Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males

Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure-function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to 3D chromosome structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) chZ expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in C. elegans) is unknown. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosome and chZ organization in somatic cells from both sexes for the first time. We find that B. mori interphase chromosomes are highly compact relative to Drosophila chromosomes. Importantly, we show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting that both male chZs are partially and equally downregulated. We also find that in the early stages of DC, the female chZ repositions toward the nuclear center concomitant with increased Z-linked gene expression, revealing the first non-sequencing-based support for Ohno's hypothesis. These studies represent the first visualization of interphase genome organization and chZ structure in Lepidoptera. We uncover striking similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting convergent evolution of DC mechanisms and a possible role for holocentricity in DC evolution.

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Finding a Balance: How Diverse Dosage Compensation Strategies Modify Histone H4 to Regulate Transcription

Genetics Research International ◽

10.1155/2012/795069 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12

Author(s):

Michael B. Wells ◽

Györgyi Csankovszki ◽

Laura M. Custer

Keyword(s):

Gene Expression ◽

Dosage Compensation ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Current Understanding ◽

Histone H4 ◽

Linked Gene ◽

Expression Levels ◽

Gene Expression Levels

Dosage compensation balances gene expression levels between the sex chromosomes and autosomes and sex-chromosome-linked gene expression levels between the sexes. Different dosage compensation strategies evolved in different lineages, but all involve changes in chromatin. This paper discusses our current understanding of how modifications of the histone H4 tail, particularly changes in levels of H4 lysine 16 acetylation and H4 lysine 20 methylation, can be used in different contexts to either modulate gene expression levels twofold or to completely inhibit transcription.

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Dosage Compensation Systems

Introduction to Epigenetics - Learning Materials in Biosciences ◽

10.1007/978-3-030-68670-3_4 ◽

2021 ◽

pp. 67-89

Author(s):

Renato Paro ◽

Ueli Grossniklaus ◽

Raffaella Santoro ◽

Anton Wutz

Keyword(s):

Gene Expression ◽

X Chromosome ◽

Dosage Compensation ◽

Molecular Mechanisms ◽

Sex Chromosome ◽

Fruit Fly ◽

X Chromosomes ◽

Compensation Systems ◽

A Cell ◽

Males And Females

AbstractThis chapter provides an introduction to chromosome-wide dosage compensation systems. We will examine the evolution of dosage compensation, which is thought to be driven by the appearance of differentiated sex chromosomes. In a subset of species with X chromosomal sex determination or XY sex chromosome systems, expression of X-linked genes is regulated by chromosome-wide modifications that equalize gene expression differences between males and females. The molecular mechanisms of X chromosome-wide dosage compensation have been studied in flies, worms, and mammals. Each of these species uses a distinct dosage compensation strategy with a different molecular mechanism. In the wormCaenorhabditis elegans, gene expression on the two X chromosomes of hermaphrodites is reduced to a level that approximates a single X chromosome in males. The fruit flyDrosophila melanogasterachieves dosage compensation by increased transcription of the single X chromosome in males to a level that is similar to the two X chromosomes in females. Lastly, in mammals, one of the two X chromosomes in female cells is transcriptionally inactive and a single X chromosome is transcribed in both sexes. Studies of dosage compensation systems provide insights into how epigenetic regulation controls gene expression and chromatin organization differentially within a cell.

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64 X-LINKED GENE EXPRESSION IN BOVINE (BOS TAURUS) MALE AND FEMALE IN VITRO- FERTILIZED AND SOMATIC CELL NUCLEAR TRANSFER-DERIVED BLASTOCYSTS

Reproduction Fertility and Development ◽

10.1071/rdv18n2ab64 ◽

2006 ◽

Vol 18 (2) ◽

pp. 140

Author(s):

M. Nino-Soto ◽

G. Mastromonaco ◽

P. Blondin ◽

W. A. King

Keyword(s):

Gene Expression ◽

Developmental Stage ◽

Somatic Cell ◽

Dosage Compensation ◽

Somatic Cell Nuclear Transfer ◽

Nuclear Transfer ◽

Regulatory Mechanisms ◽

Linked Gene ◽

Male And Female

Expression of some X-chromosome linked genes has recently been shown to be altered in bovine somatic cell nuclear transfer (SCNT) derived embryos (Wrenzycki et al. 2002 Biol. Reprod. 66, 127), implying that the regulatory mechanisms of X-linked transcription are affected by embryo in vitro production (IVP) methods. We analyzed the transcriptional pattern of X-linked genes (BIRC4, GAB3, HPRT1, MECP2, RPS4X, SLC25A6, and XIST) in bovine in vitro fertilized (IVF) and SCNT male and female blastocysts to determine X-inactivation status and changes resulting from IVP. We collected pools of male (n = 5 pools) and female (n = 3 pools) IVF-derived blastocysts (Bousquet et al. 1999 Theriogenology 51, 59) and male (n = 5 pools) and female (n = 3 pools) SCNT-derived blastocysts (Mastromonaco et al. 2004 Reprod. Domest. Anim. 39, 462). Each pool consisted of five blastocysts. Embryos were washed in phosphate buffered saline (PBS) + 0.1% polyvinyl alcohol (PVA), collected, and stored at -80�C. Total RNA was extracted with an Absolutely RNA Microprep kit (Stratagene, La Jolla, CA, USA), DNase I treated, and precipitated with isopropanol and linear acrylamide (Ambion, Inc., Austin, TX, USA) as a carrier. Reverse transcription was performed with Oligo-dT (Invitrogen, Burlington, Ontario, Canada) and Superscript II RT (Invitrogen). Transcript quantification was performed by quantitative real-time PCR using SYBR Green I (LightCycler system, Roche, Diagnostics, Laval, Quebec, Canada). Data analysis was performed with SAS (SAS Institute, Inc., Cary, SC, USA) using a mixed-model factorial ANOVA and with results presented as estimates of the median, ratios of estimates, and 95% confidence intervals with � = 0.05. IVF-derived male and female blastocysts possessed similar levels of the transcripts analyzed, suggesting successful dosage compensation at this developmental stage for embryos fertilized in vitro. XIST was not detected in male IVF embryos. GAB3 was not detected in any of the female groups and, in addition, HPRT1 transcripts were not detected in SCNT derived female embryos. Male and female SCNT-derived blastocysts possessed marked differences in their transcript levels, with males showing statistically significantly higher levels of BIRC4 and RPS4X and females possessing higher levels of MECP2 and SLC25A6 transcripts although differences between the latter two were not statistically significant. XIST was detected in both male and female SCNT blastocysts. We conclude that dosage compensation between male and female IVF blastocysts is achieved at this developmental stage for the transcripts examined. However, this pattern was markedly changed in the SCNT group, affecting especially female SCNT blastocysts, suggesting that the regulatory mechanisms of X-inactivation and X-linked gene expression are substantially altered in SCNT embryos probably due to aberrant epigenetic patterns and faulty genome reprogramming. We are currently analyzing X-linked transcription in male and female in vivo-derived blastocysts in order to compare this group with IVP-derived embryos. This work was funded by NSERC, CIHR, and CRC.

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ASSOCIATION OF FEATURE GENE EXPRESSION WITH STRUCTURAL FINGERPRINTS OF CHEMICAL COMPOUNDS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720011005446 ◽

2011 ◽

Vol 09 (04) ◽

pp. 503-519 ◽

Cited By ~ 4

Author(s):

YUN LI ◽

KANG TU ◽

SIYUAN ZHENG ◽

JINGFANG WANG ◽

YIXUE LI ◽

...

Keyword(s):

Gene Expression ◽

Structural Information ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Structural Difference ◽

Structural Features ◽

Molecular Structures ◽

Transcriptomics Data ◽

Function Relationship ◽

Relationship Of

Exploring the relationship between a chemical structure and its biological function is of great importance for drug discovery. For understanding the mechanisms of drug action, researchers traditionally focused on the molecular structures in the context of interactions with targets. The newly emerged high-throughput "omics" technology opened a new dimension to study the structure–function relationship of chemicals. Previous studies made attempts to introduce transcriptomics data into chemical function investigation. But little effort has been made to link structural fingerprints of compounds with defined intracellular functions, i.e. expression of particular genes and altered pathways. By integrating the chemical structural information with the gene expression profiles of chemical-treated cells, we developed a novel method to associate the structural difference between compounds with the expression of a definite set of genes, which were called feature genes. A subtraction protocol was designed to extract a minimum gene set related to chemical structural features, which can be utilized in practice as markers for drug screening. Case studies demonstrated that our approach is capable of finding feature genes associated with chemical structural fingerprints.

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Getting a Full Dose? Reconsidering Sex Chromosome Dosage Compensation in the Silkworm, Bombyx mori

Genome Biology and Evolution ◽

10.1093/gbe/evr036 ◽

2011 ◽

Vol 3 ◽

pp. 491-504 ◽

Cited By ~ 36

Author(s):

James R. Walters ◽

Thomas J. Hardcastle

Keyword(s):

Bombyx Mori ◽

Dosage Compensation ◽

Sex Chromosome ◽

Full Dose ◽

Silkworm Bombyx Mori

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Sex differences in gene expression and proliferation are dependent on the epigenetic modifier HP1γ

10.1101/563940 ◽

2019 ◽

Author(s):

Pui-Pik Law ◽

Ping-Kei Chan ◽

Kirsten McEwen ◽

Huihan Zhi ◽

Bing Liang ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Sex Chromosome ◽

Chromosome Complement ◽

Autosomal Gene ◽

Sexually Dimorphic ◽

Heterochromatin Protein 1 ◽

Epigenetic Modifier ◽

Early Embryos ◽

Males And Females

SummarySex differences in growth rate in very early embryos have been recognized in a variety of mammals and attributed to sex-chromosome complement effects as they occur before overt sexual differentiation. We previously found that sex-chromosome complement, rather than sex hormones regulates heterochromatin-mediated silencing of a transgene and autosomal gene expression in mice. Here, sex dimorphism in proliferation was investigated. We confirm that male embryonic fibroblasts proliferate faster than female fibroblasts and show that this proliferation advantage is completely dependent upon heterochromatin protein 1 gamma (HP1γ). To determine whether this sex-regulatory effect of HP1γ was a more general phenomenon, we performed RNA sequencing on MEFs derived from males and females, with or without HP1γ. Strikingly, HP1γ was found to be crucial for regulating nearly all sexually dimorphic autosomal gene expression because deletion of the HP1γ gene in males abolished sex differences in autosomal gene expression. The identification of a key epigenetic modifier as central in defining gene expression differences between males and females has important implications for understanding physiological sex differences and sex bias in disease.

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Characterization of the pits in parenchyma cells of the moso bamboo [Phyllostachys edulis (Carr.) J. Houz.] culm

Holzforschung ◽

10.1515/hf-2018-0236 ◽

2019 ◽

Vol 73 (7) ◽

pp. 629-636 ◽

Cited By ~ 7

Author(s):

Caiping Lian ◽

Rong Liu ◽

Cheng Xiufang ◽

Shuqing Zhang ◽

Junji Luo ◽

...

Keyword(s):

Structural Characteristics ◽

Parenchyma Cell ◽

Environmental Scanning Electron Microscopy ◽

Environmental Scanning ◽

Bordered Pits ◽

Parenchyma Cells ◽

Vascular Parenchyma ◽

Function Relationship ◽

Relationship Of ◽

First Time

Abstract The pits on parenchyma cell walls facilitate transfer of liquids between adjacent cells in the bamboo. To better understand the structure-function relationship of the pits, the structural characteristics of the pits in bamboo parenchyma cells need to be investigated. In this study, the pit structures were studied by field-emission environmental scanning electron microscopy (SEM). The samples included the native structure and the replica structure via resin castings. The results showed that the parenchyma cells possessed various shapes and the pits were diverse. Parenchyma cells exposed both simple and bordered pits. Pitting between vascular parenchyma cells (VPCs) was similar to that of the metaxylem vessel. In particular, a branched pit structure was found for the first time in the parenchyma cell.

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