Systematic Identification of Independent Functional Non-coding RNA Genes in Oxytricha trifallax

Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan Oxytricha trifallax to screen for eukaryotic independent functional noncoding RNA genes. The Oxytricha macronuclear genome consists of thousands of gene-sized nanochromosomes , each of which usually contains only a single gene. Using a draft Oxytricha trifallax genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that Oxytricha has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates

Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination, illustrating how the process of programmed genome rearrangement gives rise to evolutionary innovation

BRD2 compartmentalizes the accessible genome.

Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions

Stylonychia lemnae DDE_TNP_is1595 contigs

Contigs in fasta format

Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ~2,000 copies. We report the high-quality genome assembly of ~16,000 complete nanochromosomes (~50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ~3.2 kb) and encode ~18,500 genes. Alternative DNA fragmentation processes ~10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ~4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease

The Energetics and Physiological Impact of Cohesin Extrusion.

Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural stripes, where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development. Cell 2018 May 17; 173(5):1165-1178.e20

Oxytricha trifallax macronuclear IDBA assembly

Contigs in gzipped fasta format