Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-
<p>Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satell...
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2025
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| _version_ | 1849927626376871936 |
|---|---|
| author | Tine Struyve (22683295) |
| author2 | Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| author2_role | author author author author author author author author |
| author_facet | Tine Struyve (22683295) Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| author_role | author |
| dc.creator.none.fl_str_mv | Tine Struyve (22683295) Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| dc.date.none.fl_str_mv | 2025-11-25T18:40:41Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.ppat.1013702.g003 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Integration_site_features_of_proviruses_from_Acute_UD_Acute_UD_5_and_Chronic_UD_individuals_A_Pie_charts_displaying_proportions_of_IS_in_genic_regions_with_same_opposite_and_mixed_orientation_relative_to_the_host_gene_B_Pie_charts_displayin/30714919 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |
| dc.title.none.fl_str_mv | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_e895cba0f8e28d4a5ee34ecf711751d8 |
| identifier_str_mv | 10.1371/journal.ppat.1013702.g003 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30714919 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-Tine Struyve (22683295)Marion Pardons (6407921)Jozefien De Clercq (17737815)Liesbet Termote (22683298)Laurens Lambrechts (10532207)Ytse Noppe (22683301)Mathias Lichterfeld (57148)Sofie Rutsaert (10667718)Linos Vandekerckhove (105574)BiochemistryMedicineNeuroscienceBiotechnologyEvolutionary BiologyEcologyCancerInfectious DiseasesPlant BiologyVirologyComputational Biologyphorbol myristate acetateintegration selection mechanismsxlink "> persistencesmall reservoir sizestreatment initiation timingclonal expansion contributesart ), irrespectiveindividuals treated shortlyreservoir persistence earlyreservoir persistenceclonal expansionstarted treatmentpma ),art initiationviral reservoirtreated individualsinducible reservoirindividuals treated1 reservoirsuggesting postproviruses integratedprogressively enrichedone yearmajor barrierlongitudinal analysisheterochromatin regionsfive yearschronic cohortscell compartmentantiretroviral therapyalready detected<p>Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-</p>2025-11-25T18:40:41ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.ppat.1013702.g003https://figshare.com/articles/figure/Integration_site_features_of_proviruses_from_Acute_UD_Acute_UD_5_and_Chronic_UD_individuals_A_Pie_charts_displaying_proportions_of_IS_in_genic_regions_with_same_opposite_and_mixed_orientation_relative_to_the_host_gene_B_Pie_charts_displayin/30714919CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307149192025-11-25T18:40:41Z |
| spellingShingle | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- Tine Struyve (22683295) Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |
| status_str | publishedVersion |
| title | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| title_full | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| title_fullStr | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| title_full_unstemmed | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| title_short | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| title_sort | Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B- |
| topic | Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |