A Micronuclear Locus Containing Three Protein-Coding Genes Remains Linked During Macronuclear Development in the Spirotrichous Ciliate Holosticha

Chang, Wei‐Jen; Stover, Nicholas A.; Addis, Victoria; Landweber, Laura F.

doi:10.1078/143446104774199628

Cited by 29 publications

(47 citation statements)

References 33 publications

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“…Holosticha sp. is morphologically similar to Holosticha kessleri (17) and Uroleptus sp. is similar to Uroleptus gallina.…”

Section: Methodsmentioning

confidence: 78%

“…Species of interest were isolated and grown as described (17). Macronuclei and micronuclei were separated before DNA extraction as described (17). U. grandis DNA was a generous gift from David Prescott (University of Colorado, Boulder).…”

Section: Methodsmentioning

confidence: 99%

“…is similar to Uroleptus gallina. Species of interest were isolated and grown as described (17). Macronuclei and micronuclei were separated before DNA extraction as described (17).…”

Section: Methodsmentioning

confidence: 99%

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The evolutionary origin of a complex scrambled gene

Chang

Bryson

Liang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Some species of ciliates undergo massive DNA elimination and genome rearrangement to construct gene-sized ''chromosomes'' in their somatic nucleus. An example is the extensively scrambled DNA polymerase ␣ gene that is broken into 48 pieces and distributed over two unlinked loci in Stylonychia. To understand the emergence of this complex phenomenon during evolution, we examined DNA polymerase ␣ genes in several earlier diverging species, representing evolutionary intermediates. Mapping these data onto an evolutionary tree suggests that this gene became extensively fragmented and scrambled over evolutionary time through a series of steps, each leading to greater complexity. Our results also suggest a possible mechanism for intron loss by deletion of intron sequences as DNA during development of the somatic nucleus.ciliate ͉ DNA polymerase ͉ hypotrich ͉ intron loss ͉ spirotrich C iliates comprise a diverse group of microbial eukaryotes, or protists. These organisms contain two types of nuclei: a somatic macronucleus that is active during vegetative growth and a germ-line micronucleus that is quiescent except during sexual recombination (1). During sexual conjugation, the two mating cells exchange haploid micronuclei, after which the old macronucleus degrades, and the new diploid micronucleus develops into the new macronucleus. Extensive loss of DNA from the long micronuclear chromosomes, coupled to DNA rearrangement, removes transposons and most intergenic spacer DNA between genes, as well as intragenic spacer DNA, known as internal eliminated segments (IESs). In spirotrichous (formerly hypotrichous) ciliates, the remaining DNA sequences, known as macronuclear destined segments (MDSs), can occupy as little as 2-5% of the germ-line genome. These mostly coding regions assemble together to form Ϸ24,000 types of DNA molecules in the somatic nucleus. Because their average size is just 2.2 kbp and they usually contain only one gene, they are sometimes called ''nano-chromosomes.'' Short telomeres are added to both ends before these molecules are amplified several-thousand-fold (1-3).Furthermore, the germ-line order of the coding regions in 20-30% of the genes in stichotrichous ciliates (a subset of spirotrichous ciliates) are permuted, or scrambled, relative to their linear order in the macronucleus. Although the mechanism of reordering these segments is not well understood, short direct repeats, called pointers, may guide the unscrambling process (1, 4). Invariably, one copy of a repeated word pair is present at the 3Ј end of germ-line segment n and at the 5Ј end of segment n ϩ 1, providing the information to link them together, with only one copy of the repeated word retained in the final DNA molecule (1). Although fragmented genes do occur in other organisms [examples include V(D)J recombination in the vertebrate immune system and split ribosomal RNA genes in the mitochondria of fungi (5) and protists (6, 7)], rarely are they sewn back together at the DNA level.Three different scrambled genes, actin I (8-10), ␣ telomer...

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“…Holosticha sp. is morphologically similar to Holosticha kessleri (17) and Uroleptus sp. is similar to Uroleptus gallina.…”

Section: Methodsmentioning

confidence: 78%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The evolutionary origin of a complex scrambled gene

Chang

Bryson

Liang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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“…Bulk repetitive DNA sequences as well as unique micronucleus-specific sequences become eliminated during polytene chromosome degradation, and macronucleus-destined DNA is fragmented into small DNA molecules, the nanochromosomes, ranging in size between ∼0.4 and ∼40 kbp. In general, each of these nanochromosomes encodes only one ORF; in rare cases, up to three ORFs can be found on one nanochromosome (17). Telomeric DNA sequences are added de novo to the macronuclear nanochromosomes (18).…”

mentioning

confidence: 99%

RNA-dependent control of gene amplification

Heyse

Jönsson

Chang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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We exploit the unusual genome organization of the ciliate cell to analyze the control of specific gene amplification during a nuclear differentiation process. Ciliates contain two types of nuclei within one cell, the macronucleus and the micronucleus; and after sexual reproduction a new macronucleus is formed from a micronuclear derivative. During macronuclear differentiation, most extensive DNA reorganization, elimination, and fragmentation processes occur, resulting in a macronucleus containing short DNA molecules (nanochromosomes) representing individual genetic units and each being present in high copy number. It is believed that these processes are controlled by small nuclear RNAs but also by a template derived from the old macronucleus. We first describe the exact copy numbers of selected nanochromosomes in the macronucleus, and define the timing during nuclear differentiation at which copy number is determined. This led to the suggestion that DNA processing and copy number control may be closely related mechanisms. Degradation of an RNA template derived from the macronucleus leads to significant decrease in copy number, whereas injection of additional template molecules results in an increase in copy number and enhanced expression of the corresponding gene. These observations can be incorporated into a mechanistic model about an RNA-dependent epigenetic regulation of gene copy number during nuclear differentiation. This highlights that RNA, in addition to its well-known biological functions, can also be involved in the control of gene amplification.

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“…Oxytricha trifallax mating compatible strains JRB310 and JRB510 were cultured in inorganic salt media according to established protocol (Chang et al 2004) with Chlamydomonas reinhardtii and Klebsiella oxytoca as food sources. The cells were left overnight to exhaust their food, then filtered through gauze to remove any remaining algae before mixing them in equal proportions to initiate conjugation (Khurana et al 2014).…”

Section: Cell Culture and Harvestingmentioning

confidence: 99%

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

Lindblad

Bracht

Williams

et al. 2017

RNA

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The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.

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A Micronuclear Locus Containing Three Protein-Coding Genes Remains Linked During Macronuclear Development in the Spirotrichous Ciliate Holosticha

Cited by 29 publications

References 33 publications

The evolutionary origin of a complex scrambled gene

The evolutionary origin of a complex scrambled gene

RNA-dependent control of gene amplification

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

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