Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome

Abstract

Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level. [Supplemental material is available for this article.]The functional centromere is specified by the presence of a special histone H3 variant, known as CENH3 in plants. The establishment and maintenance of centromeres are not defined by the underlying DNA sequences but, rather, are determined by epigenetic mechanisms (Allshire and Karpen 2008). Centromeres can be inactivated (Earnshaw and Migeon 1985;Sullivan and Schwartz 1995;Han et al. 2006;Zhang et al. 2010), or they can also be activated as ''neocentromeres'' from non-centromeric regions (Williams et al. 1998;Nasuda et al. 2005;Marshall et al. 2008;Gong et al. 2009;Topp et al. 2009) or re-activated from a previously inactivated centromere (Han et al. 2009). Most strikingly, human neocentromeres were established at numerous locations associated with most chromosomes and are as fully functional as normal centromeres (Marshall et al. 2008). Despite the extensive and compelling evidence for the epigenetic regulation of centromere establishment and maintenance, there has been limited information as to what epigenetic modifications are important or specific to centromeric chromatin. The slow progress of this important research subject is largely due to the fact that centromeres in most multicellular eukaryotes are composed of megabase-sized arrays of satellite repeats (Henikoff et al. 2001;Jiang et al. 2003), which prevent DNA sequence-based fine mapping of epigenetic marks, such as DNA methylation and histone modifications.Using an immunofluorescence assay on highly stretched meiotic pachytene chromosomes, we recently demonstrated a characteristic hypomethylation pattern associated with the satellite repeats in CENH3-associated chromatin (CEN chromatin) in both Arabidopsis thaliana and maize (Zea mays). In contrast, the same satellite repeats lo...

Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

“…Similarly, the hypomethylation of DNA in the centromeric region as compared to the pericentromeric (hypermethylated) in Arabidopsis also seems to be related to the distribution of CG and CHG sites in the 178-bp satellite DNA repeats . Maize centromeres of active and inactive B chromosomes composed of the same sequences differ in terms of their activation by the presence of CENH3 which appears to inhibit the methylation of the cytosines in those regions [Koo et al, 2011]. A similar pattern of methylation was observed in the centromeric heterochromatin of P. vulgaris which was hypomethylated and surrounded by pericentromeric heterochromatin rich in 5mC.…”

Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

“…Nuclei isolation, DNA fiber preparation, and Fiber FISH were performed following published protocols (Jackson et al, 1998;Koo et al, 2011). Fiber FISH images were captured and processed as previously described in the FISH procedure.…”

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

“…The centromeric H3 subdomains positioned on the interior of the chromatin could then be modified properly for other centromeric functions, such as chromatid cohesion. The structure of alternating CENH3 and H3 nucleosome blocks was reported in a human neocentromere (Chueh et al, 2005) and is also likely associated with the maize B chromosome centromere (Koo et al, 2011). Other epigenetic modifications of CEN chromatin, such as differential cytosine methylation of centromeric DNA Koo et al, 2011;Zakrzewski et al, 2011), could also serve as barriers for the separation of H3 and CENH3 nucleosome blocks.…”

“…Indeed, both DNA sequences and histone proteins associated with CEN chromatin can be epigenetically differentially modified compared with those associated with the flanking pericentromeric chromatin (Sullivan and Karpen, 2004;Cam et al, 2005;Zhang et al, 2008;Koo et al, 2011). In humans and D. melanogaster, blocks of CENP-A/CID nucleosomes are interrupted by nucleosomes containing dimethylated H3 Lys 4 (H3K4me2), a euchromatic mark associated with permissive transcription (Sullivan and Karpen, 2004).…”