mosaicFlye: Resolving long mosaic repeats using long error-prone reads

Long-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes. However, the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of bacterial genomes and metagenomes. We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of the human genome as well as bacterial genomes and metagenomes. In particular, we show that mosaicFlye results in a complete assembly of both arms of the human chromosome 6.

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

DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal order known as the replication timing program. We previously found that disruption of the noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing and delayed mitotic chromosome condensation of human chromosome 6 and 15, respectively. ASAR6 and ASAR15 display random monoallelic expression, and display asynchronous replication between alleles that is coordinated with other random monoallelic genes on their respective chromosomes. Disruption of the expressed allele, but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously silent alleles of linked monoallelic genes, and structural instability of human chromosome 6. In this report, we describe a second lncRNA gene (ASAR6-141) on human chromosome 6 that when disrupted results in delayed replication timing in cis. ASAR6-141 is subject to random monoallelic expression and asynchronous replication, and is expressed from the opposite chromosome 6 homolog as ASAR6. ASAR6-141 RNA, like ASAR6 and ASAR15 RNAs, contains a high L1 content and remains associated with the chromosome territory where it is transcribed. Three classes of cis-acting elements control proper chromosome function in mammals: origins of replication, centromeres; and telomeres, which are responsible for replication, segregation and stability of all chromosomes. Our work supports a fourth type of essential chromosomal element, “Inactivation/Stability Centers”, which express ASAR lncRNAs responsible for proper replication timing, monoallelic expression, and structural stability of each chromosome.Author summaryMammalian cells replicate their chromosomes during a highly ordered and cell type-specific program. Genetic studies have identified two long non-coding RNA genes, ASAR6 and ASAR15, as critical regulators of the replication timing program of human chromosomes 6 and 15, respectively. There are several unusual characteristics of the ASAR6 and ASAR15 RNAs that distinguish them from other long non-coding RNAs, including: being very long (>200 kb), lacking splicing of the transcripts, lacking polyadenylation, and being retained in the nucleus on the chromosomes where they are made. ASAR6 and ASAR15 also have the unusual property of being expressed from only one copy of the two genes located on homologous chromosome pairs. Using these unusual characteristics shared between ASAR6 and ASAR15, we have identified a second ASAR lncRNA gene located on human chromosome 6, which we have named ASAR6-141. ASAR6-141 is expressed from the opposite chromosome 6 homolog as ASAR6, and disruption of the expressed allele results in delayed replication of chromosome 6. ASAR6-141 RNA had previously been annotated as vlinc273. The very long intergenic non-coding (vlinc)RNAs represent a recently annotated class of RNAs that are long (>50 kb), non-spliced, and non-polyadenlyated nuclear RNAs. There are currently >2,700 vlincRNAs expressed from every chromosome, are encoded by >15% of the human genome, and with a few exceptions have no known function. Our results suggest the intriguing possibility that the vlinc class of RNAs may be functioning to control the replication timing program of all human chromosomes.

L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing

Mammalian cells replicate their chromosomes via a temporal replication program. The ASAR6 and ASAR15 genes were identified as loci that when disrupted result in delayed replication and condensation of entire human chromosomes. ASAR6 and ASAR15 are monoallelically expressed long noncoding RNAs that remain associated with the chromosome from which they are transcribed. The chromosome-wide effects of ASAR6 map to the antisense strand of an L1 retrotransposon within ASAR6 RNA, deletion or inversion of which delayed replication of human chromosome 6. Furthermore, ectopic integration of ASAR6 or ASAR15 transgenes into mouse chromosomes resulted in delayed replication and condensation, an increase in H3K27me3, coating of the mouse chromosome with ASAR RNA, and a loss of mouse Cot-1 RNA expression in cis. Targeting the antisense strand of the L1 within ectopically expressed ASAR6 RNA restored normal replication timing. Our results provide direct evidence that L1 antisense RNA plays a functional role in chromosome-wide replication timing of mammalian chromosomes.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99–100% four-digit typing accuracy for both class I and II HLA genes, taking only∼3 min to process a 30× whole-genome BAM file on a desktop computer.