Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax

Abstract

Ciliates have two different types of nuclei per cell, with one acting as a somatic, transcriptionally active nucleus (macronucleus; abbr. MAC) and another serving as a germline nucleus (micronucleus; abbr. MIC). Furthermore, Oxytricha trifallax undergoes extensive genome rearrangements during sexual conjugation and post-zygotic development of daughter cells. These rearrangements are necessary because the precursor MIC loci are often both fragmented and scrambled, with respect to the corresponding MAC loci. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence. Here, we describe the germline organization of several nested and highly scrambled genes in Oxytricha trifallax. These include cases with multiple layers of nesting, plus highly interleaved or tangled precursor loci that appear to deviate from previously described patterns. We present mathematical methods to measure the degree of nesting between precursor MIC loci, and revisit a method for a mathematical description of scrambling. After applying these methods to the chromosome rearrangement maps of O. trifallax we describe cases of nested arrangements with up to five layers of embedded genes, as well as the most scrambled loci in O. trifallax.

Graph based analysis for gene segment organization In a scrambled genome

“…In [13] and later in [5], it was observed that an IES between consecutive MDSs of one gene can contain MDS segments from other genes, and that this process can be nested. Furthermore MDSs from different MAC genes can overlap or one MDS can be a subsegment of an MDS of another gene.…”

“…[26]). Rearranging segments of nucleotide sequences can be organized in a variety of arrangements on the locus, for example, they can be overlapping or interleaving [5]. Oxytricha trifallax is a single cell organism that is often taken as a model organism to study DNA rearrangement processes.…”

Insertions Yielding Equivalent Double Occurrence Words

“…Note that |z 3 | = |z 1 | = hν since |y i | = |u| for all i. Finally we observe that (2, 1, 3) and consider the insertions ρ(2, 1, 2) and ρ (2,14,15) into w; also, let w = 123456214365 = T τ (2, 4, 1) and consider the insertions τ (2, 1, 5) and τ (2,9,13) into w . Then…”

“…DOWs are also known as Gauss words and are closely related to linear diagrams, chord diagrams, and circle graphs. In the context of genomics, DOWs and operations on DOWs have been used in studies of DNA rearrangement [2,3,9,11]. By modeling the DNA rearrangement process using DOWs, it was observed that over 95% of the scrambled genome of the ciliate Oxytricha trifallax could be described by iterative insertions of the "repeat pattern" (αα) and the "return pattern" (αα R ) [5].…”

“…Let w = 123456653412 with the insertions ρ(2, 1, 13) and ρ(2,5,9) into w; also let w = 12345677654321 with the insertions τ (2, 1, 15) and τ (2, 6, 10) into w .…”