Development And Application Of Next Generation Sequencing Pipelines In Arabidopsis

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used assay to uncover the function of proteins of interest by generating a snapshot of the protein’s binding sites in an organism at a certain stage given specific conditions. Previous publications provide recommendations for ChIP-Seq analysis, but the guidelines are curated for human, mouse, fly, and worm genomes. More specifically, lists of regions of artificial signal for removal, called “blacklists”, were generated for only the four selected organisms, and therefore downstream analyses in other species are vulnerable to the unmasked noise. Methods to more easily identify ChIP-seq artifacts and then perform ChIP-Seq analysis is introduced and discussed in Chapter 1. In Chapters 2-4, we applied this pipeline to ChIP-Seq experiments in Arabidopsis, the plant model organism, as supportive evidence to understanding the role of specific proteins during floral development. In Chapter 2 analysis of gene expression and chromatin compaction with transcription factor LFY ChIP-seq annotation reveals the role of LFY-binding as a prerequisite for unlocking genes necessary for inflorescence. In Chapter 3, ChIP-Seq was used to reveal where bZIP transcription factor FD recruits TFL1 to compete for regulation of cell fate within the primordia of inflorescence. In Chapter 4, comparisons of ChIP-Seq experiments from different publications highlight recent advances to the collective understanding of floral reproductive development. Plants provide interesting models for studying cell fate since they are continuously generating and developing new organs for either growth or reproductive development. In this dissertation a ChIP-Seq pipeline was manufactured and applied to further the collective effort in understanding these activities

TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T

Plants monitor seasonal cues to optimize reproductive success by tuning onset of reproduction and inflorescence architecture. TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) and their orthologs antagonistically regulate these life history traits, yet their mechanism of action, antagonism and targets remain poorly understood. Here, we show that TFL1 is recruited to thousands of loci by the bZIP transcription factor FD. We identify the master regulator of floral fate, LEAFY (LFY) as a target under dual opposite regulation by TFL1 and FT and uncover a pivotal role of FT in promoting flower fate via LFY upregulation. We provide evidence that the antagonism between FT and TFL1 relies on competition for chromatin-bound FD at shared target loci. Direct TFL1-FD regulated target genes identify this complex as a hub for repressing both master regulators of reproductive development and endogenous signalling pathways. Our data provide mechanistic insight into how TFL1-FD sculpt inflorescence architecture, a trait important for reproductive success, plant architecture and yield

deeptools/deepTools: 3.5.4

error handling fix and cases for bigwigAverage for > 2 samples (@lldelisle) Tick.label deprecation to support matplotlib 3.8 matplotlib minimal supported version from 3.3 to 3.5 tag check changes in pypi upload actio

deeptools/deepTools: 3.5.4

error handling + cases for bwAverage with > 2 samples (@lldelisle ) Tick.label deprecated for matplotlib 3.8 (@lldelisle ) matplotlib minimal version is now 3.5 cicd update for pypi pus

deeptools/deepTools: 3.5.4

error handling + cases for bwAverage with > 2 samples (@lldelisle) tick.label deprecation for compatibility with matplotlib 3.8 (@lldelisle) matplotlib minimal version from 3.3 to 3.5 pypi upload cicd stricter check for tag creatio