Biology subjects

Lenhard, B.

Publications and source records attributed to Lenhard, B..

5 recordsLinked to original sources

bioRxiv2018

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

One of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the shape index, a characteristic feature of each TSS describing the spatial distribution of transcription initiation events, has a surprisingly strong negative correlation with the measured expression levels. Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.

systems biology↗

bioRxiv2018

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of rules of transcription initiation, led to discovery of new core promoter sequence features and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 micrograms), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5ends of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods by generating a complex, high quality library from mouse embryonic day (E) 11.5 primordial germ cells.

genomics↗

bioRxiv2018

HOTAIR ancient sequence suggests regulatory roles both in cis and trans

HOTAIR is a long noncoding RNA transcribed between HOXC11 and HOXC12 in mammals. The proposed function(s) of HOTAIR lacks consensus as to whether it regulates HoxD cluster genes in trans or HoxC cluster genes in cis. We have identified a 32-nucleotide long conserved noncoding element (CNE) as HOTAIR ancient sequence which has a paralogous copy embedded in HOXD11 noncoding transcript. All vertebrates except teleosts have two copies of CNE and the paralogous CNEs exhibit sequence complementarity in the transcribed orientation. Moreover, paralogous CNEs underwent compensatory mutations suggesting they co-evolved and might hybridize. In both human and mouse, HOTAIR CNE exhibits characteristic features of a poised enhancer in HOTAIR-unexpressed stem cells and of an active enhancer in HOTAIR-expressed cells. Tight correlation between the transcriptional activity of the CNE and HOTAIR promoter suggests HOTAIR transcription is crucial for enhancer activity. In HOTAIR-expressed cells, HOTAIR expression is positively correlated with HOXC11 in cis and negatively correlated with HOXD11 in trans, suggesting a dual modality of HOTAIR ancient sequence.

genomics↗

bioRxiv2017

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome

Previous studies revealed widespread transcription initiation and fast turnover of transcription start sites (TSSs) in mammalian genomes. Yet how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed [~]200,000 human TSSs by integrating evolutionary and functional genomic data, particularly focusing on TSSs that emerged in the primate lineages. We found that intrinsic factors of repetitive sequences and their proximity to established regulatory modules (extrinsic factors) contribute significantly to origin of new TSSs. In early periods, young TSSs experience rapid sequence evolution driven by endogenous mutational mechanisms that reduce the instability of associated repetitive sequences. In later periods, the regulatory functions of young TSSs are gradually modified, and with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the roles of repetitive sequences in these processes.

genomics↗

bioRxiv2017

Distinct Core Promoter Codes Drive Transcription Initiation At Key Developmental Transitions In A Marine Chordate

Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of transcription in the testis, including the male-specific use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. During oogenesis the cell cycle regulator, E2F1, has been co-opted in regulating maternal transcription in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in vertebrates and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box, which indicates that this ancient promoter motif may play a role in selecting DNA for transcription-associated methylation in invertebrate genomes.

genomics↗