ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B–H4K8ac–BRD4 axis

Abstract

Centromeres are genomic regions essential for faithful chromosome segregation. Transcription of noncoding RNA (ncRNA) at centromeres is important for their formation and functions. Here, we report the molecular mechanism by which the transcriptional regulator ZFAT controls the centromeric ncRNA transcription in human and mouse cells. Chromatin immunoprecipitation with high-throughput sequencing analysis shows that ZFAT binds to centromere regions at every chromosome. We find a specific 8-bp DNA sequence for the ZFAT-binding motif that is highly conserved and widely distributed at whole centromere regions of every chromosome. Overexpression of ZFAT increases the centromeric ncRNA levels at specific chromosomes, whereas its silencing reduces them, indicating crucial roles of ZFAT in centromeric transcription. Overexpression of ZFAT increases the centromeric levels of both the histone acetyltransferase KAT2B and the acetylation at the lysine 8 in histone H4 (H4K8ac). siRNA-mediated knockdown of KAT2B inhibits the overexpressed ZFAT-induced increase in centromeric H4K8ac levels, suggesting that ZFAT recruits KAT2B to centromeres to induce H4K8ac. Furthermore, overexpressed ZFAT recruits the bromodomain-containing protein BRD4 to centromeres through KAT2B-mediated H4K8ac, leading to RNA polymerase II-dependent ncRNA transcription. Thus, ZFAT binds to centromeres to control ncRNA transcription through the KAT2B–H4K8ac–BRD4 axis.

The transcriptional regulator Zfat is essential for maintenance and differentiation of the adipocytes

“…Here, we show that loss of Zfat in the ADSCs decreases the mRNA levels of the C/EBPα gene. On the other hand, a 8‐bp consensus DNA sequence (GAA(T/A)(C/G)TGC) for Zfat‐binding, which we previously reported, 5,6 is not located at the promoter region of C/EBP α gene. Indeed, in the Zfat ChIP‐seq analysis, Zfat‐binding was not observed in the promoter region of C/EBP α gene 5 .…”

“…Zfat controls the messenger RNA (mRNA) transcription of specific genes through binding to the proximal region of their transcription start sites 5 . Furthermore, Zfat also regulates noncoding RNA transcription at the centromeres through histone acetylation 6 . We have established several transgenic mice of the Zfat gene.…”

The Role of Human Centromeric RNA in Chromosome Stability

“…This suggests that, in mammals, the transcription at the centromere is tightly regulated, maybe by its interaction with the nucleolus that may induce its repression ( Bury et al, 2020 ). In human cells, one of the regulators of cenRNA transcription is ZFAT, which binds to a specific DNA sequence present on each centromere ( Ishikura et al, 2020 ). Its presence at the centromere increases the centromeric level of the histone acetylase KAT2B and its product the histone 4 acetylated at the lysine 8 ( Ishikura et al, 2020 ).…”

“…In human cells, one of the regulators of cenRNA transcription is ZFAT, which binds to a specific DNA sequence present on each centromere ( Ishikura et al, 2020 ). Its presence at the centromere increases the centromeric level of the histone acetylase KAT2B and its product the histone 4 acetylated at the lysine 8 ( Ishikura et al, 2020 ). This leads to the recruitment of the RNA pol II through BRD4 to the centromere, thus allowing ZFAT to control cenRNA transcription ( Ishikura et al, 2020 ).…”

“…Its presence at the centromere increases the centromeric level of the histone acetylase KAT2B and its product the histone 4 acetylated at the lysine 8 ( Ishikura et al, 2020 ). This leads to the recruitment of the RNA pol II through BRD4 to the centromere, thus allowing ZFAT to control cenRNA transcription ( Ishikura et al, 2020 ).…”