PMID- 30588288
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201001
IS  - 1993-0771 (Print)
IS  - 1993-078X (Electronic)
IS  - 1993-0771 (Linking)
VI  - 12
IP  - 4
DP  - 2018
TI  - Pilot satellitome analysis of the model plant, Physcomitrellapatens, revealed a 
      transcribed and high-copy IGS related tandem repeat.
PG  - 493-513
LID - 10.3897/CompCytogen.v12i4.31015 [doi]
AB  - Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In 
      the last decade, it has been shown that satDNA is not an inert part of the genome 
      and its function extends beyond the nuclear membrane. However, the number of 
      model plant species suitable for studying the novel horizons of satDNA 
      functionality is low. Here, we explored the satellitome of the model "basal" 
      plant, Physcomitrellapatens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which 
      has a number of advantages for deep functional and evolutionary research. Using a 
      newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) 
      coupled with fluorescence in situ hybridization (FISH), we identified five high 
      copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. 
      The nuclear organization study revealed that two TRs had distinct locations in 
      the moss genome, concentrating in the heterochromatin and knob-rDNA like 
      chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed 
      that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region 
      and transcribed into long non-coding RNAs (lncRNAs). Several specific features of 
      PpNATR76 lncRNAs make them very similar with the recently discovered human 
      lncRNAs, raising a number of questions for future studies. This work provides new 
      resources for functional studies of satellitome in plants using the model 
      organism P.patens, and describes a list of tandem repeats for further analysis.
FAU - Kirov, Ilya
AU  - Kirov I
AUID- ORCID: 0000-0003-3885-3837
AD  - Laboratory of functional genomics and proteomics of plants, Shemyakin and 
      Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation 
      Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia.
FAU - Gilyok, Marina
AU  - Gilyok M
AD  - Laboratory of functional genomics and proteomics of plants, Shemyakin and 
      Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation 
      Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia.
FAU - Knyazev, Andrey
AU  - Knyazev A
AD  - Laboratory of functional genomics and proteomics of plants, Shemyakin and 
      Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation 
      Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia.
FAU - Fesenko, Igor
AU  - Fesenko I
AD  - Laboratory of functional genomics and proteomics of plants, Shemyakin and 
      Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation 
      Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia.
LA  - eng
PT  - Journal Article
DEP - 20181213
PL  - Bulgaria
TA  - Comp Cytogenet
JT  - Comparative cytogenetics
JID - 101503807
PMC - PMC6302065
OTO - NOTNLM
OT  - Bryophyta
OT  - Physcomitrella patens
OT  - chromosomes
OT  - fluorescence in situ hybridization
OT  - long non-coding RNAs
OT  - rDNA
OT  - satellite DNA
EDAT- 2018/12/28 06:00
MHDA- 2018/12/28 06:01
PMCR- 2018/12/13
CRDT- 2018/12/28 06:00
PHST- 2018/11/02 00:00 [received]
PHST- 2018/11/27 00:00 [accepted]
PHST- 2018/12/28 06:00 [entrez]
PHST- 2018/12/28 06:00 [pubmed]
PHST- 2018/12/28 06:01 [medline]
PHST- 2018/12/13 00:00 [pmc-release]
AID - 10.3897/CompCytogen.v12i4.31015 [doi]
PST - epublish
SO  - Comp Cytogenet. 2018 Dec 13;12(4):493-513. doi: 10.3897/CompCytogen.v12i4.31015. 
      eCollection 2018.