Organization and function of the 3D genome

Bonev, Boyan; Cavalli, Giacomo

doi:10.1038/nrg.2016.112

Nat Rev Genet

2016

DOI: 10.1038/nrg.2016.112

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Organization and function of the 3D genome

Boyan Bonev

¹

,

Giacomo Cavalli

²

Abstract: Understanding how chromatin is organized within the nucleus and how this 3D architecture influences gene regulation, cell fate decisions and evolution are major questions in cell biology. Despite spectacular progress in this field, we still know remarkably little about the mechanisms underlying chromatin structure and how it can be established, reset and maintained. In this Review, we discuss the insights into chromatin architecture that have been gained through recent technological developments in quantitativ… Show more

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Cited by 1,237 publications

(890 citation statements)

References 166 publications

Supporting

18

Mentioning

866

Contrasting

1

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5

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“…Interestingly, the tight relationship between transcriptional status in a region and organization near the nuclear speckles suggests that organization around the nuclear speckle is a highly dynamic and transcriptionally-dependent process. These results contrast with previous views of genome organization that were centered around chromosome territories, a structural feature that is invariant to changes in gene expression 16,24,28 . Together, these results lead to a new picture of genome organization where regions across chromosomes organize around specific nuclear bodies to shape the overall 3-dimensional organization of the nucleus in a highly regulated and dynamic manner (Figure 7).…”

Section: Discussioncontrasting

confidence: 99%

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Quinodoz

¹

,

Ollikainen

²

,

Tabak

³

et al. 2017

Preprint

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Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Interestingly, the tight relationship between transcriptional status in a region and organization near the nuclear speckles suggests that organization around the nuclear speckle is a highly dynamic and transcriptionally-dependent process. These results contrast with previous views of genome organization that were centered around chromosome territories, a structural feature that is invariant to changes in gene expression 16,24,28 . Together, these results lead to a new picture of genome organization where regions across chromosomes organize around specific nuclear bodies to shape the overall 3-dimensional organization of the nucleus in a highly regulated and dynamic manner (Figure 7).…”

Section: Discussioncontrasting

confidence: 99%

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Quinodoz

¹

,

Ollikainen

²

,

Tabak

³

et al. 2017

Preprint

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Figure 5A summarizes the number of differential compartment bins that involve flips (A->B or B->A) or remained within the same compartment throughput the lineage transition. Consistent with the literature 2 , 5 , 49 , we showed that compartmental dynamics are strongly associated with the variability of gene expression and histone modifications (Fig. 5B ).…”

Section: Resultssupporting

confidence: 92%

dcHiC detects differential compartments across multiple Hi-C datasets

Chakraborty

¹

,

Wang

²

,

Ay

³

2022

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Figure 5A summarizes the number of differential compartment bins that involve flips (A → B or B → A) or remained within the same compartment throughput the lineage transition. Consistent with the literature [2, 5, 45], we showed that compartmental dynamics are strongly associated with the variability of gene expression and histone modifications (Figure 5B, Methods) .…”

Section: Resultssupporting

confidence: 92%

“…Previous work has shown that compartmental dynamics are strongly correlated with gene expression and histone modifications [2, 5, 45]. We observed similar trends within the significant differential compartments identified by dcHiC ( Figure 4D ).…”

Section: Resultssupporting

confidence: 85%

dcHiC: differential compartment analysis of Hi-C datasets

Chakraborty

¹

,

Wang

²

,

Ay

³

2021

Preprint

Get access via publisher Add to collection Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

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