sofia battaglia - Academia.edu (original) (raw)

Papers by sofia battaglia

Research paper thumbnail of Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Research paper thumbnail of Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies

Cell Reports, 2020

Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) t... more Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) to embryoid bodies (EBs), a heterogeneous mixture of three germ layers. Here, we combine single-cell transcriptomics and genetic recording to characterize EB differentiation. We map transcriptional states along a time course and model cell fate trajectories and branchpoints as cells progress to distinct germ layers. To validate this inferential model, we propose an innovative inducible genetic recording technique that leverages recombination to generate cell-specific, timestamp barcodes in a narrow temporal window. We validate trajectory architecture and key branchpoints, including early specification of a primordial germ cell (PGC)-like lineage from preimplantation epiblast-like cells. We further identify a temporally defined role of DNA methylation in this PGC-epiblast decision. Our study provides a high-resolution lineage map for an organoid model of embryogenesis, insights into epigenetic determinants of fate specification, and a strategy for lineage mapping of rapid differentiation processes.

Research paper thumbnail of The APT complex is involved in non-coding RNA transcription and is distinct from CPF

Nucleic Acids Research, 2018

The 3-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, ... more The 3-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes, but how these are coordinated remains poorly understood. Several subunits of CPF, including two protein phosphatases, are also found in the related 'associated with Pta1' (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1/APT has distinct, but possibly overlapping, functions from those of CPF. Syc1/APT plays a more important role in sn/snoRNA production whereas CPF processes the 3-ends of proteincoding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.

Research paper thumbnail of Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

Cell, 2019

Highlights d Technology for high-throughput single-cell RNA sequencing and genotyping d Variable ... more Highlights d Technology for high-throughput single-cell RNA sequencing and genotyping d Variable cell-type composition of AML correlates to genetics and outcome d Primitive AML cells aberrantly co-express stemness and myeloid priming genes d Differentiated AML cells express immunomodulatory factors and suppress T cells

Research paper thumbnail of Author response

Research paper thumbnail of Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Research paper thumbnail of RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

eLife, 2017

For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (... more For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction. Set1 recruitment to genes in vivo depends on its RNA recognition motifs (RRMs). These results strongly suggest that nascent RNA contributes to EF recruitment to transcribing Pol II. We propose that EF-RNA interactions facilitate assembly of the elongation complex on transcribed genes when RNA emerges from Pol II, and that loss of EF-RNA interactions upon RNA cleavage at the polyadenylation site triggers disassembly of the elongation complex.

Research paper thumbnail of Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Research paper thumbnail of Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies

Cell Reports, 2020

Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) t... more Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) to embryoid bodies (EBs), a heterogeneous mixture of three germ layers. Here, we combine single-cell transcriptomics and genetic recording to characterize EB differentiation. We map transcriptional states along a time course and model cell fate trajectories and branchpoints as cells progress to distinct germ layers. To validate this inferential model, we propose an innovative inducible genetic recording technique that leverages recombination to generate cell-specific, timestamp barcodes in a narrow temporal window. We validate trajectory architecture and key branchpoints, including early specification of a primordial germ cell (PGC)-like lineage from preimplantation epiblast-like cells. We further identify a temporally defined role of DNA methylation in this PGC-epiblast decision. Our study provides a high-resolution lineage map for an organoid model of embryogenesis, insights into epigenetic determinants of fate specification, and a strategy for lineage mapping of rapid differentiation processes.

Research paper thumbnail of The APT complex is involved in non-coding RNA transcription and is distinct from CPF

Nucleic Acids Research, 2018

The 3-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, ... more The 3-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes, but how these are coordinated remains poorly understood. Several subunits of CPF, including two protein phosphatases, are also found in the related 'associated with Pta1' (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1/APT has distinct, but possibly overlapping, functions from those of CPF. Syc1/APT plays a more important role in sn/snoRNA production whereas CPF processes the 3-ends of proteincoding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.

Research paper thumbnail of Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

Cell, 2019

Highlights d Technology for high-throughput single-cell RNA sequencing and genotyping d Variable ... more Highlights d Technology for high-throughput single-cell RNA sequencing and genotyping d Variable cell-type composition of AML correlates to genetics and outcome d Primitive AML cells aberrantly co-express stemness and myeloid priming genes d Differentiated AML cells express immunomodulatory factors and suppress T cells

Research paper thumbnail of Author response

Research paper thumbnail of Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Research paper thumbnail of RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

eLife, 2017

For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (... more For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction. Set1 recruitment to genes in vivo depends on its RNA recognition motifs (RRMs). These results strongly suggest that nascent RNA contributes to EF recruitment to transcribing Pol II. We propose that EF-RNA interactions facilitate assembly of the elongation complex on transcribed genes when RNA emerges from Pol II, and that loss of EF-RNA interactions upon RNA cleavage at the polyadenylation site triggers disassembly of the elongation complex.