Plant transcription factors – being in the right place with the right company. Curr Opin Plant Biol 2022

Transcriptional regulation underlies many of the growth and developmental processes that shape plants as well as their adaptation to their environment. Key to transcriptional control are transcription factors, DNA-binding proteins that serve two essential functions: to find the appropriate DNA contact sites in their target genes; and to recruit other proteins to execute transcriptional transactions. In recent years, protein structural, genomic, bioinformatic, and proteomic analyses have led to new insights into how these central functions are regulated. Here, we review new findings relating to plant transcription factor function and to their role in shaping transcription in the context of chromatin. Read more

Modesola’s farewell

Modesola's farewell

Thank you, Modesola Olaniyi (third from the front on the left bench) for your excellent research on overcoming Polycomb repression for the last couple of years. All the best for the next steps in your career!

H2A.Z contributes to trithorax activity at the AGAMOUS locus

In multicellular eukaryotes, Polycomb repression heritably silences gene expression programs not needed or detrimental for a given developmental stage or tissue (Schuettengruber et al., 2017). During cell fate reprogramming, Polycomb silencing can be overcome by the combined activity of multiple Trithorax group (TrxG) proteins (Wu et al., 2012; Liang et al., 2015; Schuettengruber et al., 2017). TrxG proteins are genetically defined as suppressors of homeotic defects caused by loss of Polycomb function and have diverse enzymatic activities (Schuettengruber et al., 2017). We used a genetic enhancer screen to identify candidate TrxG proteins and uncovered TrxG activity for components of the SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z (Deal et al., 2007; March-Diaz et al., 2008). Read more

Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data


Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to identify factor binding to genomic DNA and chromatin modifications. ChIP-seq data analysis is affected by genomic regions that generate ultra-high artifactual signals. To remove these signals from ChIP-seq data, the Encyclopedia of DNA Elements (ENCODE) project developed comprehensive sets of regions defined by low mappability and ultra-high signals called blacklists for human, mouse (Mus musculus), nematode (Caenorhabditis elegans), and fruit fly (Drosophila melanogaster). However, blacklists are not currently available for many model and nonmodel species. Here, we describe an alternative approach for removing false-positive peaks called greenscreen. Greenscreen is easy to implement, requires few input samples, and uses analysis tools frequently employed for ChIP-seq. Greenscreen removes artifactual signals as effectively as blacklists in Arabidopsis thaliana and human ChIP-seq dataset while covering less of the genome and dramatically improves ChIP-seq peak calling and downstream analyses. Greenscreen filtering reveals true factor binding overlap and occupancy changes in different genetic backgrounds or tissues. Because it is effective with as few as two inputs, greenscreen is readily adaptable for use in any species or genome build. Although developed for ChIP-seq, greenscreen also identifies artifactual signals from other genomic datasets including Cleavage Under Targets and Release Using Nuclease. We present an improved ChIP-seq pipeline incorporating greenscreen that detects more true peaks than other methods. Read more

Poster by fantastic intern Emily Knisely-Durham from Howard University

This Summer, the Wagner lab hosted undergraduate student Emily Knisely-Durham. Emily was an intern in the Summer Undergraduate Internship Program (SUIP), the Diversity Action Plan for PENN Genomics (DAPPG). Emily worked with PhD student Tian Huang on screening for transcription factors that regulate the Arabidopsis gene TERMINAL FLOWER 1 (TFL1) through its 3′ intergenic regulatory region, using a modified Y1H system.

This Summer, the Wagner lab hosted an undergrad, Emily …, Emily worked with PhD student Tian Huang on screening for transcription factors that regulate the Arabidopsis gene TERMINAL FLOWER 1 (TFL1) through its 3′ intergenic regulatory region, using a modified the traditional Y1H system.