X-Chromosome Target Specificity Diverged Between Dosage Compensation Mechanisms of Two Closely RelatedCaenorhabditisSpecies DOI Creative Commons
Qiming Yang, Te‐Wen Lo, Katjuša Brejc

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 5, 2022

Abstract An evolutionary perspective enhances our understanding of biological mechanisms. Comparison sex determination and X-chromosome dosage compensation mechanisms between the closely related nematode species C. briggsae ( Cbr ) elegans Cel revealed that genetic regulatory hierarchy controlling both processes is conserved, but target specificity mode binding for specialized condensin complex (DCC) X expression have diverged. We identified two motifs within DCC recruitment sites are highly enriched on X: 13-bp MEX 30-bp II. Mutating either or II in an endogenous site with multiple copies one reduced binding, only removing all eliminated vivo . Hence, to appears additive. In contrast, synergistic: mutating even motif binding. Although share sequence CAGGG, they otherwise diverged so a from cannot function other. Functional divergence was demonstrated vitro A single nucleotide position can determine whether binds. This rapid could been important factor establishing reproductive isolation contrasts dramatically conservation across Drosophila transcription factors developmental such as body-plan specification fruit flies mice.

Language: Английский

Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans DOI Creative Commons
Jun Kim,

David S Jimenez,

Bhavana Ragipani

et al.

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Nov. 4, 2022

Condensins are molecular motors that compact DNA via linear translocation. In

Language: Английский

Citations

28
Fluctuations in chromatin state at regulatory loci occur spontaneously under relaxed selection and are associated with epigenetically inherited variation in C. elegans gene expression DOI Creative Commons
Rachel Wilson, Maxime Le Bourgeois, Marcos Francisco Perez

et al.

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(3), P. e1010647 - e1010647

Published: March 2, 2023

Some epigenetic information can be transmitted between generations without changes in the underlying DNA sequence. Changes regulators, termed epimutations, occur spontaneously and propagated populations a manner reminiscent of mutations. Small RNA-based epimutations C . elegans persist for around 3–5 on average. Here, we explored whether chromatin states also undergo spontaneous change this could potential alternative mechanism transgenerational inheritance gene expression changes. We compared profiles at matched time points from three independent lineages minimal population size. Spontaneous occurred 1% regulatory regions each generation. were heritable significantly enriched nearby protein-coding genes. Most chromatin-based short-lived but subset had longer duration. Genes subject to long-lived multiple components xenobiotic response pathways. This possible role adaptation environmental stressors.

Language: Английский

Citations

12
Compensation of gene dosage on the mammalian X DOI Creative Commons
Daniela Cecalev, Beatriz Viçoso, Rafael Galupa

et al.

Development, Journal Year: 2024, Volume and Issue: 151(15)

Published: Aug. 1, 2024

Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they also lead to dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring differences their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' for chromosomes. this Review, we focus on mammalian X chromosome discuss recent new insights into dosage-compensation mechanisms that evolved along emergence chromosomes, namely X-inactivation X-upregulation. We evolution genetic loci molecular players involved, as well regulatory diversity potentially different requirements compensation across species.

Language: Английский

Citations

4
Transcriptomic and chromatin accessibility profiling unveils new regulators of heat hormesis inCaenorhabditis elegans DOI Creative Commons

Hsin-Yun Chang,

Sarah E. McMurry,

Sicheng Ma

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 14, 2025

Heat hormesis describes the beneficial adaptations from transient exposure to mild heat stress, which enhances stress resilience and promotes healthy aging. It is thought be underlying basis of popular wellness practices like sauna therapy. Despite extensive documentation across species, molecular long-term protective effects remain poorly understood. This study bridges that critical gap through a comprehensive multiomic analysis, providing key insights into transcriptomic chromatin accessibility landscapes throughout regimen adapted in C. elegans . We uncover highly dynamic dose-dependent responses reveal while most initial stress-induced changes revert baseline, differences response subsequent shock challenge are directly linked physiological benefits. identify new regulators hormesis, including MARS-1/MARS1, SNPC-4/SNAPc, ELT-2/GATA4, FOS-1/c-Fos, DPY-27/SMC4, likely orchestrate gene expression programs enhance distinct biological pathways. advances our understanding mechanisms, points multiple avenues future investigations, suggests potential strategies for promoting aging mid-life management.

Language: Английский

Citations

0
Chromatin and epigenetics in aging biology DOI
Eric Lieberman Greer, Siu Sylvia Lee, Veena Prahlad

et al.

Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Abstract This book chapter will focus on modifications to chromatin itself, how are regulated, and these deciphered by the cell impact aging. In this chapter, we review change with age, examine chromatin-modifying enzymes have been shown regulate aging healthspan, discuss some of epigenetic changes triggered they can lifespan individual its naïve descendants, speculate future directions for field.

Language: Английский

Citations

0
Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III DOI Creative Commons
Manikarna Dinda, Ryan D. Fine, Shekhar Saha

et al.

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(4), P. e1010705 - e1010705

Published: April 14, 2023

Despite recent advances in single-molecule and structural analysis of condensin activity vitro , mechanisms functional loading loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae the most prominent site is rDNA locus on chromosome XII, but its repetitiveness deters rigorous individual genes. An equally non-rDNA located III (chrIII). It lies promoter a putative non-coding RNA gene called RDT1 which segment recombination enhancer (RE) dictates MAT a-specific chrIII organization. Here, we unexpectedly find recruited cells through hierarchical interactions with Fob1, Tof2, cohibin (Lrs4/Csm1), set nucleolar factors also recruit rDNA. Fob1 directly binds this while binding vivo depends an adjacent Mcm1/α2 provides cell specificity. We uncover evidence for condensin-driven anchored by at unidirectionally extends toward right arm chrIII, supporting donor preference during mating-type switching. S . therefore new platform study programmed condensin-mediated conformation.

Language: Английский

Citations

7
Maternal H3K36 and H3K27 HMTs protect germline development via regulation of the transcription factor LIN-15B DOI Creative Commons
Chad Cockrum, Susan Strome

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Aug. 3, 2022

Maternally synthesized products play critical roles in the development of offspring. A premier example is Caenorhabditis elegans H3K36 methyltransferase MES-4, which essential for germline survival and How maternal MES-4 protects not well understood, but its role methylation hinted that it may regulate gene expression primordial germ cells (PGCs). We tested this hypothesis by profiling transcripts from nascent germlines (PGCs their descendants) dissected wild-type mes-4 mutant (lacking zygotic MES-4) larvae. displayed downregulation some genes, upregulation somatic dramatic hundreds genes on X chromosome. demonstrated one or more cause death generating analyzing mutants inherited different endowments chromosome(s). Intriguingly, removal THAP transcription factor LIN-15B reduced misexpression prevented death. lin-15B X-linked misexpressed PGCs, identifying as a target repression. The above findings extend to H3K27 MES-2/3/6, C. version polycomb repressive complex 2. propose PRC2 cooperate protect preventing synthesis germline-toxic encoded chromosome, including key LIN-15B.

Language: Английский

Citations

11
Rapid chromosome evolution and acquisition of thermosensitive stochastic sex determination in nematode androdioecious hermaphrodites DOI Creative Commons
Kohta Yoshida, Hanh Witte, Ryo Hatashima

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 7, 2024

The factors contributing to evolution of androdioecy, the coexistence hermaphrodites and males such as in Caenorhabditis elegans, remains poorly known. However, nematodes exhibit androdioecy at last 13 genera with predatory genus Pristionchus having seven independent transitions towards androdioecy. Nonetheless, associated genomic architecture sex determination mechanisms are largely known from Caenorhabditis. Here, studying 47 species, we observed repeated chromosome which abolished ancestral XX/XO system. Two phylogenetically unrelated androdioecious species have no differences between sexes mating resulted hermaphroditic offspring only. We demonstrate that stochastic is influenced by temperature P. mayeri entomophagus, CRISPR engineering indicated a conserved role transcription factor TRA-1 mayeri. Chromosome-level genome assemblies subsequent analysis related revealed be derived XY systems through chromosome-autosome fusions. Thus, rapid karyotype evolution, evolvable general features this genus, represent dynamic background against has evolved recurrently. Future studies might indicate more common than currently appreciated.

Language: Английский

Citations

2
X-chromosome target specificity diverged between dosage compensation mechanisms of two closely related Caenorhabditis species DOI Creative Commons
Qiming Yang, Te‐Wen Lo, Katjuša Brejc

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: March 23, 2023

An evolutionary perspective enhances our understanding of biological mechanisms. Comparison sex determination and X-chromosome dosage compensation mechanisms between the closely related nematode species Caenorhabditis briggsae ( Cbr ) elegans Cel revealed that genetic regulatory hierarchy controlling both processes is conserved, but target specificity mode binding for specialized condensin complex (DCC) X expression have diverged. We identified two motifs within DCC recruitment sites are highly enriched on X: 13 bp MEX 30 II. Mutating either or II in an endogenous site with multiple copies one reduced binding, only removing all eliminated vivo. Hence, to appears additive. In contrast, synergistic: mutating even motif vivo binding. Although share sequence CAGGG, they otherwise diverged so a from cannot function other. Functional divergence was demonstrated vitro. A single nucleotide position can determine whether binds. This rapid could been important factor establishing reproductive isolation contrasts dramatically conservation across Drosophila transcription factors developmental such as body-plan specification fruit flies mice.

Language: Английский

Citations

5
Regulatory divergences in dosage compensation cause hybrid male inviability inCaenorhabditis DOI Open Access
Yongbin Li, Yimeng Gao,

Jiaonv Ma

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 8, 2024

Abstract The genetic basis of Haldane’s rule, such as hybrid male incompatibility in XX systems, has long remained elusive. Here, we found that crosses Caenorhabditis nigoni males with C. briggsae females result insufficient expression Cbr-xol-1 , an X-linked master switch responsible for sex determination, consequently activating aberrant dosage compensation males, and ultimately leading to embryonic inviability. Three compensatory divergences comparable xol-1 levels between the parental species but lethal underexpression embryos: 1) a less active promoter than its ortholog; 2) loss paralog ; 3) pseudogenization autosomal repressor . Our results define evolutionary scenario sexual

Language: Английский

Citations

1