scholarly journals Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Wen Xu ◽  
Lijiang Long ◽  
Yuehui Zhao ◽  
Lewis Stevens ◽  
Irene Felipe ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Laboratory Strain ◽  
Duplication Event ◽  
C Elegans ◽  
Genetic Position ◽  
Yin And Yang ◽  
The Creation ◽  
Gene Sharing

Genes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene became fixed in two laboratory lineages of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300 kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.D and NURF-1.B, which we call Yin and Yang, respectively) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional side products necessary to transcribe the Yin and Yang transcripts in the same cells. Our work demonstrates how gene sharing, through the production of multiple isoforms, can precede the creation of new, independent genes.

scholarly journals Evolution of Yin and Yang isoforms of a chromatin remodeling subunit results in the creation of two genes

2019 ◽  
Author(s):  
Wen Xu ◽  
Lijiang Long ◽  
Yuehui Zhao ◽  
Lewis Stevens ◽  
Ronald E. Ellis ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Laboratory Strain ◽  
Duplication Event ◽  
C Elegans ◽  
Genetic Position ◽  
Long Form ◽  
Yin And Yang ◽  
The Creation

AbstractGenes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene fixed in two laboratory strains of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.B and NURF-1.D, which we call Yin and Yang) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional biproducts necessary to transcribe the Yin and Yang transcripts in the same cells. Our work suggests that evolution of nurf-1 isoforms in nematodes creates adaptive conflict that can be resolved by the creation of new, independent genes.

scholarly journals Functionally non-redundant paralogs spe-47 and spe-50 encode FB-MO associated proteins and interact with him-8

2020 ◽  
Author(s):  
Jessica N. Clark ◽  
Gaurav Prajapati ◽  
Fermina Aldaco ◽  
Thomas J. Sokolich ◽  
Steven Keung ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chromatin Remodeling ◽  
Duplication Event ◽  
Sperm Function ◽  
C Elegans ◽  
Conserved Sequence ◽  
Long Period ◽  
Normal Sperm ◽  
Number Of Genes ◽  
Associated Proteins

AbstractThe activation of C. elegans spermatids to crawling spermatozoa is affected by a number of genes including spe-47. Here, we investigate a paralog to spe-47: spe-50, which has a highly conserved sequence and expression, but which is not functionally redundant to spe-47. Phylogenetic analysis indicates that the duplication event that produced the paralogs occurred prior to the radiation of the Caenorhabditis species included in the analysis, allowing a long period for the paralogs to diverge in function. Furthermore, we observed that knockout mutations in both genes, either alone or together, have little effect on sperm function. However, hermaphrodites harboring both knockout mutations combined with a third mutation in the him-8 gene are nearly self-sterile due to a sperm defect, even though they have numerous apparently normal sperm within their spermathecae. We suggest that the sperm in these triple mutants are defective in fusing with oocytes, and that the effect of the him-8 mutation is due to its role in chromatin remodeling.

scholarly journals HDAC1 SUMOylation promotes Argonaute directed transcriptional silencing in C. elegans

2020 ◽  
Author(s):  
Heesun Kim ◽  
Yue-He Ding ◽  
Gangming Zhang ◽  
Yong-Hong Yan ◽  
Darryl Conte ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
De Novo ◽  
Transcriptional Silencing ◽  
Nurd Complex ◽  
Nucleosome Remodeling ◽  
C Elegans ◽  
Argonaute Proteins ◽  
Associated Proteins ◽  
Heterochromatin Silencing

SUMMARYEukaryotic cells use guided search to coordinately control dispersed genetic elements. The transitive effectors of these mechanisms, Argonaute proteins and their small-RNA co-factors, engage nascent RNAs and chromatin-associated proteins to direct transcriptional silencing. The small ubiquitin-like modifier (SUMO) has been shown to promote the induction and maintenance of silent chromatin (called heterochromatin) in yeast, plants, and animals. Here we show that Argonaute-directed transcriptional silencing in C. elegans requires SUMOylation of the type 1 histone deacetylase HDA-1. SUMOylation of HDA-1 promotes interactions with components of the nucleosome remodeling and deacetylase (NuRD) complex and with the nuclear Argonaute HRDE-1/WAGO-9. Our findings suggest how HDAC1 SUMOylation promotes the association of HDAC and other chromatin remodeling factors with a nuclear Argonaute in order to initiate de novo heterochromatin silencing.

scholarly journals High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

2021 ◽  
Author(s):  
Victoria L Sork ◽  
Shawn Cokus ◽  
Sorel T. Fitz-Gibbon ◽  
Alexey V. Zimin ◽  
Daniela Puiu ◽  
...  
Keyword(s):  
De Novo ◽  
Phenotypic Diversity ◽  
Duplication Event ◽  
Effective Population ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Protein Coding ◽  
Self Recognition ◽  
Intergenic Regions ◽  
Evolutionary Success

The genus Quercus, which emerged ~55 million years ago during globally warm temperatures, diversified into ~450 species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since the early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including the numerous resistance genes and also unexpected candidate genes for an incompatibility system involving multiple non-self-recognition genes. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses (another highly successful taxon). Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.

scholarly journals Author response: Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes

2019 ◽  
Author(s):  
Wen Xu ◽  
Lijiang Long ◽  
Yuehui Zhao ◽  
Lewis Stevens ◽  
Irene Felipe ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Author Response ◽  
Yin And Yang ◽  
The Creation

scholarly journals HDAC1 SUMOylation promotes Argonaute-directed transcriptional silencing in C. elegans

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Heesun Kim ◽  
Yue-He Ding ◽  
Gangming Zhang ◽  
Yong-Hong Yan ◽  
Darryl Conte ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
De Novo ◽  
Transcriptional Silencing ◽  
Silent Chromatin ◽  
Guided Search ◽  
C Elegans ◽  
Argonaute Proteins ◽  
Associated Proteins ◽  
Heterochromatin Silencing

Eukaryotic cells use guided search to coordinately control dispersed genetic elements. Argonaute proteins and their small RNA cofactors engage nascent RNAs and chromatin-associated proteins to direct transcriptional silencing. The small ubiquitin-like modifier (SUMO) has been shown to promote the formation and maintenance of silent chromatin (called heterochromatin) in yeast, plants, and animals. Here, we show that Argonaute-directed transcriptional silencing in Caenorhabditis elegans requires SUMOylation of the type 1 histone deacetylase HDA-1. Our findings suggest how SUMOylation promotes the association of HDAC1 with chromatin remodeling factors and with a nuclear Argonaute to initiate de novo heterochromatin silencing.

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals Distinct Subregions of Swi1 Manifest Striking Differences in Prion Transmission and SWI/SNF Function

2010 ◽  
Vol 30 (19) ◽  
pp. 4644-4655 ◽  
Author(s):  
Zhiqiang Du ◽  
Emily T. Crow ◽  
Hyun Seok Kang ◽  
Liming Li
Keyword(s):  
Chromatin Remodeling ◽  
De Novo ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Conformational Switch ◽  
Amyloid Fibers ◽  
Aggregation Pattern ◽  
Prion Transmission ◽  
Shed Light

ABSTRACT We have recently reported that the yeast chromatin-remodeling factor Swi1 can exist as a prion, [SWI +], demonstrating a link between prionogenesis and global transcriptional regulation. To shed light on how the Swi1 conformational switch influences Swi1 function and to define the sequence and structural requirements for [SWI +] formation and propagation, we functionally dissected the Swi1 molecule. We show here that the [SWI +] prion features are solely attributable to the first 327 amino acid residues (N), a region that is asparagine rich. N was aggregated in [SWI+ ] cells but diffuse in [swi− ] cells; chromosomal deletion of the N-coding region resulted in [SWI +] loss, and recombinant N peptide was able to form infectious amyloid fibers in vitro, enabling [SWI +] de novo formation through a simple transformation. Although the glutamine-rich middle region (Q) was not sufficient to aggregate in [SWI +] cells or essential for SWI/SNF function, it significantly modified the Swi1 aggregation pattern and Swi1 function. We also show that excessive Swi1 incurred Li+/Na+ sensitivity and that the N/Q regions are important for this gain of sensitivity. Taken together, our results provide the final proof of “protein-only” transmission of [SWI +] and demonstrate that the widely distributed “dispensable” glutamine/asparagine-rich regions/motifs might have important and divergent biological functions.

scholarly journals Costimulation of TLR8 responses by CXCL4 in Human Monocytes Mediated by TBK1-IRF5 Signaling and Epigenomic Remodeling

2021 ◽  
Author(s):  
Lionel B. Ivashkiv ◽  
Chao Yang ◽  
Mahesh Bachu ◽  
Caroline Brauner ◽  
Ruoxi Yuan ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Immune Cells ◽  
De Novo ◽  
Inflammatory Diseases ◽  
Human Monocytes ◽  
Cytokine Storm ◽  
New Paradigm ◽  
Inflammatory Genes ◽  
Synergistic Activation ◽  
Fibrotic Diseases

Abstract CXCL4 regulates responses of immune cells to endosomal TLRs and has been implicated in the pathogenesis of inflammatory and fibrotic diseases. However, mechanisms by which CXCL4 modulates TLR responses, and its functions in monocytes/macrophages, are still unclear. Here we report that CXCL4 changes the profile of the TLR8 response in human monocytes by selectively and dramatically amplifying inflammatory gene transcription and IL-1β production while partially attenuating the IFN response. Mechanistically, costimulation by CXCL4 and TLR8 synergistically activated TBK1/IKKε and repurposed these kinases towards an inflammatory response via coupling with IRF5, and by activating the NLRP3 inflammasome without the need for a second signal. CXCL4 strongly induced chromatin remodeling in a cooperative and synergistic manner with TLR8 signaling, inducing de novo enhancers associated with inflammatory genes. These findings identify signaling and epigenomic mechanisms that underly synergistic activation of inflammatory genes by CXCL4 and TLR8, provide a new paradigm for modulation of TLR responses that is relevant for cytokine storm, and suggest targeting the TBK1/IKKε-IRF5 axis may be beneficial in inflammatory diseases.

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