Customized genomes for human and mouse ribosomal DNA mapping

Abstract

Motivation: Ribosomal RNAs (rRNAs) form a majority of cellular RNA, and the loci from which they are transcribed (rDNA gene repeats) are among the most intensively transcribed regions of the genome. Due to the repetitive nature of rDNA, there has been a historical lack of genome assemblies and bioinformatic pipelines capable of yielding rDNA signal from high-throughput sequencing datasets. The study of rDNA regulation has been stunted by the lack of such tools, leading most investigators to ignore rDNA in genome wide studies, creating a significant knowledge gap in our understanding of how the most abundant RNA in the cell is regulated. Our recent work1 revealed previously-unnoticed binding of numerous mammalian transcription factors and chromatin proteins to rDNA. Several of these factors were known to play critical roles in development, tissue function, immunity, and malignancy, and had been dissected in detail for decades, but their potential rDNA roles had remained unexplored. Our work demonstrates the extent of the blind spot into which rDNA has fallen in modern genetic and epigenetic studies, and highlights an unfulfilled need for rDNA-optimized public genome assemblies and accessible mapping workflows. Results: We customized the human hg38 and mouse mm39 genomes to render them suitable for rDNA mapping. The standard builds for these genomes contain numerous partial or fragmented rDNA loci. We identified and masked all rDNA-like regions in the hg38 and mm39 assemblies, added a single rDNA reference sequence of the appropriate species as a ~45kb chromosome R. We also created annotation files to aid visualization of rDNA features in genome browser tracks. We validated the utility of these customized genomes for mapping of known rDNA binding proteins, and we present in this paper a simple workflow for mapping ChIP-seq datasets to rDNA and generating browser tracks. These resources make rDNA mapping and visualization readily accessible to a broad audience. Availability and Implementation: Customized genome assemblies (hg38-rDNA v1.0 and mm39-rDNA v1.0), annotation files, and positive and negative control mapping tracks are freely available through GitHub at: https://github.com/vikramparalkar/rDNA-Mapping-Genomes

Acute myeloid leukemias with UBTF tandem duplications are sensitive to menin inhibitors

“…19 A default quality score cutoff of Q20 is used. Quality-trimmed reads were then mapped to hg38+rDNA genome build 20 by bwa (v0.7.12-r1039) 21 and converted to a bam file by samtools (v1.2). 22 Duplicate reads were marked with biobambam2 (v2.0.87).…”

ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression

“…We generated a modified reference of the mouse rDNA sequence (NCBI Genbank BK000964.3) 107 . Because the original mouse BK000964.3 sequence begins with the TSS and ends with the Pol I promoter, we transposed a portion at the end of the rDNA reference to the beginning, as previously described 108 , to enable a continuous visualization of the promoter-TSS region. Specifically, the rDNA sequence was cut at the 36,000 nt position and the sequence downstream of the cut site were moved upstream of the TSS, such that the resulting rDNA sequence begins with ∼10kb of IGS, then the promoters and then transcribed regions.…”