TY - JOUR

T1 - Erythrocytes 3D genome organization in vertebrates

AU - Ryzhkova, Anastasia

AU - Taskina, Alena

AU - Khabarova, Anna

AU - Fishman, Veniamin

AU - Battulin, Nariman

N1 - Funding Information: The reported study was funded by RFBR, project number 19-34-90096. Hi-C libraries of mouse erythroblasts were generated with support from RFBR, project number 18-04-00668. NGS was performed with support from the Ministry of Education and Science of Russian Federation, Grant #2019-0546 (FSUS-2020-0040). Data analysis was performed with support from the computational cluster of the Novosibirsk State University and computational nodes of the Institute of Cytology and Genetics (budget project no. 0324-2019-0041-C-01). Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/2

Y1 - 2021/2

N2 - Generation of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.

AB - Generation of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.

UR - http://www.scopus.com/inward/record.url?scp=85101535098&partnerID=8YFLogxK

U2 - 10.1038/s41598-021-83903-9

DO - 10.1038/s41598-021-83903-9

M3 - Article

C2 - 33627746

AN - SCOPUS:85101535098

VL - 11

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 4414

ER -