Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability

Abstract

ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain “Inactivation/Stability Centers” that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.

ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins

“…All of the eight genetically validated ASAR genes are subject to AEI and express lncRNAs that remain associated with the chromosome territories where they are transcribed [4][5][6][7] . Examples of mono-allelic expression and chromosome territory localization of ASAR6-141 RNA are shown in Figure 1A and 1B, where ASAR6-141 RNA is localized within one of the chromosome 6 territories in two different cell types, male HTD114 cells and female GM12878 cells, respectively.…”

“…We recently identified 68 ASAR candidate genes, and genetically validated five out of five as controlling replication timing of individual human autosomes, bringing the total of genetically validated ASAR genes to eight [4][5][6][7] . These eight ASAR genes (ASAR1-187, ASAR6, ASAR6-141, ASAR8-2.7, ASAR9-23, ASAR9-24, ASAR9-30 and ASAR15) display striking epigenetically controlled differential allelic expression and replication timing, and their RNAs remain localized to their parent chromosome territories [4][5][6][7] . In this report, we used publicly available RNA-protein interaction data from ENCODE to identify RBPs that interact with multiple ASAR RNAs.…”

“…We also found that C0T-1 DNA, when used as an RNA FISH probe, can detect ASAR6 RNA that is expressed and localized to an individual chromosome territory, indicating that at least some of the RNA FISH signal detected by C0T-1 DNA represents ASAR RNA. Given our recent discovery of ASAR RNAs expressed from every autosome, and encoded by ~3% of the human genome 6 , we propose that ASAR RNAs represent functional "chromosome associated RNA" species that control chromosome dynamics within mammalian nuclei. Whether or not there are nuclear functions of other chromosome associated hnRNAs that are independent of ASARs will require genetic and/or functional validation.…”

“…The vast majority of mammalian DNA replicates in homologous regions of chromosome pairs in a highly synchronous manner 1-3 . However, genetic disruption of non-protein coding ASAR ("ASynchronous replication and Autosomal RNA") loci causes a delay in replication timing on individual human chromosomes in cis, resulting in highly asynchronous replication between pairs of autosomes [4][5][6][7] . There are eight genetically validated ASARs that are located on human chromosomes 1, 6, 8, 9 and 15 [4][5][6][7] .…”

“…However, genetic disruption of non-protein coding ASAR ("ASynchronous replication and Autosomal RNA") loci causes a delay in replication timing on individual human chromosomes in cis, resulting in highly asynchronous replication between pairs of autosomes [4][5][6][7] . There are eight genetically validated ASARs that are located on human chromosomes 1, 6, 8, 9 and 15 [4][5][6][7] . All of the known ASAR lncRNAs share several distinctive characteristics, including: 1) contiguously transcribed regions of >180 kb, 2) epigenetically regulated Allelic Expression Imbalance (AEI; including mono-allelic expression); 3) Variable Epigenetic Replication Timing (VERT; including asynchronous replication timing); 4) high density of LINE1 (L1) sequences (>30%); and 5) retention of the RNA within their parent chromosome territory.…”