scholarly journals Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Felicity C Jones
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Gill Tissue ◽  
Regulatory Control ◽  
F1 Hybrids ◽  
Adaptive Divergence ◽  
Expression Divergence ◽  
Early Stages ◽  
Specific Regulation ◽  
Cis And Trans

Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.

scholarly journals Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

2018 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Felicity C. Jones
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Gill Tissue ◽  
Regulatory Control ◽  
F1 Hybrids ◽  
Adaptive Divergence ◽  
Expression Divergence ◽  
Early Stages ◽  
Specific Regulation ◽  
Highly Correlated

AbstractRegulation of gene expression is thought to play a major role in adaptation but the relative importance of cis- and trans-regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.

scholarly journals Ecological divergence in sympatry causes gene misregulation in hybrids

2019 ◽  
Author(s):  
Joseph A. McGirr ◽  
Christopher H. Martin
Keyword(s):  
Gene Expression ◽  
Reproductive Isolation ◽  
Differentially Expressed ◽  
F1 Hybrids ◽  
Adaptive Divergence ◽  
Lower Hybrid ◽  
Hybrid Fitness ◽  
Hybrid Gene ◽  
San Salvador ◽  
Ecological Selection

AbstractEcological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. However, it is unknown whether divergent ecological selection on gene regulation can directly cause reproductive isolation. Selection favoring regulatory divergence between species could result in gene misregulation in F1 hybrids and ultimately lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to test this hypothesis in a young, sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, which consists of a dietary generalist and two novel trophic specialists – a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misregulated in their F1 hybrids. Consistent with divergent ecological selection causing misregulation, a subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle, and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length – the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can cause hybrid gene misregulation which may act as a primary reproductive barrier between nascent species.SignificanceIt is unknown whether the same genes that regulate ecological traits can simultaneously contribute to reproductive barriers between species. We measured gene expression in two trophic specialist species of Cyprinodon pupfishes that rapidly diverged from a generalist ancestor. We found genes differentially expressed between species that also showed extreme expression levels in their hybrid offspring. Many of these genes showed signs of selection and have putative effects on the development of traits that are important for ecological specialization. This suggests that genetic variants contributing to adaptive trait divergence between parental species negatively interact to cause hybrid gene misregulation, potentially producing unfit hybrids. Such loci may be important barriers to gene flow during the early stages of speciation, even in sympatry.

scholarly journals Tramtrack acts during late pupal development to direct ant caste identity

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009801
Author(s):  
Karl M. Glastad ◽  
Linyang Ju ◽  
Shelley L. Berger
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Behavioral Plasticity ◽  
Regulation Of Gene Expression ◽  
Pupal Stage ◽  
Specific Gene ◽  
Pupal Development ◽  
Camponotus Floridanus ◽  
Hormonal Function ◽  
Specific Regulation

A key question in the rising field of neuroepigenetics is how behavioral plasticity is established and maintained in the developing CNS of multicellular organisms. Behavior is controlled through systemic changes in hormonal signaling, cell-specific regulation of gene expression, and changes in neuronal connections in the nervous system, however the link between these pathways is unclear. In the ant Camponotus floridanus, the epigenetic corepressor CoREST is a central player in experimentally-induced reprogramming of caste-specific behavior, from soldier (Major worker) to forager (Minor worker). Here, we show this pathway is engaged naturally on a large genomic scale during late pupal development targeting multiple genes differentially expressed between castes, and central to this mechanism is the protein tramtrack (ttk), a DNA binding partner of CoREST. Caste-specific differences in DNA binding of ttk co-binding with CoREST correlate with caste-biased gene expression both in the late pupal stage and immediately after eclosion. However, we find a unique set of exclusive Minor-bound genes that show ttk pre-binding in the late pupal stage preceding CoREST binding, followed by caste-specific gene repression on the first day of eclosion. In addition, we show that ttk binding correlates with neurogenic Notch signaling, and that specific ttk binding between castes is enriched for regulatory sites associated with hormonal function. Overall our findings elucidate a pathway of transcription factor binding leading to a repressive epigenetic axis that lies at the crux of development and hormonal signaling to define worker caste identity in C. floridanus.

scholarly journals Gene Expression Is Differentially Regulated in the Epididymis after Orchidectomy

Endocrinology ◽  
2003 ◽  
Vol 144 (3) ◽  
pp. 975-988 ◽  
Author(s):  
Nadine Ezer ◽  
Bernard Robaire
Keyword(s):  
Gene Expression ◽  
Calcium Binding ◽  
Regulation Of Gene Expression ◽  
Brown Norway ◽  
Norway Rat ◽  
Associated Proteins ◽  
Specific Regulation ◽  
Cauda Epididymidis ◽  
Shock Proteins ◽  
And Function

The epididymis is the site for the transport, maturation, and storage of spermatozoa. Regulation of epididymal structure and function is highly dependent on the ipsilateral testis. At the molecular level, however, few studies have been undertaken to determine which genes are expressed in the epididymis under testicular regulation. The goal of this study was to identify genes for which expression is regulated after orchidectomy, both throughout the epididymis and in a segment-specific manner. Microarrays spotted with 474 rat cDNAs were used to examine gene expression changes over the first 7 d post orchidectomy in the initial segment, caput, corpus, and cauda epididymidis of the adult Brown Norway rat. Using k-means cluster analysis, we show that four patterns of gene expression are activated in each epididymal segment over the first week following orchidectomy. Transient up-regulation of gene expression in the epididymis after orchidectomy is described for the first time. Potential androgen-repressed genes, including Gpx-1, show increased expression in the epididymis after orchidectomy. Several glutathione-S-transferases and calcium-binding proteins decline throughout the epididymis after orchidectomy, indicating that these may be novel androgen-regulated epididymal genes. Other genes coding for metabolism-associated proteins, transporters, and α-1 acid glycoprotein show segment-specific regulation in the epididymis after orchidectomy. Finally, we describe the expression of the previously uncharacterized heat shock proteins, and apoptosis-associated genes in the epididymis after orchidectomy. Thus, gene expression in the epididymis is differentially affected over time after orchidectomy. These results provide novel insight into androgen-dependent and segment-specific epididymal function.

scholarly journals Locus control regions

Blood ◽  
2002 ◽  
Vol 100 (9) ◽  
pp. 3077-3086 ◽  
Author(s):  
Qiliang Li ◽  
Kenneth R. Peterson ◽  
Xiangdong Fang ◽  
George Stamatoyannopoulos
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Cell Lineage ◽  
Regulatory Elements ◽  
Dependent Manner ◽  
Long Range Interactions ◽  
Eukaryotic Gene ◽  
Specific Regulation ◽  
Locus Control Regions ◽  
Control Regions

Abstract Locus control regions (LCRs) are operationally defined by their ability to enhance the expression of linked genes to physiological levels in a tissue-specific and copy number–dependent manner at ectopic chromatin sites. Although their composition and locations relative to their cognate genes are different, LCRs have been described in a broad spectrum of mammalian gene systems, suggesting that they play an important role in the control of eukaryotic gene expression. The discovery of the LCR in the β-globin locus and the characterization of LCRs in other loci reinforces the concept that developmental and cell lineage–specific regulation of gene expression relies not on gene-proximal elements such as promoters, enhancers, and silencers exclusively, but also on long-range interactions of variouscis regulatory elements and dynamic chromatin alterations.

scholarly journals Promoter-specific regulation of gene expression by an exogenously added homeodomain that promotes neurite growth

FEBS Letters ◽  
1995 ◽  
Vol 368 (2) ◽  
pp. 311-314 ◽  
Author(s):  
Isabelle Le Roux ◽  
Sandra Duharcourt ◽  
Michel Volovitch ◽  
Alain Prochiantz ◽  
Elettra Ronchi
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Neurite Growth ◽  
Specific Regulation

scholarly journals Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression

2015 ◽  
Vol 112 (33) ◽  
pp. 10231-10238 ◽  
Author(s):  
John F. Allen
Keyword(s):  
Gene Expression ◽  
Gene Product ◽  
Redox Regulation ◽  
Regulation Of Gene Expression ◽  
Regulatory System ◽  
Regulatory Control ◽  
Protein Subunits ◽  
Expression Of Genes ◽  
Genetic Systems ◽  
Membrane Bound

Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control—control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Colocation of gene and gene product for redox regulation of gene expression (CoRR) is a hypothesis in agreement with the results of a variety of experiments designed to test it and which seem to have no other satisfactory explanation. Here, I review evidence relating to CoRR and discuss its development, conclusions, and implications. This overview also identifies predictions concerning the results of experiments that may yet prove the hypothesis to be incorrect.

scholarly journals Do Plasmodesmata Play a Prominent Role in Regulation of Auxin-Dependent Genes at Early Stages of Embryogenesis?

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 733
Author(s):  
Konrad Winnicki ◽  
Justyna Teresa Polit ◽  
Aneta Żabka ◽  
Janusz Maszewski
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
High Permeability ◽  
Cell Stage ◽  
Developmental Processes ◽  
Early Stages ◽  
Cellular Patterning ◽  
Intercellular Channels ◽  
Auxin Efflux Carriers

Plasmodesmata form intercellular channels which ensure the transport of various molecules during embryogenesis and postembryonic growth. However, high permeability of plasmodesmata may interfere with the establishment of auxin maxima, which are required for cellular patterning and the development of distinct tissues. Therefore, diffusion through plasmodesmata is not always desirable and the symplastic continuum must be broken up to induce or accomplish some developmental processes. Many data show the role of auxin maxima in the regulation of auxin-responsive genes and the establishment of various cellular patterns. However, still little is known whether and how these maxima are formed in the embryo proper before 16-cell stage, that is, when there is still a nonpolar distribution of auxin efflux carriers. In this work, we focused on auxin-dependent regulation of plasmodesmata function, which may provide rapid and transient changes of their permeability, and thus take part in the regulation of gene expression.

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