Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence

KARAKÜLAH G., Yandim C.

TURKISH JOURNAL OF BIOLOGY, cilt.44, sa.6, ss.356-370, 2020 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 44 Sayı: 6
  • Basım Tarihi: 2020
  • Doi Numarası: 10.3906/biy-2005-21
  • Dergi Adı: TURKISH JOURNAL OF BIOLOGY
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, BIOSIS, CAB Abstracts, Veterinary Science Database, TR DİZİN (ULAKBİM)
  • Sayfa Sayıları: ss.356-370
  • Anahtar Kelimeler: Senescence, senescence-associated-secretory phenotype, lncRNA, repetitive DNA, repeatome, repeat elements, bioinformatics, genomics, transcriptome, RNA-seq, LONG NONCODING RNA, REPETITIVE DNA, TRANSPOSABLE ELEMENTS, SECRETORY PHENOTYPE, CELLS, HETEROCHROMATIN, GENOMES, DAMAGE, ACTIVATION, CHROMATIN
  • Dokuz Eylül Üniversitesi Adresli: Evet

Özet

Replicative cellular senescence is the main cause of aging. It is important to note that early senescence is linked to tissue regeneration, whereas late senescence is known to trigger a chronically inflammatory phenotype. Despite the presence of various genome-wide studies, there is a lack of information on distinguishing early and late senescent phenotypes at the transcriptome level. Particularly, the changes in the noncoding RNA portion of the aging cell have not been fully elucidated. By utilising RNA sequencing data of fibroblasts, hereby, we are not only reporting changes in gene expression profiles and relevant biological processes in the early and late senescent phenotypes but also presenting significant differences in the expressions of many unravelled long noncoding RNAs (lncRNAs) and transcripts arisen from repetitive DNA. Our results indicate that, in addition to previously reported L1 elements, various LTR and DNA transposons, as well as members of the classical satellites including HSAT5 and alpha-satellites (ALR/Alpha), are expressed at higher levels in late senescence. Moreover, we revealed finer links between the expression levels of repeats with the genes located near them and known to be involved in cell cycle and senescence. Noncoding elements reported here provide a new perspective to be explored in further experimental studies.