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The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites

ABSTRACT: The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites

PROVIDER: PRJNA667735 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12781981_1.fastq.gz	Fastqsanger.gz
	SRR12781981_2.fastq.gz	Fastqsanger.gz
	SRR12781982_1.fastq.gz	Fastqsanger.gz
	SRR12781982_2.fastq.gz	Fastqsanger.gz
	SRR12781983_1.fastq.gz	Fastqsanger.gz

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The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites

Project description:We propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and the role is beyond typical enhancer activity.

2021-06-07 | GSE159130 | GEO

Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ATAC-seq]

Project description:Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.

2022-06-01 | GSE153207 | GEO

Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ChIP-seq]

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Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes of local and large-scale chromatin spatial structure

Project description:We have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. We found that, similarly to mammalian genome, the chicken genome is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation.

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Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells

Project description:Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells

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Microvirga sp. HS2

Project description:Microvirga sp. HS2 Genome sequencing

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Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [RNA-seq]

Project description:Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [RNA-seq]

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Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ChIP-seq]

Project description:Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ChIP-seq]