In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

Arzate-Mejía, Rodrigo G.; Cerecedo-Castillo, Angel Josué; Guerrero, Georgina; Furlan-Magaril, Mayra; Recillas‐Targa, Félix

doi:10.1038/s41467-020-14651-z

Cited by 40 publications

(25 citation statements)

References 74 publications

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“…These data indicate that bRNAs stabilize CTCF at the boundary thus, interactions between the genes within these TADs and their cognate enhancers is favored resulting in robust transcription of genes due to better insulation of these TAD boundaries. These results contrast the observations that deletion of boundary had no effect on E-P interaction (Yokoshi et al, 2020) but agree with other literature (Arzate-Mejía et al, 2020).…”

Section: Discussionsupporting

confidence: 83%

Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries

Islam

Saravanan

Walavalkar

et al. 2021

Preprint

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The genome is partitioned into Topologically Associating Domains (TADs). About half of the boundaries of these TADs exhibit transcriptional activity and are correlated with better TAD insulation. However, the role of these transcripts per se in TAD insulation, enhancer:promoter interactions and transcription remain unknown. Here we investigate the functional roles of these bRNAs (boundary-RNA) in boundary insulation and consequent effects on enhancer-promoter interactions and TAD transcription genome-wide and on disease relevant INK4a/ARF TAD. Using series of CTCF sites deletion and bRNA knockdown approaches at this TAD boundary, we show a direct association of CTCF with bidirectional bRNAs where the loss of bRNA triggers the concomitant loss of: CTCF clustering at TAD boundary, its insulation, enhancer:promoter interactions and gene transcription within the targeted TAD. In search of what regulates bRNA expression itself, we used another series of enhancer deletions and CRISPRi on promoters within INK4a/ARF TAD and observed that indeed, enhancers interact with boundaries and positively regulate the bRNA transcription at TAD boundaries. In return, the bRNAs recruit/stabilise the CTCF even on weaker motifs within these boundaries and supports CTCF binding in clusters, therefore enhancing TAD insulation which favors the intra-TAD enhancer:promoter interactions and robust gene transcription. Functionally, eRNAs within the boundaries are repurposed as more stable bRNAs and their knockdown exactly mimics the boundary loss. Furthermore, transcribing boundaries exhibit high TAD transcription in TCGA tumor datasets. Together, these results show that active enhancers directly mediate better insulation of TADs by activating the transcription at TAD boundaries. These transcripts trigger CTCF clustering at the boundary resulting in better insulation which favours robust intra-TAD enhancer:promoter interactions to activate the gene transcription.

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Section: Discussionsupporting

confidence: 83%

Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries

Islam

Saravanan

Walavalkar

et al. 2021

Preprint

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“…The lack of direct correlation between DEGs and DARs has been previously noted in comparable analyses ( 56 , 57 ). We acknowledge that associating DARs with the closest transcriptional unit may to some extent bias the analysis, since genes can be regulated by distal regulatory elements ( 24 , 28 , 58 ), but to date there are no methods to directly associate changes in chromatin accessibility and changes in gene expression. Analysis of GO categories of genes associated with low-Pi–induced DARs did not show a clear correlation with PSR genes, confirming that nutritional stress activates a very small set of stress-specific genes and a larger set of general stress-related genes ( 59 ).…”

Section: Discussionmentioning

confidence: 99%

“…Epigenomic approaches now allow the determination of chromatin alterations associated with developmental disorders and diseases in animals and humans (24)(25)(26)(27)(28). Numerous techniques that document genome-wide chromatin states have been developed to investigate the function of chromatin regulators (29)(30)(31)(32).…”

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confidence: 99%

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis

Barragán-Rosillo

Peralta‐Álvarez

Ojeda-Rivera³

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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As phosphorus is one of the most limiting nutrients in many natural and agricultural ecosystems, plants have evolved strategies that cope with its scarcity. Genetic approaches have facilitated the identification of several molecular elements that regulate the phosphate (Pi) starvation response (PSR) of plants, including the master regulator of the transcriptional response to phosphate starvation PHOSPHATE STARVATION RESPONSE1 (PHR1). However, the chromatin modifications underlying the plant transcriptional response to phosphate scarcity remain largely unknown. Here, we present a detailed analysis of changes in chromatin accessibility during phosphate starvation in Arabidopsis thaliana root cells. Root cells undergo a genome-wide remodeling of chromatin accessibility in response to Pi starvation that is often associated with changes in the transcription of neighboring genes. Analysis of chromatin accessibility in the phr1 phl2 double mutant revealed that the transcription factors PHR1 and PHL2 play a key role in remodeling chromatin accessibility in response to Pi limitation. We also discovered that PHR1 and PHL2 play an important role in determining chromatin accessibility and the associated transcription of many genes under optimal Pi conditions, including genes involved in the PSR. We propose that a set of transcription factors directly activated by PHR1 in Pi-starved root cells trigger a second wave of epigenetic changes required for the transcriptional activation of the complete set of low-Pi–responsive genes.

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“…Assessing whether or not CTCF-mediated domains exist in Drosophila is important for understanding their relevance for genome function. Recent studies have perturbed specific CDs in flies to address their biological roles without knowing whether they are CTCF-mediated or compartmental [22][23][24] , yet different types of CDs may have different functions.…”

mentioning

confidence: 99%

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

et al. 2021

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Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution.

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In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

Cited by 40 publications

References 74 publications

Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries

Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

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