The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

Abstract

Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.

Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells

“…Full-length hYY1 protein rescued Xist RNA localization to the Xi, with nearly identical levels of Type I/II Xist RNA patterns as wildtype B cells ( Fig 6B and 6C ). The N-terminal domain (NTD) of hYY1 (1–200 amino acids) contains the transcriptional activation domain and interacts with histone acetyltransferases and histone deacetylases [ 54 , 55 ], as well as RNA binding activity that is independent of the zinc finger domain [ 26 ]. However, we found that expression of the 1–200 amino acid protein did not rescue the Xist RNA localization defect ( Fig 6B and 6C ).…”

“…The Xist promoter region contains YY1 binding sites and YY1 enhances Xist expression during XCI initiation and maintenance in mammalian cells [ 24 ]. The YY1 protein can also bind RNA [ 25 , 26 ], and the Repeat C region of Xist contains three YY1 binding sites required for tethering Xist RNA to the chromatin of the Xi in post-XCI somatic cells [ 27 ]. YY1 mediates the long-distance DNA interactions required for V(D)J recombination of the immunoglobulin loci and for class switch recombination, and B cell specific YY1 deletion arrests B cell development at the pro-B cell stage [ 28 – 32 ].…”

The Yin and Yang of YY1 in tumor growth and suppression

“…For example, recent studies by Wai et al . using systematic evolution of ligands by exponential enrichment (SELEX) and related approaches have determined that the zinc fingers of YY1 bind with low sequence‐specificity to single‐stranded RNA in a manner distinct from its binding to DNA . Recent work has also found that YY1 is tyrosine‐phosphorylated by Src family kinases.…”

How do lncRNAs regulate transcription?

“…A lncRNA transcribed from the YY1 gene promoter (linc-YY1) interacts with YY1 through its middle domain to evict YY1-PRC2 from target promoters, thus activating gene expression in trans ( 124 ). A recent SELEX (systematic evolution of ligands by exponential enrichment) study found that YY1 interacts with RNA with low sequence specificity ( 125 ), and the lack of RNA sequence specificity has been commonly observed among chromatin binders more generally. The biochemical and structure nature of the protein-RNA interaction may determine the inhibition or activation mechanism.…”