Precise identification of cascading alpha satellite higher order repeats in T2TCHM13 assembly of human chromosome 3

Scientific paper - Conference paper

• Author: Matko Glunčić
• Author: Ines Vlahović
• Author: Marija Rosandić
• Author: Vladimir Paar
• Author's institution: University of Zagreb; Faculty of Science; (Department of Physics)
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Physics

Abstract (english)

Aim. To precisely identify and analyze alpha-satellite higher-order repeats (HORs) in T2T-CHM13 assembly of human chromosome 3. Methods. From the recently sequenced complete T2TCHM13 assembly of human chromosome 3, the precise alpha satellite HOR structure was computed by using the novel high-precision GRM2023 algorithm with global repeat map (GRM) and monomer distance (MD) diagrams. Results. The major alpha satellite HOR array in chromosome 3 revealed a novel cascading HOR, housing 17mer HOR copies with subfragments of periods 15 and 2. Within each row in the cascading HOR, the monomers were of different types, but different rows within the same cascading 17mer HOR contained more than one monomer of the same type. Each canonical 17mer HOR copy comprised 17 monomers belonging to 16 different monomer types. Another pronounced 10mer HOR array was of the regular Willard’s type. Conclusion. Our findings emphasize the complexity within the chromosome 3 centromere as well as deviations from expected highly regular patterns.

• Keywords (english): cascading alpha satellite higher order repeats
• Language: english
• Publication type: Scientific paper - Conference paper
• Publication status: Published
• Peer review: Peer review - international
• Publication version: Published version
• Journal title: Croatian Medical Journal
• Numbering: vol. 65, 209
• p-ISSN: 0353-9504
• e-ISSN: 1332-8166
• URN:NBN: urn:nbn:hr:217:903234
• Publication: 2024
• Project: Number: KK.01.1.1.01.0004; Title (croatian): Provedba vrhunskih istraživanja u sklopu Znanstvenog centra izvrsnosti za kvantne i kompleksne sustave te reprezentacije Liejevih algebri; Title (english): Implementation of top research within the Scientific Center of Excellence for Quantum and Complex Systems, and Representations of Lie Algebras; Acronym: QuantiXLie; Leader: Hrvoje Buljan; Jurisdiction: eu; Funding stream: European Regional Development Fund
• Project: Number: IP-2019-04-2757; Title (croatian): Varijante u repetitivnim strukturama višeg reda u centromernim i NBPF dijelovima genoma čovjeka i viših primata; Title (english): Variants in higher order repeat structures in centromeric and NBPF regions of human and higher primates genomes; Acronym: HORVAR; Leader: Matko Glunčić; Jurisdiction: Croatia; Funding stream: Research Projects
• Conference: Title: 13th International Society for Applied Biological Sciences; Acronym: ISABS; Location: Split, Croatia; Start date: 2024-06-17; End date: 2024-06-22
• Document URL: http://www.cmj.hr/2024/65/3/38868967.htm
• Type of resource: Text
• Access conditions: Open access
• Public note: Received: April 10, 2024. Accepted: May 28, 2024.
• Created on: 2024-07-23 20:53:57