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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 epigenetically defined regulatory regions.(A) Dynamics of promoter and enhancer chromatin signatures upon HSPC commitment. Venn diagrams show the overlap of strong (H3K27ac+) and weak/inactive (H3K27ac−) promoters (H3K4me3 > H3K4me1) and enhancers (H3K4me1 > H3K4me3) identified in HSPC, EPP and MPP. The fraction of non-overlapping HSPC, EPP and MPP regulatory regions is indicated. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. (B) Top enriched TF motifs in epigenetically defined regulatory regions. Putative TFBS in cell-specific promoters and enhancers were identified using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated. (C) Expression levels of CAGE promoters surrounding HSPC-, EPP- and MPP-specific enhancers (±5 kb interval) in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, expression levels of total HSPC, EPP and MPP CAGE promoters were analyzed. A t-test was used to determine significant differences in the expression values associated to CAGE promoters in the different cell types (*P < 0.05). The median expression levels of genes close to weak/inactive enhancers was similar among the different cell populations (data not shown). Comparable results were obtained by analyzing the expression levels of CAGE promoters in a 100-Kb window (data not shown).
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f4: Analysis of epigenetically defined regulatory regions.(A) Dynamics of promoter and enhancer chromatin signatures upon HSPC commitment. Venn diagrams show the overlap of strong (H3K27ac+) and weak/inactive (H3K27ac−) promoters (H3K4me3 > H3K4me1) and enhancers (H3K4me1 > H3K4me3) identified in HSPC, EPP and MPP. The fraction of non-overlapping HSPC, EPP and MPP regulatory regions is indicated. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. (B) Top enriched TF motifs in epigenetically defined regulatory regions. Putative TFBS in cell-specific promoters and enhancers were identified using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated. (C) Expression levels of CAGE promoters surrounding HSPC-, EPP- and MPP-specific enhancers (±5 kb interval) in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, expression levels of total HSPC, EPP and MPP CAGE promoters were analyzed. A t-test was used to determine significant differences in the expression values associated to CAGE promoters in the different cell types (*P < 0.05). The median expression levels of genes close to weak/inactive enhancers was similar among the different cell populations (data not shown). Comparable results were obtained by analyzing the expression levels of CAGE promoters in a 100-Kb window (data not shown).

Mentions: Next, we evaluated the dynamics of ChIP-defined regulatory elements upon HSPC commitment. The vast majority of strong EPP and MPP promoter regions (92% and 93%, respectively), and a low proportion of the weak/inactive ones, were shared with HSPC (Fig. 4A). On the contrary, a much lower proportion of both strong and weak enhancers were shared upon lineage commitment while the majority was cell-specific (Fig. 4A), suggesting that enhancers play a major role in HSPC commitment. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. ChIP-defined cell-specific regulatory regions were modestly enriched in binding motifs of general and hematopoietic TFs, the majority of which were shared by the three populations (Fig. 4B).


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 epigenetically defined regulatory regions.(A) Dynamics of promoter and enhancer chromatin signatures upon HSPC commitment. Venn diagrams show the overlap of strong (H3K27ac+) and weak/inactive (H3K27ac−) promoters (H3K4me3 > H3K4me1) and enhancers (H3K4me1 > H3K4me3) identified in HSPC, EPP and MPP. The fraction of non-overlapping HSPC, EPP and MPP regulatory regions is indicated. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. (B) Top enriched TF motifs in epigenetically defined regulatory regions. Putative TFBS in cell-specific promoters and enhancers were identified using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated. (C) Expression levels of CAGE promoters surrounding HSPC-, EPP- and MPP-specific enhancers (±5 kb interval) in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, expression levels of total HSPC, EPP and MPP CAGE promoters were analyzed. A t-test was used to determine significant differences in the expression values associated to CAGE promoters in the different cell types (*P < 0.05). The median expression levels of genes close to weak/inactive enhancers was similar among the different cell populations (data not shown). Comparable results were obtained by analyzing the expression levels of CAGE promoters in a 100-Kb window (data not shown).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4837375&req=5

f4: Analysis of epigenetically defined regulatory regions.(A) Dynamics of promoter and enhancer chromatin signatures upon HSPC commitment. Venn diagrams show the overlap of strong (H3K27ac+) and weak/inactive (H3K27ac−) promoters (H3K4me3 > H3K4me1) and enhancers (H3K4me1 > H3K4me3) identified in HSPC, EPP and MPP. The fraction of non-overlapping HSPC, EPP and MPP regulatory regions is indicated. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. (B) Top enriched TF motifs in epigenetically defined regulatory regions. Putative TFBS in cell-specific promoters and enhancers were identified using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated. (C) Expression levels of CAGE promoters surrounding HSPC-, EPP- and MPP-specific enhancers (±5 kb interval) in HSPC, EPP, MPP, embryonic stem cells (ES) and keratinocytes (KER). As control, expression levels of total HSPC, EPP and MPP CAGE promoters were analyzed. A t-test was used to determine significant differences in the expression values associated to CAGE promoters in the different cell types (*P < 0.05). The median expression levels of genes close to weak/inactive enhancers was similar among the different cell populations (data not shown). Comparable results were obtained by analyzing the expression levels of CAGE promoters in a 100-Kb window (data not shown).
Mentions: Next, we evaluated the dynamics of ChIP-defined regulatory elements upon HSPC commitment. The vast majority of strong EPP and MPP promoter regions (92% and 93%, respectively), and a low proportion of the weak/inactive ones, were shared with HSPC (Fig. 4A). On the contrary, a much lower proportion of both strong and weak enhancers were shared upon lineage commitment while the majority was cell-specific (Fig. 4A), suggesting that enhancers play a major role in HSPC commitment. Overall, we identified 7,107, 1,026 and 2,675 cell-specific promoters and 35,318, 19,465 and 43,120 cell-specific enhancers in HSPC, EPP and MPP, respectively. ChIP-defined cell-specific regulatory regions were modestly enriched in binding motifs of general and hematopoietic TFs, the majority of which were shared by the three populations (Fig. 4B).

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