Wagner A (2001) Trends Genet "Birth and death of duplicated genes in completely sequenced eukaryotes."

Wagner A

[Trends Genet, 2001]

Gene and genome duplications are commonly regarded as being of major evolutionary significance. But how often does gene duplication occur? And, once duplicated, what are the fates of duplicated genes? How do they contribute to evolution? In a recent article, Lynch and Conery analyze divergence between duplicate genes from six eukaryotic genomes. They estimate the rate of gene duplication, the rate of gene loss after duplication and the strength of selection experienced by duplicate genes. They conclude that although the rate of gene duplications is high, so is the rate of gene loss, and they argue that gene duplications could be a major factor in speciation.

Hobert O et al. (2010) Trends Neurosci "The molecular and gene regulatory signature of a neuron."

Hobert O, Carrera I, Stefanakis N

[Trends Neurosci, 2010]

Neuron-type specific gene batteries define the morphological and functional diversity of cell types in the nervous system. Here, we discuss the composition of neuron-type specific gene batteries and illustrate gene regulatory strategies which determine the unique gene expression profiles and molecular composition of individual neuronal cell types from C. elegans to higher vertebrates. Based on principles learned from prokaryotic gene regulation, we argue that neuronal terminal gene batteries are functionally grouped into parallel-acting 'regulons'. The theoretical concepts discussed here provide testable hypotheses for future experimental analysis of the exact gene-regulatory mechanisms employed in the generation of neuronal diversity and identity.

Hunter CP (1999) Curr Biol "Genetics: A touch of elegance with RNAi."

Hunter CP

[Curr Biol, 1999]

RNA -mediated gene interference (RNAi), a rapid, convenient tool for inhibiting gene function in Caenorhabditis elegans, has recently been shown to work in other organisms.

Walker JE et al. (1993) J Bioenerg Biomembr "The mitochondrial transport protein superfamily."

Runswick MJ, Walker JE

[J Bioenerg Biomembr, 1993]

The ADP/ATP, phosphate, and oxoglutarate/malate carrier proteins found in the inner membranes of mitochondria, and the uncoupling protein from mitochondria in mammalian brown adipose tissue, belong to the same protein superfamily. Established members of this superfamily have polypeptide chains approximately 300 amino acids long that consist of three tandem related sequences of about 100 amino acids. The tandem repeats from the different proteins are interrelated, and probably have similar secondary structures. The common features of this superfamily are also present in nine proteins of unknown functions characterized by DNA sequencing in various species, most notably in Caenorhabditis elegans and Saccharomyces cerevisiae. The high level expression in Escherichia coli of the bovine oxoglutarate/malate carrier, and the reconstitution of active carrier from the expressed protein, offers encouragement that the identity of superfamily members of known sequence but unknown function may be uncovered by a similar route.

Waterhouse PM et al. (2003) Nat Rev Genet "Exploring plant genomes by RNA-induced gene silencing."

Helliwell CA, Waterhouse PM

[Nat Rev Genet, 2003]

The nucleotide sequences of several animal, plant and bacterial genomes are now known, but the functions of many of the proteins that they are predicted to encode remain unclear. RNA interference is a gene-silencing technology that is being used successfully to investigate gene function in several organisms--for example, Caenorhabditis elegans. We discuss here that RNA-induced gene silencing approaches are also likely to be effective for investigating plant gene function in a high-throughput, genome-wide manner.

Hobert O (2006) Cold Spring Harb Symp Quant Biol "Architecture of a microRNA-controlled gene regulatory network that diversifies neuronal cell fates."

Hobert O

[Cold Spring Harb Symp Quant Biol, 2006]

Individual cell types are defined by the expression of specific gene batteries. Regulatory networks that control cell-typespecific gene expression programs in the nervous system are only beginning to be understood. This paper summarizes a complex gene regulatory network, composed of several transcription factors and microRNAs (miRNAs), that controls neuronal subclass specification in the nervous system of the nematode Caenorhabditis elegans.

Gordon KL et al. (2012) PLoS Genet "Tempo and mode in evolution of transcriptional regulation."

Ruvinsky I, Gordon KL

[PLoS Genet, 2012]

Perennial questions of evolutionary biology can be applied to gene regulatory systems using the abundance of experimental data addressing gene regulation in a comparative context. What is the tempo (frequency, rate) and mode (way, mechanism) of transcriptional regulatory evolution? Here we synthesize the results of 230 experiments performed on insects and nematodes in which regulatory DNA from one species was used to drive gene expression in another species. General principles of regulatory evolution emerge. Gene regulatory evolution is widespread and accumulates with genetic divergence in both insects and nematodes. Divergence in cis is more common than divergence in trans. Coevolution between cis and trans shows a particular increase over greater evolutionary timespans, especially in sex-specific gene regulation. Despite these generalities, the evolution of gene regulation is gene- and taxon-specific. The congruence of these conclusions with evidence from other types of experiments suggests that general principles are discoverable, and a unified view of the tempo and mode of regulatory evolution may be achievable.

Freedman JH et al. (2002) Cell Mol Life Sci "Differential display analysis of gene expression in invertebrates."

Freedman JH, Liao VH

[Cell Mol Life Sci, 2002]

Screening for differentially expressed genes is a straightforward approach to study the molecular basis for changes in gene expression. Differential display analysis has been used by investigators in diverse fields of research since it was developed. Differential display has also been the approach of choice to investigate changes in gene expression in response to various biological challenges in invertebrates. We review the application of differential display analysis of gene expression in invertebrates, and provide a specific example using this technique for novel gene discovery in the nematode

Wu W et al. (2011) Mol Cell Endocrinol "Nuclear hormone receptors in parasitic helminths."

Wu W, LoVerde PT

[Mol Cell Endocrinol, 2011]

Nuclear receptors (NRs) belong to a large protein superfamily that are important transcriptional modulators in metazoans. Parasitic helminths include parasitic worms from the Lophotrochozoa (Platyhelminths) and Ecdysozoa (Nematoda). NRs in parasitic helminths diverged into two different evolutionary lineages. NRs in parasitic Platyhelminths have orthologues in Deuterostomes, in arthropods or both with a feature of extensive gene loss and gene duplication within different gene groups. NRs in parasitic Nematoda follow the nematode evolutionary lineage with a feature of multiple duplication of SupNRs and gene loss.

Azimzadeh Jamalkandi S et al. (2011) Funct Integr Genomics "RNAi pathway integration in Caenorhabditis elegans development."

Azimzadeh Jamalkandi S, Masoudi-Nejad A

[Funct Integr Genomics, 2011]

In this review, the pathways involving small RNAs are provided followed by a new and updated network that illustrates their interplay with diverse cellular mechanisms in Caenorhabditis elegans. The RNA silencing pathways are now recognized as key factors that connect together the many variations in biological processes, including transcriptional gene regulation, post-transcriptional gene silencing, translational gene silencing, apoptosis, meiosis, and antiviral defense. The utilization of small RNAs represents a specific, energy conserving, and fast mechanism of gene regulation via a core system known as RNA interference.