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51 results for “TAD boundaries”
CTCF BINDING PATTERNS DEFINE TADS AND BOUNDARY ELEMENTS IN HUMAN AND MOUSE GENOMES
<p><em><strong>Msci thesis from Industrial Placement at Politecnico di Milano</strong></em></p> <p> </p> <p><strong>Abstract</strong></p> <p>In eukaryotes, the genome is highly packaged inside the nucleus. This hierarchical structure requires complex compartmentation and organization. Topologically associating domains (TADs) serve as architectural units in the 3D genome, functioning to regulate and constrain gene interaction. TAD boundaries are enriched in the CCCTC-binding factor (CTCF). Due to the asymmetric nature of the CTCF motif, it exhibits differing orientations based on the strand it is localized. Motif orientation is crucial for loop formation, which is facilitated in a convergent orientation. While the relationship between TADs and CTCF motif patterns has been described in humans, the model remained to be corroborated in other mammals. </p> <p>We conducted a comparative analysis by applying the research conducted in humans to the mouse genome. By integrating ChIP-seq data, we examined the CTCF sites based on ChIP-seq peak consolidation, signal value, and motif p-value. This analysis aimed to comprehend the binding profile of CTCF and elucidate its complexity in terms of binding strength and cross-tissue conservation. Mouse genome CTCF motifs were categorized into cluster patterns based on their relative orientation. Following this classification, the distribution of each pattern was studied using ChIP-seq-related descriptors. We then built a TAD boundary collection based on the insulation score. Boundary consolidation and length, insulation score, and CTCF number were used to reconcile CTCF to TAD boundary function. The cluster patterns were then mapped to TAD and TAD boundaries to elucidate their structure based on the spatial arrangement of CTCF.</p> <p>The distribution of ChIP-seq-validated CTCF sites within TAD boundaries revealed a well-defined structure, characterized by an abundance of the divergent pattern. Boundaries with the highest insulation scores exhibited both a high consolidation and CTCF enrichment. This set of boundaries was used to study TAD structure. An increment of the convergent pattern was observed inside TADs. The individual CTCF sites on the interior of the TAD were further organized into left and right sections, corresponding to an opposing directional arrangement to TAD boundaries. Significantly, the ChIP-seq data contained many unannotated peaks and non-signal motifs. These were associated with a high motif p-value, low ChIP-seq signal, low consolidation, and a less structured arrangement of CTCF clustering. Moreover, non-signal motifs were underrepresented within TAD boundaries and displayed a disorderly distribution.</p> <p>The human model of CTCF-dependent TAD structure was confirmed in mice. The model suggested the inherent alternation between convergent and divergent patterns, with these CTCF sites conferring characteristic properties upon TADs and their boundaries. These traits encompass the change of preferential genomic interaction and boundary insulation capability. Thus, the orientation-based clustering of CTCF sites was further validated as a good method to define TADs in a precise organized manner.</p>
A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]
GEO Series GSE101715. Mus musculus. 6 samples. Type: Other; Third-party reanalysis.
The essential role of CTCF binding site at TAD boundaries in modulating Ifng locus chromatin interactions and transcriptional regulation [RNA-seq]
GEO Series GSE300740. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [Hi-C]
GEO Series GSE245527. Solanum lycopersicum. 5 samples. Type: Other.
Invariant TAD boundaries constrain cell type-specific looping interactions between promoters and distal elements around the CFTR locus.
GEO Series GSE75634. Homo sapiens. 10 samples. Type: Other.
Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties
GEO Series GSE263270. Drosophila melanogaster. 11 samples. Type: Other.
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_mESC]
GEO Series GSE104814. Mus musculus. 4 samples. Type: Other.
A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes
GEO Series GSE101717. Mus musculus. 91 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Induction of a chromatin boundary in vivo upon insertion of a TAD border (Hi-C)
GEO Series GSE166578. Mus musculus. 2 samples. Type: Other.
Deletion of an evolutionary conserved TAD boundary leads to changes in gene expression, histology and function in mouse testis.
GEO Series GSE242235. Mus musculus. 27 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Induction of a chromatin boundary in vivo upon insertion of a TAD border (ChIP-Seq)
GEO Series GSE166574. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
GEO Series GSE197926. Macaca mulatta; Homo sapiens; Mus musculus; Mus pahari; Hylobates moloch; Mus caroli; Rattus norvegicus; Nomascus leucogenys. 87 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.
GEO Series GSE116862. Callithrix jacchus; Pan paniscus; Pan troglodytes; Homo sapiens. 115 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Induction of a chromatin boundary in vivo upon insertion of a TAD border (MinION-nCATS)
GEO Series GSE166583. Mus musculus. 1 samples. Type: Other.
Induction of a chromatin boundary in vivo upon insertion of a TAD border
GEO Series GSE166584. Mus musculus. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [RNA-Seq, HiC_C2C12, ChIP-Seq]
GEO Series GSE104427. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing.
A conserved noncoding locus modulates random monoallelic Xist expression across a TAD boundary
GEO Series GSE124596. Mus musculus. 56 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [RNA-seq]
GEO Series GSE245528. Solanum lycopersicum. 6 samples. Type: Expression profiling by high throughput sequencing.
TAD boundary deletion causes PITX2-related cardiac electrical and structural defects
GEO Series GSE242698. Mus musculus. 29 samples. Type: Expression profiling by high throughput sequencing.
KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-Seq]
GEO Series GSE264430. Solanum lycopersicum. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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