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Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment.

Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A - Sci Rep (2016)

Bottom Line: A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment.Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers.Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

ABSTRACT
Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.

No MeSH data available.


Related in: MedlinePlus

Analysis of super-enhancers.(A) The plots represents the distribution of H3K27ac ChIP-seq signal (in units of reads per million, on y-axis) across all the H3K27ac-containing enhancers (x-axis). Enhancers were ranked by increasing H3K27ac ChIP-seq signal. H3K27ac is not evenly distributed across the enhancer regions, with a subset of enhancers containing exceptionally high amounts of H3K27ac (SEs), as defined by surpassing the inflection point. (B) Differential SE usage upon erythroid and myeloid commitment. Venn diagrams showed the fraction of non-overlapping HSPC, EPP and MPP SEs. Overall, we identified 415 HSPC-specific, 245 EPP-specific and 337 MPP-specific SEs. (C) Expression levels of CAGE promoters driving the expression of genes targeted by cell-specific SE were analyzed in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, we analyzed the expression levels of total HSPC, EPP and MPP CAGE promoters. Statistical significance was calculated as described in Fig. 4C legend (*P < 0.05; **P < 0.01; ***P < 0.001). (D) GREAT analysis of cell-specific SEs.
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f5: Analysis of super-enhancers.(A) The plots represents the distribution of H3K27ac ChIP-seq signal (in units of reads per million, on y-axis) across all the H3K27ac-containing enhancers (x-axis). Enhancers were ranked by increasing H3K27ac ChIP-seq signal. H3K27ac is not evenly distributed across the enhancer regions, with a subset of enhancers containing exceptionally high amounts of H3K27ac (SEs), as defined by surpassing the inflection point. (B) Differential SE usage upon erythroid and myeloid commitment. Venn diagrams showed the fraction of non-overlapping HSPC, EPP and MPP SEs. Overall, we identified 415 HSPC-specific, 245 EPP-specific and 337 MPP-specific SEs. (C) Expression levels of CAGE promoters driving the expression of genes targeted by cell-specific SE were analyzed in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, we analyzed the expression levels of total HSPC, EPP and MPP CAGE promoters. Statistical significance was calculated as described in Fig. 4C legend (*P < 0.05; **P < 0.01; ***P < 0.001). (D) GREAT analysis of cell-specific SEs.

Mentions: Super-enhancers (SEs) have been described as clusters of enhancers, involved in the specification of cell identity8. By using H3K27ac ChIP-seq data, we defined 755 SEs in HSPC, 513 in EPP and 600 in MPP (Supplementary Table 6 and Fig. 5A), all actively transcribed as previously described9. The majority of SEs were cell-specific (Fig. 5B) and showed a moderate enrichment in common and cell-specific TF motifs (Supplementary Fig. 9). Expression of CAGE promoters close to EPP- and MPP- specific SEs tended to be higher than the average expression of the total CAGE promoter population in the same cells, or the expression of the same promoters in other cell types (Fig. 5C). HSPC-specific SEs were associated with genes involved in metabolic processes, RNA processing, and T cell phenotypes, while EPP- and MPP-specific SEs were associated to erythroid and myeloid phenotypes, respectively (Fig. 5D).


Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment.

Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A - Sci Rep (2016)

Analysis of super-enhancers.(A) The plots represents the distribution of H3K27ac ChIP-seq signal (in units of reads per million, on y-axis) across all the H3K27ac-containing enhancers (x-axis). Enhancers were ranked by increasing H3K27ac ChIP-seq signal. H3K27ac is not evenly distributed across the enhancer regions, with a subset of enhancers containing exceptionally high amounts of H3K27ac (SEs), as defined by surpassing the inflection point. (B) Differential SE usage upon erythroid and myeloid commitment. Venn diagrams showed the fraction of non-overlapping HSPC, EPP and MPP SEs. Overall, we identified 415 HSPC-specific, 245 EPP-specific and 337 MPP-specific SEs. (C) Expression levels of CAGE promoters driving the expression of genes targeted by cell-specific SE were analyzed in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, we analyzed the expression levels of total HSPC, EPP and MPP CAGE promoters. Statistical significance was calculated as described in Fig. 4C legend (*P < 0.05; **P < 0.01; ***P < 0.001). (D) GREAT analysis of cell-specific SEs.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4837375&req=5

f5: Analysis of super-enhancers.(A) The plots represents the distribution of H3K27ac ChIP-seq signal (in units of reads per million, on y-axis) across all the H3K27ac-containing enhancers (x-axis). Enhancers were ranked by increasing H3K27ac ChIP-seq signal. H3K27ac is not evenly distributed across the enhancer regions, with a subset of enhancers containing exceptionally high amounts of H3K27ac (SEs), as defined by surpassing the inflection point. (B) Differential SE usage upon erythroid and myeloid commitment. Venn diagrams showed the fraction of non-overlapping HSPC, EPP and MPP SEs. Overall, we identified 415 HSPC-specific, 245 EPP-specific and 337 MPP-specific SEs. (C) Expression levels of CAGE promoters driving the expression of genes targeted by cell-specific SE were analyzed in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, we analyzed the expression levels of total HSPC, EPP and MPP CAGE promoters. Statistical significance was calculated as described in Fig. 4C legend (*P < 0.05; **P < 0.01; ***P < 0.001). (D) GREAT analysis of cell-specific SEs.
Mentions: Super-enhancers (SEs) have been described as clusters of enhancers, involved in the specification of cell identity8. By using H3K27ac ChIP-seq data, we defined 755 SEs in HSPC, 513 in EPP and 600 in MPP (Supplementary Table 6 and Fig. 5A), all actively transcribed as previously described9. The majority of SEs were cell-specific (Fig. 5B) and showed a moderate enrichment in common and cell-specific TF motifs (Supplementary Fig. 9). Expression of CAGE promoters close to EPP- and MPP- specific SEs tended to be higher than the average expression of the total CAGE promoter population in the same cells, or the expression of the same promoters in other cell types (Fig. 5C). HSPC-specific SEs were associated with genes involved in metabolic processes, RNA processing, and T cell phenotypes, while EPP- and MPP-specific SEs were associated to erythroid and myeloid phenotypes, respectively (Fig. 5D).

Bottom Line: A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment.Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers.Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

ABSTRACT
Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.

No MeSH data available.


Related in: MedlinePlus