PMID- 25056159
OWN - NLM
STAT- MEDLINE
DCOM- 20150331
LR  - 20211021
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 15
DP  - 2014 Jul 23
TI  - LTR retroelements are intrinsic components of transcriptional networks in frogs.
PG  - 626
LID - 10.1186/1471-2164-15-626 [doi]
LID - 626
AB  - BACKGROUND: LTR retroelements (LTR REs) constitute a major group of transposable 
      elements widely distributed in eukaryotic genomes. Through their own mechanism of 
      retrotranscription LTR REs enrich the genomic landscape by providing genetic 
      variability, thus contributing to genome structure and organization. Nonetheless, 
      transcriptomic activity of LTR REs still remains an obscure domain within cell, 
      developmental, and organism biology. RESULTS: Here we present a first comparative 
      analysis of LTR REs for anuran amphibians based on a full depth coverage 
      transcriptome of the European pool frog, Pelophylax lessonae, the genome of the 
      African clawed frog, Silurana tropicalis (release v7.1), and additional 
      transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 
      1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, 
      Retroviridae) in the genome of S. tropicalis and discovered transcripts of 
      several of these elements in all RNA-seq datasets analyzed. Elements of the 
      Ty3/Gypsy family were most active, especially Amn-san elements, which accounted 
      for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue 
      specific expression patterns, for example Hydra1.1 and MuERV-like elements in 
      Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed 
      during embryogenesis as soon as the embryonic genome became activated, i.e. at 
      midblastula transition. In the course of embryonic development the spectrum of 
      transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and 
      SnRV like retroviruses were abundantly transcribed while during organogenesis 
      transcripts of the XEN1 retroviruses became much more active. CONCLUSIONS: The 
      differential expression of LTR REs during embryogenesis in concert with their 
      tissue-specificity and the protein domains they encode are evidence for the 
      functional roles these elements play as integrative parts of complex regulatory 
      networks. Our results support the meanwhile widely accepted concept that 
      retroelements are not simple "junk DNA" or "harmful genomic parasites" but 
      essential components of the transcriptomic machinery in vertebrates.
FAU - Grau, Jose Horacio
AU  - Grau JH
AD  - Dahlem Center for Genome Research and Medical Systems Biology, Fabeckstrasse 
      60-62, 14195 Berlin, Germany. jose.grau@mfn-berlin.de.
FAU - Poustka, Albert J
AU  - Poustka AJ
FAU - Meixner, Martin
AU  - Meixner M
FAU - Plotner, Jorg
AU  - Plotner J
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140723
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (RNA, Messenger)
RN  - 0 (Retroelements)
SB  - IM
MH  - Animals
MH  - Anura/embryology/*genetics/virology
MH  - Endogenous Retroviruses/genetics
MH  - Gene Expression Profiling
MH  - *Gene Regulatory Networks
MH  - Genetic Variation
MH  - *Genomics
MH  - Molecular Sequence Annotation
MH  - Organ Specificity
MH  - RNA, Messenger/genetics/metabolism
MH  - Retroelements/*genetics
MH  - Terminal Repeat Sequences/*genetics
MH  - Transcription, Genetic
PMC - PMC4131045
EDAT- 2014/07/25 06:00
MHDA- 2015/04/01 06:00
PMCR- 2014/07/23
CRDT- 2014/07/25 06:00
PHST- 2014/03/18 00:00 [received]
PHST- 2014/07/15 00:00 [accepted]
PHST- 2014/07/25 06:00 [entrez]
PHST- 2014/07/25 06:00 [pubmed]
PHST- 2015/04/01 06:00 [medline]
PHST- 2014/07/23 00:00 [pmc-release]
AID - 1471-2164-15-626 [pii]
AID - 6338 [pii]
AID - 10.1186/1471-2164-15-626 [doi]
PST - epublish
SO  - BMC Genomics. 2014 Jul 23;15:626. doi: 10.1186/1471-2164-15-626.