3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

Luo, Xin; Liu, Yuting; Dang, Dachang; Hu, Ting; Hou, Yingping; Meng, Xiaoyu; Zhang, Fengyun; Li, Tingting; Wang, Can; Li, Min; Wu, Haixu; Shen, Qingwu; Hu, Yan; Zeng, Xuerui; He, Xiaorong; Yan, Lei; Zhang, Shihua; Li, Cheng; Su, Bing

doi:10.1016/j.cell.2021.01.001

Cited by 95 publications

(97 citation statements)

References 104 publications

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“…Principal component analysis was conducted using the cwold-dekker software with default parameters (https://github.com/dekkerlab/cworld-dekker/releases, v1.01) based on the ICE-normalized contact matrix at 100 kb resolution. Following many published studies 40,[81][82][83] , the first principal component (PC1) was used to identify compartment A/B. Positive or negative values of the PC1 separate chromatin regions into two spatially segregated compartments and regions with higher gene density and GC content were assigned as compartment A, while the rest were compartment B.…”

Section: Methodsmentioning

confidence: 99%

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

et al. 2021

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Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs’ recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.

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Section: Methodsmentioning

confidence: 99%

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

et al. 2021

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“…The reorganization of TADs will lead to the change of chromatin interaction around TAD boundaries, which may affect the expression of genes [ 38 , 39 ]. Using the 20-kb resolution matrices, we identified a total of 10,571 TAD-like structures including 7169, 7411, 7325, and 7314 at 0, 5, 10, and 20 DPA respectively (Additional file 9 : Table S8).…”

Section: Resultsmentioning

confidence: 99%

Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation

et al. 2022

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Background Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. Results To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. Conclusions This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.

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“…These new regulatory interactions resulted in the co-option (which refers to the redeployment of pre-existing genetic or regulatory mechanisms for the acquisition of new functions or expression domains) of rac3b and rfng in the rhombomeres margins, thus promoting the formation of actomyosin cables characteristic of these structures ( Letelier et al, 2018b ). Moreover, it has been found that human brain tissue shows a subset of species-specific TADs compared with macaques that are associated with human-specific expression changes that are likely responsible of the higher complexity of the human brain ( Luo et al, 2021 ). Similarly, interspecies differences in chromatin structure between human and chimpanzees are commonly associated with differences in gene expression ( Eres et al, 2019 ).…”

Section: Tad Reshuffling Underlies the Emergence Of Evolutionary Noveltiesmentioning

confidence: 99%

Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease

Tena

Santos-Pereira

2021

Front. Cell Dev. Biol.

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Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.

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3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

Cited by 95 publications

References 104 publications

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation

Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease

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