Human nuclear protein interacting with a conservative sequence motif of Alu‐family DNA repeats

Abstract

Human retrotransposons, Alu‐family DNA repeats (AFRs), have variable nucleotide sequence but conservative short elements, which may have important functions, are also present. In our previous reports we have described human nuclear DNA‐binding protein interacting with AFRs and evidence was presented that the protein recognizes sequence motif 5′‐GGAGGC‐3′ which is conserved in the spacer of RNA polymerase III promoter of AFRs and in the SV40 T‐antigen‐dependent replication origin of AFRS. In this study it was found that double‐stranded synthetic oligonucleotides containing indicated conservative sequences of AFRs actually have high‐affinity binding site for HeLa nuclear protein. The data suggest that non‐infected human cells contain nuclear DNA‐binding protein which recognizes the conservative sequence motif of AFRs — GGAGGC.

Evidence for a regulatory protein complex on RNA polymerase III promoter of human retroposons of Alu family

“…This model does not exclude the existence of other factors contributing to Alu silencing, such as DNA methylation (Labuda & Striker, 1989;Schmid, 1991;Kochanek, Renz & Doerfler, 1993;Kochanek, Renz & Doerfler, 1995) or Alu sequence-specific chromatin structure (Englander, Wolffe & Howard, 1993;Russanova, Driscoll & Howard, 1995). It is also possible that protein interacting with a conserved GCrich sequence located between the A-and B-boxes of the Alu promoter, ABP (Bozhkov & Tomilin, 1989;Tomilin, Iguchi-Ariga & Ariga, 1990;Chesnokov et al, 1991;Saegusa et al, 1993), or some unknown protein contribute to Alu transcription repression. ABP may interfere with the TFIIIC2-directed binding to the Alu A-box of TFIIIC1 (Dean & Berk, 1988).…”

“…Transcriptional activity of the 'master' or 'source' gene may depend on the presence of flanking sequences containing binding sites for RNA polymerase II transcription factors (Chesnokov & Schmid, 1996). Another hypothesis suggests that the bulk of retroposed Alu copies has potentially active internal and external promoter elements, but transcription is blocked in vivo by a specific repressor protein (Tomilin & Bozhkov, 1989;Tomilin, Iguchi-Ariga & Ariga, 1990), by Alu-specific chromatin structure (Englander, Wolffe & Howard, 1993), or by DNA methylation (Labuda & Striker, 1989;Schmid, 1991;Kochanek, Renz & Doerfler, 1993;Kochanek, Renz & Doerfler, 1995). Recent analysis indicates that the vast majority of transcriptionally competent Alu elements in nuclei of the HeLa cells are masked from the pdlII transcriptional machinery, and the repression is relieved by adenovirus infection (Panning & Smiley, 1995;Russanova, Driscoll & Howard, 1995) or by heat shock (Liu et al, 1995).…”

“…In an attempt to understand the basis of relative transcriptional inactivity of Alu repeats, we have identified earlier a number of human nuclear Alu-binding proteins interacting with different Alu subsequences (Perelygina, Tomilin & Podgornaya, 1987;Tomilin & Bozhkov, 1989;Tomilin, Iguchi-Ariga & Ariga, 1990;Chesnokov et al, 1991;Tomilin et al, 1992). One of these proteins (ABP) was found to bind a highly conserved GC-rich Alu subsequence located between the A and B boxes of Alu RNA polymerase III promoter (Tomilin & Bozhkov, 1989;Tomilin, IguchiAriga & Ariga, 1990;Chesnokov et al, 1991).…”

“…One of these proteins (ABP) was found to bind a highly conserved GC-rich Alu subsequence located between the A and B boxes of Alu RNA polymerase III promoter (Tomilin & Bozhkov, 1989;Tomilin, IguchiAriga & Ariga, 1990;Chesnokov et al, 1991). Other proteins were found to interact with a less conserved Alu subsequence covering the B-box and downstream nucleotides, including the sequence that covers clustered diagnostic differences between Alu subfamilies (Tomilin et al, 1992).…”

Increased concentration of some transcription factor binding sites in human retroposons of theAlu family

“…One of the signals which is highly conserved in Alu repeats (GGAGGCPyGAGGCA) was identified as a pal II transcription modulator interacting with a human nuclear protein (Tomilin & Bozhkov, 1989;Tomilin, Iguchi-Ariga & Ariga, 1990;Chesnokov et al, 199 1;Saegusa et al, 1993). This conserved block overlaps with consensus binding sites for T-cell-specific transcription factor LyF-1 present in many genomic Ah repeats (Hambor et al, 1993), opening an apparent question about the presence in ALU repeats of other consensus sites for known transcription factors.…”