scholarly journals The conservation landscape of the human ribosomal RNA gene repeats

2018 ◽  
Author(s):  
Saumya Agrawal ◽  
Austen R.D. Ganley
Keyword(s):  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Metabolic Regulation ◽  
De Novo ◽  
Intergenic Spacer ◽  
Phylogenetic Footprinting ◽  
Genomic Region ◽  
Primate Species ◽  
Ribosomal Rna Gene ◽  
Conserved Regions

ABSTRACTRibosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed usingde novowhole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS, and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.

Characterization of the Gyrodactylus salaris Malmberg, 1957 (Platyhelminthes: Monogenea) ribosomal intergenic spacer (IGS) DNA

Parasitology ◽  
2000 ◽  
Vol 121 (5) ◽  
pp. 555-563 ◽  
Author(s):  
C. M. COLLINS ◽  
C. O. CUNNINGHAM
Keyword(s):  
Ribosomal Rna ◽  
Tandem Repeats ◽  
Gene Array ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Sequence Motifs ◽  
Ribosomal Rna Gene ◽  
Intergenic Spacers ◽  
Transcription Start Sites ◽  
Pcr Products

The intergenic spacer of the ribosomal RNA gene array from the monogenean Gyrodactylus salaris was isolated using PCR amplification. PCR products were cloned and sequenced. Three different fragments of 0·63, 1·0 and 2·62 kb, were consistently obtained. These showed homology at the 5′ and 3′ termini but differed in their overall size and intervening sequence. The 5′ end showed homology to various 28S ribosomal RNA gene sequences, suggesting that this represented the 3′ terminus of the G. salaris 28S ribosomal RNA gene. A number of features common to other eukaryotic intergenic spacers were found in the longest sequence, including A + T rich sequences, palindromic sequences and tandemly repeated elements. Two regions of 23 bp sequences arranged in non-identical tandem repeats were identified. There were 9 repeats in both regions, separated by 81 bp of non-repetitive sequence. The repeat units from the two regions shared some similarity at their 3′ ends. The G. salaris intergenic spacer sequence was examined for sequence motifs involved in the transcription of the ribosomal RNA genes in other species. Several regions with homology to transcription start sites were identified.

scholarly journals ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1418 ◽  
Author(s):  
Adam R. Rivers ◽  
Kyle C. Weber ◽  
Terrence G. Gardner ◽  
Shuang Liu ◽  
Shalamar D. Armstrong
Keyword(s):  
Ribosomal Rna ◽  
Large Subunit ◽  
Marker Gene ◽  
Its Region ◽  
Small Subunit ◽  
Sequence Variant ◽  
Ribosomal Rna Gene ◽  
Conserved Regions ◽  
Conserved Genes ◽  
Internally Transcribed Spacer

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.

scholarly journals The intergenic spacer region of the ribosomal RNA gene of Penicillium marneffei shows almost no DNA sequence diversity

2010 ◽  
Vol 54 (11) ◽  
pp. 714-716 ◽  
Author(s):  
Nanthawan Mekha ◽  
Takashi Sugita ◽  
Koichi Makimura ◽  
Natteewan Poonwan ◽  
Pathom Sawanpanyalert ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ribosomal Rna ◽  
Intergenic Spacer ◽  
Sequence Diversity ◽  
Penicillium Marneffei ◽  
Ribosomal Rna Gene ◽  
Intergenic Spacer Region

A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil

2006 ◽  
Vol 64 (3) ◽  
pp. 366-379 ◽  
Author(s):  
Valéria Maia de Oliveira ◽  
Gilson Paulo Manfio ◽  
Heitor Luiz da Costa Coutinho ◽  
Anneke Christina Keijzer-Wolters ◽  
Jan Dirk van Elsas
Keyword(s):  
Ribosomal Rna ◽  
Intergenic Spacer ◽  
Ribosomal Rna Gene ◽  
Fingerprinting Method
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