Barr body

Last updated January 15, 2025

Nucleus of a female amniotic fluid cell. Top: Both X-chromosome territories are detected by FISH. Shown is a single optical section made with a confocal microscope. Bottom: Same nucleus stained with DAPI and recorded with a CCD camera. The Barr body is indicated by the arrow, it identifies the inactive X (Xi). Sd4hi-unten-crop.jpg — Nucleus of a female amniotic fluid cell. Top: Both X-chromosome territories are detected by FISH. Shown is a single optical section made with a confocal microscope. Bottom: Same nucleus stained with DAPI and recorded with a CCD camera. The Barr body is indicated by the arrow, it identifies the inactive X (Xi).

A Barr body (named after discoverer Murray Barr)^[1] or X-chromatin is an inactive X chromosome. In species with XY sex-determination (including humans), females typically have two X chromosomes,^[2] and one is rendered inactive in a process called lyonization. Errors in chromosome separation can also result in male and female individuals with extra X chromosomes. The Lyon hypothesis states that in cells with multiple X chromosomes, all but one are inactivated early in embryonic development in mammals.^[3]^[4] The X chromosomes that become inactivated are chosen randomly, except in marsupials and in some extra-embryonic tissues of some placental mammals, in which the X chromosome from the sperm is always deactivated.^[5]

In humans with euploidy, a genotypical female (46, XX karyotype) has one Barr body per somatic cell nucleus, while a genotypical male (46, XY) has none. The Barr body can be seen in the interphase nucleus as a darkly staining small mass in contact with the nucleus membrane. Barr bodies can be seen in neutrophils at the rim of the nucleus.

In humans with more than one X chromosome, the number of Barr bodies visible at interphase is always one fewer than the total number of X chromosomes. For example, people with Klinefelter syndrome (47, XXY) have a single Barr body, and people with a 47, XXX karyotype have two Barr bodies.

Mechanism

Someone with two X chromosomes (such as the majority of human females) has only one Barr body per somatic cell, while someone with one X chromosome (such as most human males) has none.

Mammalian X-chromosome inactivation is initiated from the X inactivation centre or Xic, usually found near the centromere.^[6] The center contains twelve genes, seven of which code for proteins, five for untranslated RNAs, of which only two are known to play an active role in the X inactivation process, Xist and Tsix .^[6] The centre also appears to be important in chromosome counting: ensuring that random inactivation only takes place when two or more X-chromosomes are present. The provision of an extra artificial Xic in early embryogenesis can induce inactivation of the single X found in male cells.^[6]

The roles of Xist and Tsix appear to be antagonistic. The loss of Tsix expression on the future inactive X chromosome results in an increase in levels of Xist around the Xic. Meanwhile, on the future active X Tsix levels are maintained; thus the levels of Xist remain low.^[7] This shift allows Xist to begin coating the future inactive chromosome, spreading out from the Xic.^[2] In non-random inactivation this choice appears to be fixed and current evidence suggests that the maternally inherited gene may be imprinted.^[3] Variations in Xi frequency have been reported with age, pregnancy, the use of oral contraceptives, fluctuations in menstrual cycle and neoplasia.^[8]

It is thought that this constitutes the mechanism of choice, and allows downstream processes to establish the compact state of the Barr body. These changes include histone modifications, such as histone H3 methylation (i.e. H3K27me3 by PRC2 which is recruited by Xist)^[9] and histone H2A ubiquitination,^[10] as well as direct modification of the DNA itself, via the methylation of CpG sites.^[11] These changes help inactivate gene expression on the inactive X-chromosome and to bring about its compaction to form the Barr body.

Reactivation of a Barr body is also possible, and has been seen in breast cancer patients.^[12] One study showed that the frequency of Barr bodies in breast carcinoma were significantly lower than in healthy controls, indicating reactivation of these once inactivated X chromosomes.^[12]

Uses

Barr Bodies in Ancient Samples: Observation and Relevance in Gender Identification of Extinct Species

Barr bodies are condensed, inactive X chromosomes found in the somatic cells of female mammals. Their detection in ancient samples provides a powerful tool for gender identification in extinct species, offering insights into population dynamics, biology, and evolution.

Recent advancements in histological and genomic techniques have made it possible to observe Barr bodies in ancient remains, including fossilized bones and tissues:

Histological Staining: Techniques like hematoxylin-eosin staining can highlight chromatin structures, including Barr bodies, in well-preserved osteocytes embedded within bone matrix.^[13]
Fluorescence Microscopy: Fluorescent dyes can differentiate X-chromosome condensation patterns, aiding in the visualization of Barr bodies.^[13]
Integration with Genomic Tools: Techniques such as PaleoHi-C enable the spatial reconstruction of chromosomal interactions, confirming the presence of inactivated X chromosomes in ancient samples.

In a notable example, Barr bodies were detected in osteocytes from ancient mammalian remains, demonstrating the potential of this approach for studying gender in extinct populations.^[13]

Relevance in Gender Identification

Population Studies:
- Identifying sex ratios in extinct species sheds light on social structures, reproductive strategies, and extinction dynamics.
Reconstruction of Lifeways:
- Understanding the distribution of genders within ancient populations allows bioarchaeologists to analyze sex-based differences in diet, health, and activity patterns.^[14]
Preservation of Chromatin:
- The discovery of intact Barr bodies in fossils underscores the potential for studying chromosomal and epigenetic features in ancient samples

Limitations and Challenges

Degradation of Samples: The fragmentation and chemical damage of ancient DNA and chromatin often hinder Barr body detection.
Sample Availability: Successful detection depends on the preservation of osteocytes or other cells within the sample matrix.
Replicability: Variability in preservation conditions can limit the reproducibility of results across samples.

Future Directions

Further research into the detection of Barr bodies may enhance our ability to:

Identify gender in a broader range of extinct species.
Study X-chromosome inactivation patterns across evolutionary timescales.
Integrate histological and genomic methods to reconstruct detailed population dynamics.

Related Research Articles

<span class="mw-page-title-main">Euchromatin</span> Lightly packed form of chromatin that is enriched in genes

Euchromatin is a lightly packed form of chromatin that is enriched in genes, and is often under active transcription. Euchromatin stands in contrast to heterochromatin, which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.

Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed; however, according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO₄ staining reveal that the dense packing is not due to the chromatin.

A karyotype is the general appearance of the complete set of chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is discerned by determining the chromosome complement of an individual, including the number of chromosomes and any abnormalities.

Dosage compensation is the process by which organisms equalize the expression of genes between members of different biological sexes. Across species, different sexes are often characterized by different types and numbers of sex chromosomes. In order to neutralize the large difference in gene dosage produced by differing numbers of sex chromosomes among the sexes, various evolutionary branches have acquired various methods to equalize gene expression among the sexes. Because sex chromosomes contain different numbers of genes, different species of organisms have developed different mechanisms to cope with this inequality. Replicating the actual gene is impossible; thus organisms instead equalize the expression from each gene. For example, in humans, female (XX) cells randomly silence the transcription of one X chromosome, and transcribe all information from the other, expressed X chromosome. Thus, human females have the same number of expressed X-linked genes per cell as do human males (XY), both sexes having essentially one X chromosome per cell, from which to transcribe and express genes.

X-inactivation is a process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packaged into a transcriptionally inactive structure called heterochromatin. As nearly all female mammals have two X chromosomes, X-inactivation prevents them from having twice as many X chromosome gene products as males, who only possess a single copy of the X chromosome.

Histone H2A is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells.

Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated, and how many methyl groups are attached. Methylation events that weaken chemical attractions between histone tails and DNA increase transcription because they enable the DNA to uncoil from nucleosomes so that transcription factor proteins and RNA polymerase can access the DNA. This process is critical for the regulation of gene expression that allows different cells to express different genes.

<span class="mw-page-title-main">ATR-X syndrome</span> Medical condition

Alpha-thalassemia mental retardation syndrome (ATRX), also called alpha-thalassemia X-linked intellectual disability syndrome, nondeletion type or ATR-X syndrome, is an X-linked recessive condition associated with a mutation in the ATRX gene. Males with this condition tend to be moderately intellectually disabled and have physical characteristics including coarse facial features, microcephaly, hypertelorism, a depressed nasal bridge, a tented upper lip and an everted lower lip. Mild or moderate anemia, associated with alpha-thalassemia, is part of the condition. Females with this mutated gene have no specific signs or features, but if they do, they may demonstrate skewed X chromosome inactivation.

Polycomb-group proteins are a family of protein complexes first discovered in fruit flies that can remodel chromatin such that epigenetic silencing of genes takes place. Polycomb-group proteins are well known for silencing Hox genes through modulation of chromatin structure during embryonic development in fruit flies. They derive their name from the fact that the first sign of a decrease in PcG function is often a homeotic transformation of posterior legs towards anterior legs, which have a characteristic comb-like set of bristles.

Core histone macro-H2A.1 is a protein that in humans is encoded by the H2AFY gene.

<span class="mw-page-title-main">XIST</span> Non-coding RNA

Xist is a non-coding RNA transcribed from the X chromosome of the placental mammals that acts as a major effector of the X-inactivation process. It is a component of the Xic – X-chromosome inactivation centre – along with two other RNA genes and two protein genes.

Chromodomain-helicase-DNA-binding protein 8 is an enzyme that in humans is encoded by the CHD8 gene.

Long non-coding RNAs are a type of RNA, generally defined as transcripts more than 200 nucleotides that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. Given that some lncRNAs have been reported to have the potential to encode small proteins or micro-peptides, the latest definition of lncRNA is a class of transcripts of over 200 nucleotides that have no or limited coding capacity. However, John S. Mattick and colleagues suggested to change definition of long non-coding RNAs to transcripts more than 500 nt, which are mostly generated by Pol II. That means that question of lncRNA exact definition is still under discussion in the field. Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of transcripts that do not overlap protein-coding genes.

Skewed X-chromosome inactivation occurs when the X-inactivation of one X chromosome is favored over the other, leading to an uneven number of cells with each chromosome inactivated. It is usually defined as one allele being found on the active X chromosome in over 75% of cells, and extreme skewing is when over 90% of cells have inactivated the same X chromosome. It can be caused by primary nonrandom inactivation, either by chance due to a small cell pool or directed by genes, or by secondary nonrandom inactivation, which occurs by selection.

Tsix is a non-coding RNA gene that is antisense to the Xist RNA. Tsix binds Xist during X chromosome inactivation. The name Tsix comes from the reverse of Xist, which stands for X-inactive specific transcript.

Epigenetics of human development is the study of how epigenetics effects human development.

X chromosome inactivation (XCI) is the phenomenon that has been selected during the evolution to balance X-linked gene dosage between XX females and XY males.

Jeannie T. Lee is a Professor of Genetics at Harvard Medical School and the Massachusetts General Hospital, and a Howard Hughes Medical Institute Investigator. She is known for her work on X-chromosome inactivation and for discovering the functions of a new class of epigenetic regulators known as long noncoding RNAs (lncRNAs), including Xist and Tsix.

Neil Alexander Steven Brockdorff is a British biochemist who is a Wellcome Trust Principal Research Fellow and professor in the department of biochemistry at the University of Oxford. Brockdorff's research investigates gene and genome regulation in mammalian development. His interests are in the molecular basis of X-inactivation, the process that evolved in mammals to equalise X chromosome gene expression levels in XX females relative to XY males.

X chromosome reactivation (XCR) is the process by which the inactive X chromosome (the Xi) is re-activated in the cells of eutherian female mammals. Therian female mammalian cells have two X chromosomes, while males have only one, requiring X-chromosome inactivation (XCI) for sex-chromosome dosage compensation. In eutherians, XCI is the random inactivation of one of the X chromosomes, silencing its expression. Much of the scientific knowledge currently known about XCR comes from research limited to mouse models or stem cells.

References

Links to full text articles are provided where access is free, in other cases only the abstract has been linked.

↑ Barr, M. L.; Bertram, E. G. (1949). "A Morphological Distinction between Neurones of the Male and Female, and the Behaviour of the Nucleolar Satellite during Accelerated Nucleoprotein Synthesis". Nature . 163 (4148): 676–677. Bibcode:1949Natur.163..676B. doi:10.1038/163676a0. PMID 18120749. S2CID 4093883.
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1 2 Brown, C.J., Robinson, W.P., (1997), XIST Expression and X-Chromosome Inactivation in Human Preimplantation Embryos Am. J. Hum. Genet. 61, 5–8 (Full Text PDF)
↑ Lyon, M. F. (1961). "Gene Action in the X-chromosome of the Mouse (Mus musculus L.)". Nature . 190 (4773): 372–373. Bibcode:1961Natur.190..372L. doi:10.1038/190372a0. PMID 13764598. S2CID 4146768.
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↑ Lee, J. T.; Davidow, L. S.; Warshawsky, D. (1999). "Tisx, a gene antisense to Xist at the X-inactivation centre". Nat. Genet. 21 (4): 400–404. doi:10.1038/7734. PMID 10192391. S2CID 30636065.
↑ Sharma, Deepti (January 10, 2018). "Deciphering the Role of the Barr Body in Malignancy". Sultan Qaboos University Medical Journal. 17 (4): 389–397. doi:10.18295/squmj.2017.17.04.003. PMC 5766293 . PMID 29372079.
↑ Heard, E.; Rougeulle, C.; Arnaud, D.; Avner, P.; Allis, C. D. (2001). "Methylation of Histone H3 at Lys-9 Is an Early Mark on the X Chromosome during X Inactivation". Cell. 107 (6): 727–738. doi: 10.1016/S0092-8674(01)00598-0 . PMID 11747809. S2CID 10124177.
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↑ Chadwick, B.P.; Willard, H.F. (2003). "Barring gene expression after XIST: maintaining faculative heterochromatin on the inactive X.". Seminars in Cell & Developmental Biology. 14 (6): 359–367. doi:10.1016/j.semcdb.2003.09.016. PMID 15015743.
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