HOR-track, classification and monomer-by-monomer annotation of human alpha satellite higher-order repeats in T2T CHM13 human genome assembly release v2.0.
Annotation tables are shown at: How_to_read_AS_annotation
Based on the phylogenetic and genomic analysis of alpha satellites in hg38 genome assembly. Alpha satellite HOR monomer sequences were established as single-sequence HMM profiles (two copies of the same monomer were used for alignment), but any number of slightly different profiles could be used for a given HOR monomer. The profile sets were processed by HMMER to create a monomer-by-monomer annotation track for UCSC Genome Browser as described in Uralsky et al., 2019. Unpublished profiles for S4CYH1L were provided by F. Ryabov and I. Alexandrov.
See details: Altemose et al., 2021, Supplementary Materials and Methods, Section I. Sequence content and organization of centromeric regions. Classification of alpha satellite monomers into HOR monomers.
Nicolas Altemose, Glennis Logsdon, Andrey V Bzikadze, Pragya Sidhwani, Sasha A Langley, Gina V. Caldas, Savannah J. Hoyt, Lev Uralsky, Fedor D. Ryabov, Colin Shew, Michael E.G. Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A. Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R Vollger, Arang Rhie, Ann M. McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Sergey Aganezov, Daniel Olson, Leonardo Gomes de Lima, Tamara Potapova, Gabrielle A. Hartley, Marina Haukness, Peter Kerpedjiev, Fedor Gusev, Kristof Tigyi, Shelise Y. Brooks, Alice Young, Sergey Nurk, Sergey Koren, Sofie Salama, Benedict Paten, Evgeny I. Rogaev, Aaron M Streets, Gary H Karpen, Abby Dernburg, Beth A Sullivan, Aaron F Straight, Travis Wheeler, Jennifer L. Gerton, Evan Eichler, Adam M. Phillippy, Winston Timp, Megan Y. Dennis, Rachel J O'Neill, Justin M Zook, Michael Schatz, Pavel A Pevzner, Mark Diekhans, Charles H. Langley, Ivan A. Alexandrov, Karen H Miga. bioRxiv 2021.07.12.452052; doi: doi.org/10.1101/2021.07.12.452052
Uralsky, L. I.; Shepelev, V. A.; Alexandrov, A. A.; Yurov, Y. B.; Rogaev, E. I.; Alexandrov, I. A. Classification and Monomer-by-Monomer Annotation Dataset of Suprachromosomal Family 1 Alpha Satellite Higher-Order Repeats in Hg38 Human Genome Assembly. Data Brief 2019, 24, 103708. doi: doi.org/10.1016/j.dib.2019.103708.
Shepelev, V. A.; Uralsky, L. I.; Alexandrov, A. A.; Yurov, Y. B.; Rogaev, E. I.; Alexandrov, I. A. Annotation of Suprachromosomal Families Reveals Uncommon Types of Alpha Satellite Organization in Pericentromeric Regions of Hg38 Human Genome Assembly. Genom Data 2015, 5, 139–146. doi: doi.org/10.1016/j.gdata.2015.05.035.
Shepelev, V. A.; Alexandrov, A. A.; Yurov, Y. B.; Alexandrov, I. A. The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes. PLoS Genet. 2009, 5 (9), e1000641. doi: doi.org/10.1371/journal.pgen.1000641.
Contact Lev I. Uralsky <uralsky@rogaevlab.ru>
Contact Fedor Ryabov <fedorrik1@gmail.com>
Contact Ivan A. Alexandrov <ivanalx@hotmail.com>
Lev I. Uralsky (1. Sirius University of Science and Technology, Sochi, Russia; 2. Vavilov Institute of General Genetics, Moscow, Russia)
Valery A. Shepelev (Vavilov Institute of General Genetics, Moscow, Russia)
Fedor Ryabov (Moscow Polytechnic University, Russia)
Ivan A. Alexandrov (1. Vavilov Institute of General Genetics, Moscow, Russia; 2. Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia)