Limits...
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 novel CAGE promoters.(A) Distribution of total and differentially used unannotated CAGE promoters overlapping with epigenetically defined promoters and enhancers. (B,C) Gene ontology analysis of unannotated CAGE promoters. CAGE promoters (EPP- specific and down-regulated upon HSPC commitment), which were not assigned to any known gene or transcript, were analyzed using GREAT. (D) Top enriched TF motifs within annotated and unannotated CAGE promoters. Cell-specific annotated and unannotated CAGE promoters were enriched for similar cell-specific and ubiquitous transcription factor motifs. TF motif analysis was performed using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4837375&req=5

f3: Analysis of novel CAGE promoters.(A) Distribution of total and differentially used unannotated CAGE promoters overlapping with epigenetically defined promoters and enhancers. (B,C) Gene ontology analysis of unannotated CAGE promoters. CAGE promoters (EPP- specific and down-regulated upon HSPC commitment), which were not assigned to any known gene or transcript, were analyzed using GREAT. (D) Top enriched TF motifs within annotated and unannotated CAGE promoters. Cell-specific annotated and unannotated CAGE promoters were enriched for similar cell-specific and ubiquitous transcription factor motifs. TF motif analysis was performed using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated.

Mentions: Next, we analyzed CAGE promoters not assigned to known genes. Around 22% of these unannotated promoters harbored an epigenetic enhancer signature, a frequency that increased up to 45% for DU promoters (Fig. 3A), suggesting that they may represent regulatory regions associated with enhancer-derived RNA acting in cis on adjacent target genes. Regions surrounding EPP-specific unannotated promoters were associated with erythroid phenotypes (Fig. 3B), while those surrounding promoters down-regulated upon erythroid and myeloid commitment were associated with leukocyte phenotypes and RNA processing/macromolecular complex assembly, respectively (Fig. 3C). Finally, both annotated and unannotated promoters were enriched for the same ubiquitous and cell-specific TF motifs (Fig. 3D), indicating that novel promoters are in fact regulated by the same TFs binding to annotated promoters.


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 novel CAGE promoters.(A) Distribution of total and differentially used unannotated CAGE promoters overlapping with epigenetically defined promoters and enhancers. (B,C) Gene ontology analysis of unannotated CAGE promoters. CAGE promoters (EPP- specific and down-regulated upon HSPC commitment), which were not assigned to any known gene or transcript, were analyzed using GREAT. (D) Top enriched TF motifs within annotated and unannotated CAGE promoters. Cell-specific annotated and unannotated CAGE promoters were enriched for similar cell-specific and ubiquitous transcription factor motifs. TF motif analysis was performed using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Analysis of novel CAGE promoters.(A) Distribution of total and differentially used unannotated CAGE promoters overlapping with epigenetically defined promoters and enhancers. (B,C) Gene ontology analysis of unannotated CAGE promoters. CAGE promoters (EPP- specific and down-regulated upon HSPC commitment), which were not assigned to any known gene or transcript, were analyzed using GREAT. (D) Top enriched TF motifs within annotated and unannotated CAGE promoters. Cell-specific annotated and unannotated CAGE promoters were enriched for similar cell-specific and ubiquitous transcription factor motifs. TF motif analysis was performed using HOMER. The frequency of target (background) sequences enriched in TF motifs and p-values are indicated.
Mentions: Next, we analyzed CAGE promoters not assigned to known genes. Around 22% of these unannotated promoters harbored an epigenetic enhancer signature, a frequency that increased up to 45% for DU promoters (Fig. 3A), suggesting that they may represent regulatory regions associated with enhancer-derived RNA acting in cis on adjacent target genes. Regions surrounding EPP-specific unannotated promoters were associated with erythroid phenotypes (Fig. 3B), while those surrounding promoters down-regulated upon erythroid and myeloid commitment were associated with leukocyte phenotypes and RNA processing/macromolecular complex assembly, respectively (Fig. 3C). Finally, both annotated and unannotated promoters were enriched for the same ubiquitous and cell-specific TF motifs (Fig. 3D), indicating that novel promoters are in fact regulated by the same TFs binding to annotated promoters.

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