Transcriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells

Abstract

Nucleotide excision repair (NER) removes DNA helix-distorting lesions induced by UV light and various chemotherapeutic agents such as cisplatin. These lesions efficiently block the elongation of transcription and need to be rapidly removed by transcription-coupled NER (TC-NER) to avoid the induction of apoptosis. Twenty-nine genes have been classified to code for proteins participating in nucleotide excision repair (NER) in human cells. Here we explored the transcriptional and post-transcriptional regulation of these NER genes across 13 human cell lines using Bru-seq and BruChase-seq, respectively. Many NER genes are relatively large in size and therefore will be easily inactivated by UV-induced transcription-blocking lesions. Furthermore, many of these genes produce transcripts that are rather unstable. Thus, these genes are expected to rapidly lose expression leading to a diminished function of NER. One such gene is ERCC6 that codes for the CSB protein critical for TC-NER. Due to its large gene size and high RNA turnover rate, the ERCC6 gene may act as dosimeter of DNA damage so that at high levels of damage, ERCC6 RNA levels would be diminished leading to the loss of CSB expression, inhibition of TC-NER and the promotion of cell death.

KMT2D links TGF‐β signaling to noncanonical activin pathway and regulates pancreatic cancer cell plasticity

“…The downregulation of E‐cadherin and upregulation of mesenchymal markers resemble what was seen in cells treated with TGF‐β and was reversible with TGF‐β inhibitor SB505124 (Figure S2E). To confirm that these findings are due to the loss of KMT2D, we used two different siRNAs to knockdown KMT2D in two additional cell lines, including a patient‐derived primary PDAC cell line, UM28 15 . Indeed, in both cell lines, E‐cadherin expression was attenuated in KMT2D‐knockdown cells (Figure 4C), confirming the promesenchymal effect of KMT2D deficiency.…”

“…UM28 was a patient-derived primary PDAC cell line developed by Dr. Diane Simeone. 15 All human cell lines have been authenticated using short tandem repeat profiling within the last 3 years. All experiments were performed with mycoplasma-free cells.…”

The Tardigrade Damage Suppressor Protein Modulates Transcription Factor and DNA Repair Genes in Human Cells Treated with Hydroxyl Radicals and UV-C

“…ATR activation, occurring during the S phase, allows repairing stalled replication forks and avoiding the arrest of replication or premature entry into mitosis [16]. In addition, Dsup+ cells exhibited increased expression in other genes related to the ATR rescue pathway: BRCA1, which is recruited during the S/G2 phase and contributes to the UV irradiation response operating in gap repair at photoproduct-stalled replication forks level [42]; XRCC6, which participates in the UV-G2 checkpoint [43]; ERCC6, whose gene represents a potential target for inactivation by UV light and seems to act as a "dosimeter" of DNA damage (though DNA damage exceeds a certain threshold, ERCC6 transcript is depleted and cell death is promoted) [44]. In Dsup+ cells, ATM expression was similar or lower than that in untransfected cells.…”

KMT2D links TGF-β Signalling to Non-Canonical Activin Pathway and Regulates Pancreatic Cancer Cell Plasticity

“…1g). To confirm that these findings are due to the loss of KMT2D, we used two different siRNAs to knock-down KMT2D in 2 additional cell lines, including a patient-derived primary PDAC cell line, UM28 22 . Indeed, in both cell lines, E-cadherin expression was attenuated in KMT2D-knockdown cells ( Fig.…”