affinity to synthetic mRNAs that contain interspersed Alus in their untranslated regions.