Edinburgh Research Explorer Centromere chromatin structure - Lessons from neocentromeres Citation for published version: Naughton, C & Gilbert, N 2020, 'Centromere chromatin structure - Lessons from neocentromeres', Experimental Cell Research, pp. 111899. https://doi.org/10.1016/j.yexcr.2020.111899 Digital Object Identifier (DOI): 10.1016/j.yexcr.2020.111899 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Experimental Cell Research General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 28. Sep. 2021 Experimental Cell Research xxx (xxxx) xxxx Contents lists available at ScienceDirect Experimental Cell Research journal homepage: www.elsevier.com/locate/yexcr Centromere chromatin structure – Lessons from neocentromeres ∗ Catherine Naughton , Nick Gilbert Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK ARTICLE INFO ABSTRACT Keywords: Centromeres are highly specialized genomic loci that function during mitosis to maintain genome stability. Centromere Formed primarily on repetitive α-satellite DNA sequence characterisation of native centromeric chromatin Neocentromere structure has remained challenging. Fortuitously, neocentromeres are formed on a unique DNA sequence and α -satellite represent an excellent model to interrogate centromeric chromatin structure. This review uncovers the specific Chromatin findings from independent neocentromere studies that have advanced our understanding of canonical cen- tromere chromatin structure. Centromeres are highly specialized genomic loci, that function experiments revealed the heterochromatic nature of centromeres [12], during mitosis to ensure accurate chromosome segregation and main- the underlying structure and organisation of this chromatin has re- tain genome stability. Cytogenetically centromeres can be identified as mained obscure. This is primarily due to centromeres being located on the primary constriction of metaphase chromosomes where they serve highly repetitive DNA sequences and the difficulties associated with as the assembly site for the kinetochore, a multiprotein structure that analysing these loci. fvdorms attachments to the microtubules of the mitotic and meiotic Human centromeres are composed of tandem arrays of α-satellite spindles. Whilst kinetochore architecture and microtubule interactions DNA, a repeat based on a 171bp monomer which are 50–70% identical, have been described in detail [1] less is known about their underlying arranged to create a higher order repeat (HOR) unit [13]. Due to the chromatin organisation. Our interest in centromeres arises from a desire challenge in assembling these near-identical DNA sequences the re- to understand their chromatin architecture and determine how im- ference human genome lacked sequence information for all cen- portant this is for function. This information could prove ther- tromeres until its most recent build (GRCh38/hg38) which contains apeutically useful as centromeric breaks and rearrangements are com- sequence representation for all human centromeres although these do monly associated with human diseases such as cancer [2]. not yet completely represent the linear DNA structure [14,15]. This Chromatin is a complex of DNA and proteins within the nucleus of repetitive property of centromeres hinders the use of many chromatin mammalian cells. It functions to package and compress the large structural assays where the readout often requires microarray, or more amounts of DNA into the nucleus and to regulate gene expression. frequently nowadays next generation sequencing. However a recent Nucleosomes represent the primary level of chromatin folding where by advance in understanding centromere organisation comes from using double-stranded DNA is wrapped around eight core histone proteins, Nanopore long DNA sequence reads to assemble the centromeric se- these nucleosomes are then folded into a higher-order fibre which is quence of the human Y chromosome [16]. This study examined the further packaged into the large-scale chromatin structures observed in haploid satellite array present on the Y centromere and using BACs interphase cells [3–6]. We and others have shown that within these spanning from the proximal p-arm to proximal q-arm determined the packaging levels, chromatin structure regulates gene expression by DNA sequence underpinning the functional Y centromere and packaged controlling accessibility of the transcriptional machinery and tran- as chromatin enriched in CENP-A. New sequencing methodologies will scription factors to DNA. For instance, transcription start sites are often make these repetitive centromeric regions easier to structurally char- depleted of nucleosomes [7], forming open or disrupted 30-nm chro- acterise in the future. However, one method we previously used to in- matin fibres [8,9] whilst large-scale chromatin fibres can be decom- terrogate chromatin structure was sucrose gradient sedimentation. pacted in a transcription dependent manner [9–11]. Interphase chro- Using this approach we demonstrated that repetitive satellite-con- matin is characterised as either ‘euchromatin’ or ‘heterochromatin’: taining chromatin fibres have a more compact structure compared to euchromatin often corresponds to gene-rich regions; in contrast, het- bulk chromatin fibres, indicating that canonical centromeric domains erochromatin is transcriptionally silent. Whilst early cytological might have distinct properties [17]. ∗ Corresponding author. E-mail address: [email protected] (C. Naughton). https://doi.org/10.1016/j.yexcr.2020.111899 Received 5 November 2019; Received in revised form 1 February 2020; Accepted 7 February 2020 0014-4827/ © 2020 Elsevier Inc. All rights reserved. Please cite this article as: Catherine Naughton and Nick Gilbert, Experimental Cell Research, https://doi.org/10.1016/j.yexcr.2020.111899 C. Naughton and N. Gilbert Experimental Cell Research xxx (xxxx) xxxx Neocentromeres are a special class of centromere that form in an for the emergence of neocentromeres [35]. Importantly, this experi- ectopic location on a chromosome [18]. In stark contrast to canonical ment did not identify any specific DNA sequence or motif associated centromeres, neocentromeres form on a unique DNA sequence, an im- with neocentromere formation, supporting the requirement for an portant feature that can be exploited to investigate centromere chro- epigenetic component or feature for centromere locus specification. matin structure. Significantly, neocentromeres bind all known essential Although the mechanisms for centromere locus specification are centromere proteins and form a fully functional kinetochore making unclear, CENP-A, a variant of histone H3 [36], was long considered to this a useful model to understand native centromere function [19,20]. be a key component for defining centromere identity. First identified in How neocentromeres emerge is still unclear but they appear in the case 1980 as a protein detected by one of a number of anti-centromere an- of centromere inactivation or loss, and are a feature of certain cancers tibodies found in patients suffering from the autoimmune disorder where they seem to rescue acentric fragments [2]. Intriguingly in a few scleroderma [37], CENP-A was the smallest antigen detected, the larger rare cases neocentromeres have been discovered for seemingly un-re- two were termed CENP-B and CENP-C [38]. Since then CENP-A has arranged chromosomes, including human chromosome 3, 4, 7 and Y been the focus of biochemical and molecular research identifying it as [21–24]. These are often identified through cytogenetic screening, the undeniable epigenetic component necessary for centromere identity which observed a shift in the primary constriction away from the ca- [39–41] and an essential component in kinetochore formation and nonical block of original α-satellite centromeric DNA. Concomitantly, centromere function (reviewed in Ref. [42]). the original centromere is functionally inactivated creating a pseudo- dicentric chromosome but with one functioning centromere in an ec- 2. Centromeres accumulate α-satellite DNA topic site. Indeed, we actually have no clear understanding of the fre- quency of these centromere repositioning events as they have only been The observation that centromere specification is sequence in- detected serendipitously and can be phenotypically silent. Another type dependent but yet all human centromeres are associated with α-satellite of centromere are the evolutionary new centromeres (ENCs) and like DNA presents an intriguing paradox that implies some role for the α- neocentromeres these may result from the seeding of a new centromere satellite DNA sequences in centromere stability. This is also consistent at an ectopic location which have since been inherited through gen- with other eukaryotic species,