Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Genet Sel Evol
2019 Oct 26;511:59. doi: 10.1186/s12711-019-0501-7.
Show Gene links
Show Anatomy links
Structure of the intergenic spacers in chicken ribosomal DNA.
Dyomin A
,
Galkina S
,
Fillon V
,
Cauet S
,
Lopez-Roques C
,
Rodde N
,
Klopp C
,
Vignal A
,
Sokolovskaya A
,
Saifitdinova A
,
Gaginskaya E
.
???displayArticle.abstract???
BACKGROUND: Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals.
METHODS: We used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data.
RESULTS: Three complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences.
CONCLUSIONS: Due to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization.
???displayArticle.pubmedLink???
31655542
???displayArticle.pmcLink???PMC6815422 ???displayArticle.link???Genet Sel Evol ???displayArticle.grants???[+]
18-04-01276A Russian Foundation for Basic Research, 1.40.1625.2017 Saint Petersburg State University, ANR-10-INBS-09 Agence Nationale pour la Recherche, Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 GET-PACBIO
Fig. 1. Chicken rDNA repeat structure. Structure of the WAG137G4_utg0 contig obtained by PacBio sequencing of the WAG137G04 chicken BAC clone. The positions of three complete and one incomplete rRNA gene clusters together with three intercalary IGS are indicated. An enlarged diagram of the rRNA gene cluster is shown separately
Fig. 2. Chicken IGS length variants. Structure of three IGS from the WAG137G04 BAC clone (IGS_I, IGS_II, IGS_III) and an IGS present in the AADN04001305.1 contig of Gallus_gallus-5.0. a Detailed comparative figures of IGS structural elements distribution. Repeat deficiency regions are designated with fine black lines. b Contracted IGS figures, central block repeats are organized into tetrads
Fig. 3. Tandem repeats at the chicken IGS 5′ end. a
Svetlana (SV) repeat unit; b
Alsu (AL) repeat unit. Both repeats are consensus sequences
Fig. 4. Elena repeats in chicken IGS. Relationships between repeats in the Elena (EL) group. The figure was plotted using the maximum likelihood method. The numbers following the repeat names indicate the repeat ordinal position in the IGS, and the numbers following after a space—the IGS ordinal position in WAG137G4_utg0 contig. An expanded figure is attached in Additional file 4
Fig. 5. Consensus sequences of Elena (EL) repeat variants. Elena (EL) repeat variants: alignment of the sequences
Fig. 6. Valerie repeats in chicken IGS. Relationships between repeats in the Valerie group. The figure was plotted using the maximum likelihood method. The numbers following the repeat names indicate the repeat ordinal position in the IGS, and the numbers following a space—the IGS ordinal position in WAG137G4_utg0 contig
Fig. 7. Consensus sequences of Valerie (VAL) repeat variants. Valerie (VAL) repeat variants: alignment of the sequences
Fig. 8. GC content in Sauropsida and Mammalia IGS. (C+G) content and putative CpG island distribution in the IGS of chicken Gallus gallus, terrapin Malaclemys terrapin, human Homo sapiens, and mouse Mus musculus. Regions containing repeats are designated with horizontal green blocks (Rep); putative CpG islands—with light-green boxes (CpG Island); GC pairs distribution is shown in the graphs (GC content)
Fig. 9. IGS transcription. Analysis of the IGS transcription in different chicken organs. The vertical axis represents read counts aligned to each nucleotide position
Agrawal,
Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data.
2016, Pubmed
Agrawal,
Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data.
2016,
Pubmed
Akamatsu,
The Human RNA Polymerase I Transcription Terminator Complex Acts as a Replication Fork Barrier That Coordinates the Progress of Replication with rRNA Transcription Activity.
2015,
Pubmed
Banditt,
Transcriptional activity and chromatin structure of enhancer-deleted rRNA genes in Saccharomyces cerevisiae.
1999,
Pubmed
Bloom,
Linkage of the major histocompatibility (B) complex and the nucleolar organizer in the chicken. Assignment to a microchromosome.
1985,
Pubmed
Brewer,
The arrest of replication forks in the rDNA of yeast occurs independently of transcription.
1992,
Pubmed
Caudy,
Xenopus ribosomal RNA gene intergenic spacer elements conferring transcriptional enhancement and nucleolar dominance-like competition in oocytes.
2002,
Pubmed
,
Xenbase
Crooijmans,
Two-dimensional screening of the Wageningen chicken BAC library.
2000,
Pubmed
Delany,
Molecular characterization of ribosomal gene variation within and among NORs segregating in specialized populations of chicken.
1999,
Pubmed
Delany,
Architecture and organization of chicken microchromosome 16: order of the NOR, MHC-Y, and MHC-B subregions.
2009,
Pubmed
Dyomin,
Chicken rRNA Gene Cluster Structure.
2016,
Pubmed
Grozdanov,
Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer.
2003,
Pubmed
Grummt,
Transcription of mouse rDNA terminates downstream of the 3' end of 28S RNA and involves interaction of factors with repeated sequences in the 3' spacer.
1985,
Pubmed
Hastings,
Mechanisms of change in gene copy number.
2009,
Pubmed
Jacob,
Regulation of ribosomal gene transcription.
1995,
Pubmed
Kim,
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.
2018,
Pubmed
Kimura,
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
1980,
Pubmed
Kobayashi,
Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae.
1992,
Pubmed
Kobayashi,
Ribosomal RNA gene repeats, their stability and cellular senescence.
2014,
Pubmed
Kumar,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
2016,
Pubmed
Masabanda,
Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype.
2004,
Pubmed
Mason,
RNA polymerase I transcription termination: similar mechanisms are employed by yeast and mammals.
1997,
Pubmed
Massin,
Cloning of the chicken RNA polymerase I promoter and use for reverse genetics of influenza A viruses in avian cells.
2005,
Pubmed
Mayer,
Intergenic transcripts regulate the epigenetic state of rRNA genes.
2006,
Pubmed
McCarthy,
Chickspress: a resource for chicken gene expression.
2019,
Pubmed
Pfleiderer,
An undecamer DNA sequence directs termination of human ribosomal gene transcription.
1990,
Pubmed
Pikaard,
Enhancers for RNA polymerase I in mouse ribosomal DNA.
1990,
Pubmed
,
Xenbase
Santoro,
Epigenetic engineering of ribosomal RNA genes enhances protein production.
2009,
Pubmed
Solinhac,
Integrative mapping analysis of chicken microchromosome 16 organization.
2010,
Pubmed
Su,
Ribosomal RNA gene copy number and nucleolar-size polymorphisms within and among chicken lines selected for enhanced growth.
1998,
Pubmed