Biology subjects

Klasfeld, S.

Publications and source records attributed to Klasfeld, S..

4 recordsLinked to original sources

bioRxiv2023

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinias i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinias stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.

genomics↗

bioRxiv2022

Greenscreen decreases Type I Errors and increases true peak detection in genomic datasets including ChIP-seq

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is used widely to identify both factor binding to genomic DNA and chromatin modifications. Analysis of ChIP-seq data is impacted by regions of the genome which generate ultra-high artifactual signals. To remove these signals from ChIP-seq data, ENCODE developed blacklists, comprehensive sets of regions defined by low mappability and ultra-high signals for human, mouse, worm, and flies. Currently, blacklists are not available for many model and non-model species. Here we describe an alternative approach for removing false-positive peaks we called "greenscreen". Greenscreen is facile to implement, requires few input samples, and uses analysis tools frequently employed for ChIP-seq. We show that greenscreen removes artifact signal as effectively as blacklists in Arabidopsis and human ChIP-seq datasets while covering less of the genome, dramatically improving ChIP-seq data quality. Greenscreen filtering reveals true factor binding overlap and of occupancy changes in different genetic backgrounds or tissues. Because it is effective with as few as three inputs, greenscreen is readily adaptable for use in any species or genome build. Although developed for ChIP-seq, greenscreen also identifies artifact signals from other genomic datasets including CUT&RUN. Finally, we present an improved ChIP-seq pipeline which incorporates greenscreen, that detects more true peaks than published methods. One Sentence SummaryA facile method for removing artifact signal from ChIP-seq that improves downstream analyses

genomics↗

bioRxiv2020

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet no bonafide pioneer transcription factor has - been identified in this kingdom. Here we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds in a sequence-specific manner and with high affinity to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1, where it co-occupies DNA with histones. Moreover, the LFY DNA contact helix shares defining properties with those of strong nucleosome binding pioneer factors. At the AP1 locus, LFY unlocks chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later and require activity of additional, non-pioneer transcription, factors. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between plant and animal pioneer transcription factors. Further analyses aimed at elucidating the defining characteristics of pioneer transcription factors will allow harnessing these for enhanced cell fate reprogramming.

plant biology↗

bioRxiv2020

Florigen family chromatin recruitment, competition and target genes

Plants monitor seasonal cues, such as day-length, to optimize life history traits including onset of reproduction and inflorescence architecture 1-3. Florigen family transcriptional co-regulators TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) antagonistically regulate these vital processes 4-6 yet how TFL1 and FT execute their roles and what the mechanism is for their antagonism remains poorly understood. We show genome-wide, that TFL1 is recruited to the chromatin by the bZIP transcription factor FLOWERING LOCUS D (FD) in Arabidopsis. We find that seasonal cue-mediated upregulation of FT competes TFL1 from chromatin-bound FD at key target loci. We identify the master regulator of floral fate, LEAFY (LFY) as a target under dual opposite regulation by TFL1 and FT. Exonic bZIP motifs in LFY are critical for repression by TFL1, upregulation by FT and adoption of floral fate. Transcriptomic identification of target genes directly repressed by the TFL1-FD complex not only identifies key regulators of onset of reproduction and floral fate, but reveals that TFL1-FD repress sugar and hormone signalling pathways and chromatin regulators. Our data provide mechanistic insight into how florigen family member sculpt inflorescence architecture, a trait important for reproductive success and yield.

plant biology↗