Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Li, Diyan; Ning, Chunyou; Zhang, Jiaman; Wang, Yujie; Tang, Qianzi; Kui, Hua; Wang, Tao; He, Mengnan; Jin, Long; Li, Jing; Lin, Yu; Zeng, Bo; Yin, Huadong; Zhao, Xiaoling; Zhang, Yao; Xu, Huailiang; Zhu, Qing; Li, Mingzhou

doi:10.1038/s41467-021-27800-9

Cited by 29 publications

(7 citation statements)

References 103 publications

(125 reference statements)

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“…1 c). Such contact domains have been detected on both macro- and microchromosomes, similar to previous data for other chicken cell types [ 39 , 48 , 56 ]. In many cases, TADs exhibit a hierarchical structure; that is, large contact-enriched domains can be subdivided into several smaller domains.…”

Section: Resultssupporting

confidence: 89%

“…For domain calling, we applied the Armatus [ 47 ] algorithm to the HD3 Hi-C heatmap binned at 50 kb resolution and parameter γ = 0.2–0.3. Hi-C heatmaps, TAD annotations and compartment boundaries for chicken embryonic fibroblasts and granulosa cells from preovulatory follicles were obtained from Fishman et al, 2019 [ 39 ] and Li et al, 2022 [ 48 ], respectively. To compare sets of domains between different cell lines, we either directly compared the genomic coordinates of domain borders at an accuracy level of 50 kb, which corresponds to 1 bin, or used variation of information coefficient.…”

Section: Methodsmentioning

confidence: 99%

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Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

et al. 2023

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Background Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line. Results We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling “chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH. Conclusions In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure–function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.

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Section: Resultssupporting

confidence: 89%

Section: Methodsmentioning

confidence: 99%

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

et al. 2023

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“…In addition, regions enriched with local contacts, namely topologically associating domains (TADs), were identi ed in the genome of chicken HD3 cells (Figure 1 c). Such contact domains have been detected on both macro-and microchromosomes similar to previous data for other chicken cell types [39,55,47]. In many cases, TADs exhibited a hierarchical structure, that is, large contact-enriched domains could be subdivided into several smaller ones.…”

Section: Tads and A/b Compartments Conservation Between Chicken Eryth...supporting

confidence: 85%

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

Maslova

Плотников

Nuriddinov

et al. 2022

Preprint

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Background: Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in HD3 cell line were not assessed. In the present study we apply high throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in HD3 cell line. Results: We obtained Hi-C maps of genomic interactions for HD3 cell line and compared A/B compartments and topologically-associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells we identified more than 25 interchromosomal translocations of regions ≥200 Kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling “chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter, between GGA5, GGA4p and GGA7p, between GAA4q, GGA6 and GGA19 and duplication of the sex chromosome GGAW, were confirmed by FISH. Conclusions: In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, genome is organized into distinct topologically-associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in the studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.

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“…Ribosome and peptide biosynthetic processes were important parts of the protein synthesis process. During the follicular development, numerous biological processes occurred including a series of protein synthetic ( Zhou et al, 2020 ; Li et al, 2022 ). Many proteins such as bone morphogenetic protein 4 ( Yao et al, 2020 ), and transcription factor CTIP2 ( Bhattacharya et al, 2015 ) play important roles in chicken follicular development.…”

Section: Discussionmentioning

confidence: 99%

Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

Cai¹,

Wang²,

Zhou³

et al. 2023

Poultry Science

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Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Cited by 29 publications

References 103 publications

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

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