Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression

AbstractCells regulate transcription by coordinating the activities of multiple histone modifying complexes. We recently identified the yeast histone H4 methyltransferase Set5 and discovered functional overlap with the histone H3 methyltransferase Set1 in gene expression. Specifically, using next-generation RNA sequencing (RNA-Seq), we found that Set5 and Set1 function synergistically to regulate specific transcriptional programs at subtelomeres and transposable elements. Here we provide a comprehensive description of the methodology and analysis tools corresponding to the data deposited in NCBI's Gene Expression Omnibus (GEO) under the accession number GSE52086. This data complements the experimental methods described in Mas Martín G et al. (2014) and provides the means to explore the cooperative functions of histone H3 and H4 methyltransferases in the regulation of transcription. Furthermore, a fully annotated R code is included to enable researchers to use the following computational tools: comparison of significant differential expression (SDE) profiles; gene ontology enrichment of SDE; and enrichment of SDE relative to chromosomal features, such as centromeres, telomeres, and transposable elements. Overall, we present a bioinformatics platform that can be generally implemented for similar analyses with different datasets and in different organisms

Resultats primera fase de l’estudi ENE-COVID a Catalunya

Coronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiologia; AnticossosCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiologia; AnticuerposCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiology; AntibodiesENE-COVID és un ampli estudi longitudinal sero-epidemiològic de base poblacional, que té com a objectiu estimar la prevalença d’infecció per SARS-CoV-2 a l’Estat espanyol mitjançant la determinació d’anticossos enfront del virus, així com avaluar-ne l’evolució temporal. Aquest estudi ha estat coordinat pel Ministeri de Sanitat en col·laboració amb l’Institut de Salut Carlos III, l’Institut Nacional d’Estadística i els departaments de Salut Públicai serveis de salut de totes lescomunitats autònomes i de les ciutats autònomes de Ceuta i Melilla. La informació recollida s’ha analitzat en l’àmbit de les comunitats autònomes, províncies, grups d’edat i sexes. S’ha seleccionat a l’atzar un nombre de llars de cada província perquè sigui representatiu de la població d’Espanya. Als participants se’ls fa una enquesta, un test ràpid d’anticossos mitjançant punxada al dit i una extracció de sang venosa per conèixer la presència d’anticossos d’una forma més precisa. L’estudi es va dur a terme en tres rondes durant els mesos d’abril a juny de 2020 (la primera, del 27 d’abril a l’11 de maig; la segona, del 18 de maig a l’1 de juny, i la tercera, del 8 de juny al 22 de juny)

Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response

The YEATS domain, found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation. Here, we show that the YEATS domain of Taf14, a member of key transcriptional and chromatin-modifying complexes in yeast, is a selective reader of histone H3 Lys9 acetylation (H3K9ac). Structural analysis reveals that acetylated Lys9 is sandwiched in an aromatic cage formed by F62 and W81. Disruption of this binding in cells impairs gene transcription and the DNA damage response. Our findings establish a highly conserved acetyllysine reader function for the YEATS domain protein family and highlight the significance of this interaction for Taf14

Novel mechanisms of transcriptional regulation by the yeast hog 1 mapk

En la levadura S. cerevisiae, un incremento de la osmolaridad extracelular activa la vía de Hog1, lo que produce una compleja respuesta adaptativa. Entre las respuestas adaptativas que Hog1 coordina, está un importante cambio en el partón de expresión génica. La tesis presentada se centra en la respuesta a nivel de regulación génica, y en ella se ponen de manifiesto nuevos mecanismos por los cuales Hog1 regula la transcripción para inducir genes necesarios para la adaptación celular en respuesta a estrés osmótico. Este trabajo demuestra que Hog1 controla la iniciación y la elongación de la transcripción, interacciona con la RNA polimerasa elongando, y es reclutado en toda la región codificante de los genes que se inducen por estrés osmótico a traves del 3'UTR. Asimismo, Hog1 recluta el complejo remodelador de cromatina RSC para promover un dramático cambio en el posicionamiento de nucleosomas, permitiendo una correcta inducción de la expresión génica.In the yeast S.cerevisiae, an increase in extra cellular osmolarity activates the Hog1 Pathway, which produces a very complex adaptive response. Among these adaptive responses coordinated by Hog1, there is an important change in the gene expression pattern. The presented Thesis focuses on the response triggered at the genomic level, showing novel mechanisms by which Hog1 regulates transcription to efficiently and properly induce a subset of genes critical for the cellular adaptation to osmotic stress. This work demonstrates that Hog1 promotes and regulates transcription not only at the initiation level, as was previously described, but it also interacts with the RNA Polymerase while elongating, and travels along the coding regions of genes induced upon osmotic stress through recognition of the 3'UTR. Furthermore, Hog1 recruits a chromatin-remodeling complex known as RSC to promote a dramatic change in nucleosome positioning of target genes, allowing a proper induction of the transcriptio

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.

A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.

A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons

A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity

Resultats primera fase de l’estudi ENE-COVID a Catalunya

Coronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiologia; AnticossosCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiologia; AnticuerposCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Sero-epidemiology; AntibodiesENE-COVID és un ampli estudi longitudinal sero-epidemiològic de base poblacional, que té com a objectiu estimar la prevalença d’infecció per SARS-CoV-2 a l’Estat espanyol mitjançant la determinació d’anticossos enfront del virus, així com avaluar-ne l’evolució temporal. Aquest estudi ha estat coordinat pel Ministeri de Sanitat en col·laboració amb l’Institut de Salut Carlos III, l’Institut Nacional d’Estadística i els departaments de Salut Públicai serveis de salut de totes lescomunitats autònomes i de les ciutats autònomes de Ceuta i Melilla. La informació recollida s’ha analitzat en l’àmbit de les comunitats autònomes, províncies, grups d’edat i sexes. S’ha seleccionat a l’atzar un nombre de llars de cada província perquè sigui representatiu de la població d’Espanya. Als participants se’ls fa una enquesta, un test ràpid d’anticossos mitjançant punxada al dit i una extracció de sang venosa per conèixer la presència d’anticossos d’una forma més precisa. L’estudi es va dur a terme en tres rondes durant els mesos d’abril a juny de 2020 (la primera, del 27 d’abril a l’11 de maig; la segona, del 18 de maig a l’1 de juny, i la tercera, del 8 de juny al 22 de juny)

Not all H3K4 Methylations are created equal: Mll2/COMPASS dependency in primordial germ cell specification

The spatiotemporal regulation of gene expression is central for cell-lineage specification during embryonic development and is achieved through the combinatorial action of transcription factors/co-factors and epigenetic states at cis-regulatory elements. Here, we show that in addition to implementing H3K4me3 at promoters of bivalent genes, Mll2 (KMT2B)/COMPASS can also implement H3K4me3 at a subset of non-TSS regulatory elements, a subset of which shares epigenetic signatures of active enhancers. Our mechanistic studies reveal that association of Mll2's CXXC domain with CpG-rich regions plays an instrumental role for chromatin targeting and subsequent implementation of H3K4me3. Although Mll2/COMPASS is required for H3K4me3 implementation on thousands of loci, generation of catalytically mutant MLL2/COMPASS demonstrated that H3K4me3 implemented by this enzyme was essential for expression of a subset of genes, including those functioning in the control of transcriptional programs during embryonic development. Our findings suggest that not all H3K4 trimethylations implemented by MLL2/COMPASS are functionally equivalent.D.H. was supported by the Robert H. Lurie Comprehensive Cancer Center - Translational Bridge Program Fellowship in Lymphoma Research. G.M. received the support of Ia Convocatoria de Ayudas Fundación BBVA a Investigadores, Innovadores y Creadores Culturales. A.V. was supported by NIH training grant T32CA080621. These studies were further supported by grants from the Spanish “Ministerio de Educación y Ciencia” (SAF2013-48926-P) and AGAUR to L.D.C., and NIH grants R01CA101774 to J.D.C., R50CA211428 to E.R.S., and R35CA197569 to A.S