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Article ; Online: Keep Them Close: PRC2 Poises Enhancer-Promoter Interactions at Anterior Neuronal Genes.

Caglio, Giulia / Torlai Triglia, Elena / Pombo, Ana

2017 Volume 20, Issue 5, Page(s) 573–575

Abstract: Enhancers exist in different epigenetic states: active, primed, or poised. However, it is not yet understood how the different enhancer states influence gene activation. In this issue of Cell Stem Cell, Cruz-Molina et al. (2017) unravel how poised ... ...

Abstract	Enhancers exist in different epigenetic states: active, primed, or poised. However, it is not yet understood how the different enhancer states influence gene activation. In this issue of Cell Stem Cell, Cruz-Molina et al. (2017) unravel how poised enhancers activate anterior neural genes and the role of Polycomb proteins in enhancer-promoter contacts.
Language	English
Publishing date	2017-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2375354-7
ISSN	1875-9777 ; 1934-5909
ISSN (online)	1875-9777
ISSN	1934-5909
DOI	10.1016/j.stem.2017.04.006
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Article ; Online: A Finer Print Than TADs: PRC1-Mediated Domains.

Torlai Triglia, Elena / Rito, Tiago / Pombo, Ana

Molecular cell

2017 Volume 65, Issue 3, Page(s) 373–375

Abstract: Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon ... ...

Abstract	Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts.
MeSH term(s)	Animals ; Cell Differentiation ; Chromatin/metabolism ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Epigenesis, Genetic ; Humans ; Polycomb Repressive Complex 1/chemistry ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 1/metabolism ; Protein Domains
Chemical Substances	Chromatin ; Polycomb Repressive Complex 1 (EC 2.3.2.27)
Language	English
Publishing date	2017-02-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2017.01.028
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Article: A Finer Print Than TADs: PRC1-Mediated Domains

Torlai Triglia, Elena / Ana Pombo / Tiago Rito

Molecular cell. 2017 Feb. 02, v. 65, no. 3

2017

Abstract	Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts.
Keywords	chromatin ; epigenetics ; stem cells
Language	English
Dates of publication	2017-0202
Size	p. 373-375.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2017.01.028
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Article ; Online: R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes.

Skourti-Stathaki, Konstantina / Torlai Triglia, Elena / Warburton, Marie / Voigt, Philipp / Bird, Adrian / Pombo, Ana

Molecular cell

2019 Volume 73, Issue 5, Page(s) 930–945.e4

Abstract: R-loops are three-stranded nucleic acid structures that form during transcription, especially over unmethylated CpG-rich promoters of active genes. In mouse embryonic stem cells (mESCs), CpG-rich developmental regulator genes are repressed by the ... ...

Abstract	R-loops are three-stranded nucleic acid structures that form during transcription, especially over unmethylated CpG-rich promoters of active genes. In mouse embryonic stem cells (mESCs), CpG-rich developmental regulator genes are repressed by the Polycomb complexes PRC1 and PRC2. Here, we show that R-loops form at a subset of Polycomb target genes, and we investigate their contribution to Polycomb repression. At R-loop-positive genes, R-loop removal leads to decreased PRC1 and PRC2 recruitment and Pol II activation into a productive elongation state, accompanied by gene derepression at nascent and processed transcript levels. Stable removal of PRC2 derepresses R-loop-negative genes, as expected, but does not affect R-loops, PRC1 recruitment, or transcriptional repression of R-loop-positive genes. Our results highlight that Polycomb repression does not occur via one mechanism but consists of different layers of repression, some of which are gene specific. We uncover that one such mechanism is mediated by an interplay between R-loops and RING1B recruitment.
MeSH term(s)	Animals ; Binding Sites ; Cell Line ; CpG Islands ; Down-Regulation ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Gene Expression Regulation, Developmental ; Mice ; Mouse Embryonic Stem Cells/metabolism ; Mouse Embryonic Stem Cells/physiology ; Nucleic Acid Conformation ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 1/metabolism ; Promoter Regions, Genetic ; Protein Binding ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Structure-Activity Relationship ; Transcription, Genetic ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; Ezh2 protein, mouse (EC 2.1.1.43) ; Polycomb Repressive Complex 1 (EC 2.3.2.27) ; Rnf2 protein, mouse (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2019-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2018.12.016
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Article: R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes

Skourti-Stathaki, Konstantina / Torlai Triglia, Elena / Warburton, Marie / Voigt, Philipp / Bird, Adrian / Pombo, Ana

Molecular cell. 2019 Mar. 07, v. 73, no. 5

2019

Abstract	R-loops are three-stranded nucleic acid structures that form during transcription, especially over unmethylated CpG-rich promoters of active genes. In mouse embryonic stem cells (mESCs), CpG-rich developmental regulator genes are repressed by the Polycomb complexes PRC1 and PRC2. Here, we show that R-loops form at a subset of Polycomb target genes, and we investigate their contribution to Polycomb repression. At R-loop-positive genes, R-loop removal leads to decreased PRC1 and PRC2 recruitment and Pol II activation into a productive elongation state, accompanied by gene derepression at nascent and processed transcript levels. Stable removal of PRC2 derepresses R-loop-negative genes, as expected, but does not affect R-loops, PRC1 recruitment, or transcriptional repression of R-loop-positive genes. Our results highlight that Polycomb repression does not occur via one mechanism but consists of different layers of repression, some of which are gene specific. We uncover that one such mechanism is mediated by an interplay between R-loops and RING1B recruitment.
Keywords	embryonic stem cells ; messenger RNA ; mice ; regulator genes ; transcription (genetics)
Language	English
Dates of publication	2019-0307
Size	p. 930-945.e4.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2018.12.016
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Article ; Online: Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment.

Science (New York, N.Y.)

2022 Volume 376, Issue 6592, Page(s) eabi8175

Abstract: Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly ... ...

Abstract	Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.
MeSH term(s)	Humans ; Melanocytes/metabolism ; Melanoma/pathology ; Mutation ; Skin Neoplasms/genetics ; Skin Neoplasms/pathology ; Tumor Microenvironment/genetics
Language	English
Publishing date	2022-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abi8175
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Article ; Online: B-cell-specific checkpoint molecules that regulate anti-tumour immunity.

Bod, Lloyd / Kye, Yoon-Chul / Shi, Jingwen / Torlai Triglia, Elena / Schnell, Alexandra / Fessler, Johannes / Ostrowski, Stephen M / Von-Franque, Max Y / Kuchroo, Juhi R / Barilla, Rocky M / Zaghouani, Sarah / Christian, Elena / Delorey, Toni Marie / Mohib, Kanishka / Xiao, Sheng / Slingerland, Nadine / Giuliano, Christopher J / Ashenberg, Orr / Li, Zhaorong /

Rothstein, David M / Fisher, David E / Rozenblatt-Rosen, Orit / Sharpe, Arlene H / Quintana, Francisco J / Apetoh, Lionel / Regev, Aviv / Kuchroo, Vijay K

Nature

2023 Volume 619, Issue 7969, Page(s) 348–356

Abstract: The role of B cells in anti-tumour immunity is still debated and, accordingly, immunotherapies have focused on targeting T and natural killer cells to inhibit tumour ... ...

Abstract	The role of B cells in anti-tumour immunity is still debated and, accordingly, immunotherapies have focused on targeting T and natural killer cells to inhibit tumour growth
MeSH term(s)	Animals ; Mice ; B-Lymphocytes/cytology ; B-Lymphocytes/immunology ; B-Lymphocytes/metabolism ; Lymphocyte Activation ; Melanoma/immunology ; Melanoma/pathology ; Melanoma/prevention & control ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology ; Flow Cytometry ; Melanoma, Experimental/immunology ; Melanoma, Experimental/pathology ; Lymph Nodes/cytology ; Lymph Nodes/immunology ; Antigen Presentation ; Receptors, Antigen, B-Cell/genetics ; Single-Cell Gene Expression Analysis ; Tumor Burden ; Interferon Type I
Chemical Substances	Havcr1 protein, mouse ; Lag3 protein, mouse ; T cell Ig and ITIM domain protein, mouse ; Receptors, Antigen, B-Cell ; Interferon Type I
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06231-0
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Article ; Online: Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

Dias, João D / Rito, Tiago / Torlai Triglia, Elena / Kukalev, Alexander / Ferrai, Carmelo / Chotalia, Mita / Brookes, Emily / Kimura, Hiroshi / Pombo, Ana

eLife

2015 Volume 4

Abstract: Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the ... ...

Abstract	Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels.
MeSH term(s)	Animals ; Consensus ; Gene Expression Regulation ; Lysine/metabolism ; Methylation ; Mice ; NIH 3T3 Cells ; Phosphorylation ; Protein Processing, Post-Translational ; RNA Polymerase II/metabolism ; Serine/metabolism ; Transcription, Genetic
Chemical Substances	Serine (452VLY9402) ; RNA Polymerase II (EC 2.7.7.-) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2015-12-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.11215
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Article ; Online: Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Kar, Gozde / Kim, Jong Kyoung / Kolodziejczyk, Aleksandra A / Natarajan, Kedar Nath / Torlai Triglia, Elena / Mifsud, Borbala / Elderkin, Sarah / Marioni, John C / Pombo, Ana / Teichmann, Sarah A

Nature communications

2017 Volume 8, Issue 1, Page(s) 36

Abstract: Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive ... ...

Abstract	Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive complex is to dampen expression of these PRC-active genes. However, it is unclear how this flipping between chromatin states alters the kinetics of transcription. Here, we integrate histone modifications and RNAPII states derived from bulk ChIP-seq data with single-cell RNA-sequencing data. We find that Polycomb repressive complex-active genes have greater cell-to-cell variation in expression than active genes, and these results are validated by knockout experiments. We also show that PRC-active genes are clustered on chromosomes in both two and three dimensions, and interactions with active enhancers promote a stabilization of gene expression noise. These findings provide new insights into how chromatin regulation modulates stochastic gene expression and transcriptional bursting, with implications for regulation of pluripotency and development.Polycomb repressive complexes modify histones but it is unclear how changes in chromatin states alter kinetics of transcription. Here, the authors use single-cell RNAseq and ChIPseq to find that actively transcribed genes with Polycomb marks have greater cell-to-cell variation in expression.
MeSH term(s)	Animals ; Base Sequence ; Cell Line, Tumor ; Gene Expression Regulation/physiology ; Genetic Markers ; Mice ; Mice, Knockout ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 1/metabolism ; Polycomb-Group Proteins/genetics ; Polycomb-Group Proteins/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription, Genetic ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Genetic Markers ; Polycomb-Group Proteins ; RNA, Messenger ; Polycomb Repressive Complex 1 (EC 2.3.2.27) ; Ring1 protein, mouse (EC 2.3.2.27) ; Rnf2 protein, mouse (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2017-06-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-017-00052-2
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Article ; Online: Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.

Barbieri, Mariano / Xie, Sheila Q / Torlai Triglia, Elena / Chiariello, Andrea M / Bianco, Simona / de Santiago, Inês / Branco, Miguel R / Rueda, David / Nicodemi, Mario / Pombo, Ana

Nature structural & molecular biology

2017 Volume 24, Issue 6, Page(s) 515–524

Abstract: Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation ... ...

Abstract	Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF. Single-cell imaging of the locus folding was performed to test model predictions. While CTCF occupancy alone fails to predict the in vivo folding at genomic length scale of 10 kb, we found that homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber fully explain the HoxB folding patterns imaged in single cells. We identify state-dependent promoter interactions as major drivers of chromatin folding in gene-dense regions.
MeSH term(s)	Animals ; Chromatin/metabolism ; Computer Simulation ; DNA/chemistry ; DNA/metabolism ; Embryonic Stem Cells/physiology ; Fluorescent Antibody Technique ; Genetic Loci ; In Situ Hybridization, Fluorescence ; Mice ; Microscopy, Confocal ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Binding ; Single-Cell Analysis ; Transcription Factors/metabolism
Chemical Substances	Chromatin ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2017-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.3402
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