scholarly journals Rate variation in the evolution of non-coding DNA associated with social evolution in bees

2018 ◽  
Author(s):  
Benjamin E.R. Rubin ◽  
Beryl M. Jones ◽  
Brendan G. Hunt ◽  
Sarah D. Kocher
Keyword(s):  
Division Of Labor ◽  
Social Evolution ◽  
Molecular Mechanisms ◽  
Regulatory Elements ◽  
Rate Variation ◽  
Putative Gene ◽  
Coding Sequences ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Convergent Rate

AbstractThe evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioral transitions have been hypothesized to go hand-in-hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in eleven diverse bee species, encompassing three independent origins of reproductive division of labor and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behavior, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labor within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioral evolution.

scholarly journals Rate variation in the evolution of non-coding DNA associated with social evolution in bees

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180247 ◽  
Author(s):  
Benjamin E. R. Rubin ◽  
Beryl M. Jones ◽  
Brendan G. Hunt ◽  
Sarah D. Kocher
Keyword(s):  
Social Evolution ◽  
Molecular Mechanisms ◽  
Regulatory Elements ◽  
Division Of Labour ◽  
Rate Variation ◽  
Putative Gene ◽  
Coding Sequences ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Convergent Rate

The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals The interdependence of gene-regulatory elements and the 3D genome

2018 ◽  
Vol 218 (1) ◽  
pp. 12-26 ◽  
Author(s):  
Marit W. Vermunt ◽  
Di Zhang ◽  
Gerd A. Blobel
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Regulatory Elements ◽  
3D Genome ◽  
Gene Positioning ◽  
Transcriptional Changes ◽  
Gene Regulatory Elements ◽  
Chromatin Folding ◽  
Gene Regulatory ◽  
Relationship Of

Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.

scholarly journals Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 729-742 ◽  
Author(s):  
Lena Annika Street ◽  
Ana Karina Morao ◽  
Lara Heermans Winterkorn ◽  
Chen-Yu Jiao ◽  
Sarah Elizabeth Albritton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Protein Complexes ◽  
Regulatory Elements ◽  
Evolutionarily Conserved ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

scholarly journals Identification and Computational Analysis of Gene Regulatory Elements

2015 ◽  
Vol 2015 (1) ◽  
pp. pdb.top083642 ◽  
Author(s):  
Leila Taher ◽  
Leelavati Narlikar ◽  
Ivan Ovcharenko
Keyword(s):  
Computational Analysis ◽  
Regulatory Elements ◽  
Gene Regulatory Elements ◽  
Gene Regulatory

Gene-regulatory elements may change the amount, timing, or location of gene expression, cis-Regulation therapy platforms might become a gene therapy to treat many genetic diseases

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Gene Expression ◽  
Genetic Diseases ◽  
Regulatory Elements ◽  
Tissue Type ◽  
Gene Promoters ◽  
Expression Levels ◽  
Cis Regulation ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Gene Expression Levels

Changes in gene expression levels above or below a particular threshold may have a dramatic impact on phenotypes, leading to a wide spectrum of human illnesses. Gene-regulatory elements, also known as cis-regulatory elements (CREs), may change the amount, timing, or location (cell/tissue type) of gene expression, whereas mutations in a gene's coding sequence may result in lower or higher gene expression levels resulting in protein loss or gain. Loss-of-function mutations in both genes produce recessive human illness, while haploinsufficient mutations in 65 genes are also known to be deleterious due to function gain, according to the ClinVar1 and ClinGen3 databases. CREs are promoters living near to a gene's transcription start site and switching it on at predefined times, places, and levels. Other distal CREs, like enhancers and silencers, are temporal and tissue-specific control promoters. Enhancers activate promoters, commonly referred to as "promoters," whereas silencers turn them off. Insulators also restrict promiscuous interactions between enhancers and gene promoters. Systematic genomic approaches can help understand the cis-regulatory circuitry of gene expression by highly detecting and functionally defining these CREs. This includes the new use of CRISPR–CRISPR-associated protein 9 (CRISPR–Cas9) and other editing approaches to discover CREs. Cis-Regulation therapy (CRT) provides many promises to heal human ailments. CRT may be used to upregulate or downregulate disease-causing genes due to lower or higher levels of expression, and it may also be used to precisely adjust the expression of genes that assist in alleviating disease features. CRT may employ proteins that generate epigenetic modifications like methylation, histone modification, or gene expression regulation looping. Weighing CRT's advantages and downsides against alternative treatment methods is crucial. CRT platforms might become a practical technique to treat many genetic diseases that now lack treatment alternatives if academics, patient communities, clinicians, regulators and industry work together.

scholarly journals Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

PLoS ONE ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. e0198463
Author(s):  
Bhaven B. Patel ◽  
Andres M. Lebensohn ◽  
Ganesh V. Pusapati ◽  
Jan E. Carette ◽  
Julia Salzman ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Regulatory Elements ◽  
Genetic Screens ◽  
Gene Regulatory Elements ◽  
Gene Regulatory
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