Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6

Abstract

25 DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal 26 order known as the replication timing program. We previously found that disruption of the 27 noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing 28 and delayed mitotic chromosome condensation of human chromosome 6 and 15, 29 respectively. ASAR6 and ASAR15 display random monoallelic expression, and display 30 asynchronous replication between alleles that is coordinated with other random 31 monoallelic genes on their respective chromosomes. Disruption of the expressed allele, 32 but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously 33 silent alleles of linked monoallelic genes, and structural instability of human chromosome 34 6. In this report, we describe a second lncRNA gene (ASAR6-141) on human 35 chromosome 6 that when disrupted results in delayed replication timing in cis. ASAR6-36 141 is subject to random monoallelic expression and asynchronous replication, and is 37 expressed from the opposite chromosome 6 homolog as ASAR6. ASAR6-141 RNA, like 38 ASAR6 and ASAR15 RNAs, contains a high L1 content and remains associated with the 39 chromosome territory where it is transcribed. Three classes of cis-acting elements control 40 proper chromosome function in mammals: origins of replication, centromeres; and 41 telomeres, which are responsible for replication, segregation and stability of all 42 chromosomes. Our work supports a fourth type of essential chromosomal element, 43 "Inactivation/Stability Centers", which express ASAR lncRNAs responsible for proper 44 replication timing, monoallelic expression, and structural stability of each chromosome. 45 3 46 Author summary 47 Mammalian cells replicate their chromosomes during a highly ordered and cell type-48 specific program. Genetic studies have identified two long non-coding RNA genes, 49 ASAR6 and ASAR15, as critical regulators of the replication timing program of human 50 chromosomes 6 and 15, respectively. There are several unusual characteristics of the 51 ASAR6 and ASAR15 RNAs that distinguish them from other long non-coding RNAs, 52 including: being very long (>200 kb), lacking splicing of the transcripts, lacking 53 polyadenylation, and being retained in the nucleus on the chromosomes where they are 54 made. ASAR6 and ASAR15 also have the unusual property of being expressed from only 55 one copy of the two genes located on homologous chromosome pairs. Using these 56 unusual characteristics shared between ASAR6 and ASAR15, we have identified a 57 second ASAR lncRNA gene located on human chromosome 6, which we have named 58 ASAR6-141. ASAR6-141 is expressed from the opposite chromosome 6 homolog as 59 ASAR6, and disruption of the expressed allele results in delayed replication of 60 chromosome 6. ASAR6-141 RNA had previously been annotated as vlinc273. The very 61 long intergenic non-coding (vlinc)RNAs represent a recently annotated class of RNAs that 62 are long (>50 kb), non-spliced, and non-polyade...