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| STARK LAB
Understanding transcription regulation. Transcription — the copying of genomic DNA into RNA — is one of the most fascinating processes in biology, particularly in animals in which different cell types transcribe different genes to acquire different morphologies andfunctions.
MEET US AT CONFERENCES AND MEETINGS 2021. 14.04.2021-15.04.2021: Abcam Meeting Chromatin & Epigenetics: from Mechanisms to Function, Munich, Germany - virtual 2020; 26.01.2020-31.01.2020: KeystoneALEXANDER STARK
STARK LAB | FLY ENHANCERS | HOME The Fly Enhancers resource assesses the in vivo activity of 7793 enhancer candidates (tiles), which cover about 13.5% of the entire non-coding, non-repetitive Drosophila melanogaster genome, across embryonic stages 4 to 16. Enhancer activity patterns were recorded by whole slide imaging of ~400 embryos of various stages per enhancer candidate and enhancer activity was manually annotated with a STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna WELCOME TO OUR NEW MEMBER PETER A warm welcome to our new PhD student Peter Zöscher who has recently joined our group. We wish him all the best for tackling gene regulation computationally! STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA sequence and measured as presence of the resulting reporter transcripts among STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Assessing activity differences of different cis-regulatory genomes – comparative genomics. STARR-seq allows screening multiple cis-regulatory genomes in a single cell type, i.e. in the same trans-regulatory environment, enabling powerful comparative analyses of differential enhancer activities that arise from sequencevariation.
STARK LAB | FLY ENHANCERS | ADVANCED SEARCH Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Understanding transcription regulation. The regulation of gene expression in response to developmental or environmental stimuli is a crucial mechanism in all organisms.| STARK LAB
Understanding transcription regulation. Transcription — the copying of genomic DNA into RNA — is one of the most fascinating processes in biology, particularly in animals in which different cell types transcribe different genes to acquire different morphologies andfunctions.
MEET US AT CONFERENCES AND MEETINGS 2021. 14.04.2021-15.04.2021: Abcam Meeting Chromatin & Epigenetics: from Mechanisms to Function, Munich, Germany - virtual 2020; 26.01.2020-31.01.2020: KeystoneALEXANDER STARK
STARK LAB | FLY ENHANCERS | HOME The Fly Enhancers resource assesses the in vivo activity of 7793 enhancer candidates (tiles), which cover about 13.5% of the entire non-coding, non-repetitive Drosophila melanogaster genome, across embryonic stages 4 to 16. Enhancer activity patterns were recorded by whole slide imaging of ~400 embryos of various stages per enhancer candidate and enhancer activity was manually annotated with a STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna WELCOME TO OUR NEW MEMBER PETER A warm welcome to our new PhD student Peter Zöscher who has recently joined our group. We wish him all the best for tackling gene regulation computationally! STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA sequence and measured as presence of the resulting reporter transcripts among STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Assessing activity differences of different cis-regulatory genomes – comparative genomics. STARR-seq allows screening multiple cis-regulatory genomes in a single cell type, i.e. in the same trans-regulatory environment, enabling powerful comparative analyses of differential enhancer activities that arise from sequencevariation.
STARK LAB | FLY ENHANCERS | ADVANCED SEARCH Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna| STARK LAB
See dedicated STARR-seq and STAP-seq pages for detailed information, protocols, and plasmids 2020. Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar J, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaefer J, Hufnagl P, Zoufaly A, Seitz T, VCDI, Foedinger M, Allerberger F, Stark A, Cochella L § & Elling U §. MEET US AT CONFERENCES AND MEETINGS 2021. 14.04.2021-15.04.2021: Abcam Meeting Chromatin & Epigenetics: from Mechanisms to Function, Munich, Germany - virtual 2020; 26.01.2020-31.01.2020: Keystone| STARK LAB
Next journal club on Friday May 21 st: (virtual meeting): . Oliver: Dixon et al, QSER1 protects DNA methylation valleys from de novo methylation. Science 2021. 10.1126/science.abd0875| STARK LAB
Stark Lab Research Institute of Molecular Pathology Campus-Vienna-Biocenter 1 1030 Vienna, AustriaALEXANDER STARK
2008 - Present Group-leader, Research Institute of Molecular Pathology (IMP), Vienna, Austria 2005 - 2008 Postdoctoral Fellow, Kellis & Lander Groups, The Broad Institute of MIT and Harvard and CSAIL MIT, Cambridge, USA 2001 - 2005 STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna JOINT GROUP RETREAT WITH THE SCHUEBELER LAB We had our first online Joint Group Retreat with Dirk Schuebeler’s Lab from the Friedrich Miescher Institute for Biomedical Research in Basel. Thank you to Dirk and Alex for preparing such a fun meeting and for giving us the chance to get to know and learn from each other! STARK LAB | FACTORS | DMEL:COREST 1 H. sapiens orthologs were obtained from InParanoid8, in particular D.melanogaster-H.sapiens.orthoXML. 2 Genomic sequences of the transcription factors were obtained from the dm3/BDGP Release 5 genome assembly.In the case of cofactors, the genomic sequences stand for our results obtained by deep sequencing. STARK LAB | FACTORS | DMEL:TAF11 1 H. sapiens orthologs were obtained from InParanoid8, in particular D.melanogaster-H.sapiens.orthoXML. 2 Genomic sequences of the transcription factors were obtained from the dm3/BDGP Release 5 genome assembly.In the case of cofactors, the genomic sequences stand for our results obtained by deep sequencing. STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA sequence and measured as presence of the resulting reporter transcripts among STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY The regulation of gene expression in response to developmental or environmental stimuli is a crucial mechanism in all organisms. We are fascinated by the question how transcription is regulated at the level of the two key types of regulatory genomic elements — enhancers and core-promoters — and the transcription factor and cofactor proteins| STARK LAB
Cracking the transcriptional regulatory code. We use bioinformatics and machine-learning to dissect regulatory sequences and determine sequence features (e.g. TF motifs) that are predictive of regulatory function and required for enhancer activity. Our goal is to achieve a systematic understanding of the structure and functions of enhancers,i
MEET US AT CONFERENCES AND MEETINGS 2021. 14.04.2021-15.04.2021: Abcam Meeting Chromatin & Epigenetics: from Mechanisms to Function, Munich, Germany - virtual 2020; 26.01.2020-31.01.2020: Keystone| STARK LAB
Next journal club on Friday May 21 st: (virtual meeting): . Oliver: Dixon et al, QSER1 protects DNA methylation valleys from de novo methylation. Science 2021. 10.1126/science.abd0875| STARK LAB
Stark Lab Research Institute of Molecular Pathology Campus-Vienna-Biocenter 1 1030 Vienna, Austria STARK LAB | FLY ENHANCERS | HOME The Fly Enhancers resource assesses the in vivo activity of 7793 enhancer candidates (tiles), which cover about 13.5% of the entire non-coding, non-repetitive Drosophila melanogaster genome, across embryonic stages 4 to 16. Enhancer activity patterns were recorded by whole slide imaging of ~400 embryos of various stages per enhancer candidate and enhancer activity was manually annotated with a STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Stark Lab | STARR-seq | Home. Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Assessing activity differences of different cis-regulatory genomes – comparative genomics. STARR-seq allows screening multiple cis-regulatory genomes in a single cell type, i.e. in the same trans-regulatory environment, enabling powerful comparative analyses of differential enhancer activities that arise from sequencevariation.
STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA sequence and measured as presence of the resulting reporter transcripts among STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY The regulation of gene expression in response to developmental or environmental stimuli is a crucial mechanism in all organisms. We are fascinated by the question how transcription is regulated at the level of the two key types of regulatory genomic elements — enhancers and core-promoters — and the transcription factor and cofactor proteins| STARK LAB
Cracking the transcriptional regulatory code. We use bioinformatics and machine-learning to dissect regulatory sequences and determine sequence features (e.g. TF motifs) that are predictive of regulatory function and required for enhancer activity. Our goal is to achieve a systematic understanding of the structure and functions of enhancers,i
MEET US AT CONFERENCES AND MEETINGS 2021. 14.04.2021-15.04.2021: Abcam Meeting Chromatin & Epigenetics: from Mechanisms to Function, Munich, Germany - virtual 2020; 26.01.2020-31.01.2020: Keystone| STARK LAB
Next journal club on Friday May 21 st: (virtual meeting): . Oliver: Dixon et al, QSER1 protects DNA methylation valleys from de novo methylation. Science 2021. 10.1126/science.abd0875| STARK LAB
Stark Lab Research Institute of Molecular Pathology Campus-Vienna-Biocenter 1 1030 Vienna, Austria STARK LAB | FLY ENHANCERS | HOME The Fly Enhancers resource assesses the in vivo activity of 7793 enhancer candidates (tiles), which cover about 13.5% of the entire non-coding, non-repetitive Drosophila melanogaster genome, across embryonic stages 4 to 16. Enhancer activity patterns were recorded by whole slide imaging of ~400 embryos of various stages per enhancer candidate and enhancer activity was manually annotated with a STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Stark Lab | STARR-seq | Home. Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Assessing activity differences of different cis-regulatory genomes – comparative genomics. STARR-seq allows screening multiple cis-regulatory genomes in a single cell type, i.e. in the same trans-regulatory environment, enabling powerful comparative analyses of differential enhancer activities that arise from sequencevariation.
STARK LAB | DECIPHERING THE TRANSCRIPTIONAL CIS-REGULATORY Self-transcribing active regulatory region sequencing (STARR-seq) is a massively parallel reporter assay to identify transcriptional enhancers directly based on their activity in entire genomes and to assess their activity quantitatively (Arnold 2013). Enhancer activity is directly linked to the underlying DNA sequence and measured as presence of the resulting reporter transcripts among| STARK LAB
Pubmed 24402316. Meireles-Filho AC, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A. cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock. Current Biology. 2014 Jan;24 (1):1-10. Pubmed 24332542 . Featured in: ** Circadian Clocks: The Tissue Is the Issue. Current Biology 24 (2014).| STARK LAB
Pubmed 28369070. DATA. Arnold CD*, Zabidi MA*, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A. Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nature Biotechnology, 2017 Feb;35 (2):136-144. Pubmed28024147.
| STARK LAB
Next journal club on Friday May 21 st: (virtual meeting): . Oliver: Dixon et al, QSER1 protects DNA methylation valleys from de novo methylation. Science 2021. 10.1126/science.abd0875ALEXANDER STARK
Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 339 (6123):1074-1077. Yáñez-Cuna JO*, Kvon EZ*, Stark A. (2013). Deciphering the transcriptional cis-regulatory code. WELCOME TO OUR NEW MEMBER PETER Welcome to our new member Peter. A warm welcome to our new PhD student Peter Zöscher who has recently joined our group. We wish him all the best for tackling gene regulation computationally! See Members.Before.
STARK LAB | FLY ENHANCERS | BROWSE Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna JOINT GROUP RETREAT WITH THE SCHUEBELER LAB We had our first online Joint Group Retreat with Dirk Schuebeler’s Lab from the Friedrich Miescher Institute for Biomedical Research in Basel. Thank you to Dirk and Alex for preparing such a fun meeting and for giving us the chance to get to know and learn from each other! STARK LAB | FLY ENHANCERS | ADVANCED SEARCH Presentation of Fly Enhancers by the Alexander Stark Group at the Research Institute of Molecular Pathology (IMP), Vienna| STARK LAB
Stark Lab Research Institute of Molecular Pathology Campus-Vienna-Biocenter 1 1030 Vienna, Austria STARR-SEQ LIBRARY PREPARATION PROTOCOL STARR-seq Library preparation protocol G e n o m e - w i d e l i b r a r y U s e 5 0 µ g o f ge n o m i c D N A ( Pro m ega; hum an g enomic D NA (gDN A ); Cat N o .* Stark Lab
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STARK LAB
UNDERSTANDING TRANSCRIPTION REGULATION The regulation of gene expression in response to developmental or environmental stimuli is a crucial mechanism in all organisms. We are fascinated by the question how transcription is regulated at the level of the two key types of regulatory genomic elements — enhancers and core-promoters — and the transcription factor and cofactor proteins that mediate transcription activation. We follow an interdisciplinary approach, using genome-wide functional assays, bioinformatics, biochemistry, and mass-spectrometry. We develop and employ highly-controllable reporter assays that provide a reliable functional readout for each of the questions we ask, while circumventing the many confounding issues that exist in complex gene regulatory systems in vivo. Our goal is to understand transcription and — ultimately — how transcriptional networks define cellular and developmentalprograms.
NEWS
* Congratulations to Alex and the whole lab for being awarded the Austrian Science Fund (FWF) grant! 20 Dec 2019 * Congratulations to Lorena and Vincent for receiving fellowships!20 Dec 2019
* Welcome to our new intern29 Oct 2019
NEWS ARCHIVE
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