Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

Lopes, Mariana da Silva; Louzada, Sandra; Gama‐Carvalho, Margarida; Chaves, Raquel

doi:10.3390/ijms22094707

Cited by 10 publications

(7 citation statements)

References 197 publications

(328 reference statements)

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“…Human satellite DNA [18] is an essential part of so-called "constitutive" heterochromatin (defined as a transcriptionally inactive chromatin that remains compact throughout Genes 2021, 12, 1524 2 of 18 the cell cycle) comprising 3% of the genomic repetitive elements [19] and predominantly located at the centromeric and pericentromeric regions of the chromosomes, and their terminal ends-telomeric and subtelomeric regions [20,21]. In mammals, two types of satellite DNA sequences are usually described: major satellite repeats that are generally located at the pericentromeric regions and minor satellite repeats at the centromeric regions [22].…”

Section: Introductionmentioning

confidence: 99%

The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model

Porokhovnik

Veiko

Ershova

et al. 2021

Genes

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The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.

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Section: Introductionmentioning

confidence: 99%

The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model

Porokhovnik

Veiko

Ershova

et al. 2021

Genes

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“…The sequences of HSAT2 and HSAT3 are closely related and originated from the same pentameric repeat, though HSAT2 is more diverged and based on 23 or 26 units [ 4 ]. Before the publication of the CHM13-T2T assembly, both satellites were sometimes referred to as HS2/3 or HSII/HSIII [ 36 , 37 ] due to the lack of a proper bioinformatic/sequencing approach and their short irregular nature. The gapless assembly where satellites are annotated using the K-mer approach gives a possibility for precise classification of a sequence.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of Pericentromeric HSAT2 DNA Increases Expression of EMT Markers in Human Epithelial Cancer Cell Lines

Ponomartsev

Zilov

Gushcha

et al. 2023

IJMS

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Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome assembly. The aim of our study was to map a transcript that we have previously described as HS2/HS3 on chromosomes using a newly published gapless genome assembly T2T-CHM13, and create a plasmid overexpressing the transcript to assess the influence of HS2/HS3 transcription on cancer cells. We report here that the sequence of the transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). A detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to HSAT2 (HS2) but not to the HS3 family of tandemly repeated DNA. The transcript was found on both strands of HSAT2 arrays. The overexpression of the HSAT2 transcript increased the transcription of the genes encoding the proteins involved in the epithelial-to-mesenchymal transition, EMT (SNAI1, ZEB1, and SNAI2), and the genes that mark cancer-associated fibroblasts (VIM, COL1A1, COL11A1, and ACTA2) in cancer cell lines A549 and HeLa. Co-transfection of the overexpression plasmid and antisense nucleotides eliminated the transcription of EMT genes observed after HSAT2 overexpression. Antisense oligonucleotides also decreased transcription of the EMT genes induced by tumor growth factor beta 1 (TGFβ1). Thus, our study suggests HSAT2 lncRNA transcribed from the pericentromeric tandemly repeated DNA is involved in EMT regulation in cancer cells.

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“…Repetitive DNA sequences play a key role in driving karyotype evolution and genome structure ( Lopes et al, 2021 ). At the same time, they are also involved in various basic genome functions and are closely related to a variety of diseases.…”

Section: Discussionmentioning

confidence: 99%

Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility

Xu¹,

Pang

2022

Front. Cell Dev. Biol.

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The male-specific Y chromosome, which is well known for its diverse and complex repetitive sequences, has different sizes, genome structures, contents and evolutionary trajectories from other chromosomes and is of great significance for testis development and function. The large number of repetitive sequences and palindrome structure of the Y chromosome play an important role in maintaining the stability of male sex determining genes, although they can also cause non-allelic homologous recombination within the chromosome. Deletion of certain Y chromosome sequences will lead to spermatogenesis disorders and male infertility. And Y chromosome genes are also involved in the occurrence of reproductive system cancers and can increase the susceptibility of other tumors. In addition, the Y chromosome has very special value in the personal identification and parentage testing of male-related cases in forensic medicine because of its unique paternal genetic characteristics. In view of the extremely high frequency and complexity of gene rearrangements and the limitations of sequencing technology, the analysis of Y chromosome sequences and the study of Y-gene function still have many unsolved problems. This article will introduce the structure and repetitive sequence of the Y chromosome, summarize the correlation between Y chromosome various sequence deletions and male infertility for understanding the repetitive sequence of Y chromosome more systematically, in order to provide research motivation for further explore of the molecules mechanism of Y-deletion and male infertility and theoretical foundations for the transformation of basic research into applications in clinical medicine and forensic medicine.

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Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

Cited by 10 publications

References 197 publications

The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model

The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model

Overexpression of Pericentromeric HSAT2 DNA Increases Expression of EMT Markers in Human Epithelial Cancer Cell Lines

Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility

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