Author: klasfeld

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

Citation:

Xiao, J., Jin, R., Yu, X., Shen, M., Wagner, J. D., Pai, A., Song, C., Zhuang, M., Klasfeld, S., He, C., Santos, A. M., Helliwell, C., Pruneda-Paz, J. L., Kay, S. A., Lin, X., Cui, S., Garzia, M. F., Clarenz, O., Goodrich, J., Zhang, X., Austin, R., Bonasio, R., & Wagner, D. (2017). Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet, advance online publication.

Abstract:

Disruption of gene silencing by Polycomb protein complexes leads to homeotic transformations and altered developmental-phase identity in plants1, 2, 3, 4, 5. Here we define short genomic fragments, known as Polycomb response elements (PREs), that direct Polycomb repressive complex 2 (PRC2) placement at developmental genes regulated by silencing in Arabidopsis thaliana. We identify transcription factor families that bind to these PREs, colocalize with PRC2 on chromatin, physically interact with and recruit PRC2, and are required for PRC2-mediated gene silencing in vivo. Two of the cis sequence motifs enriched in the PREs are cognate binding sites for the identified transcription factors and are necessary and sufficient for PRE activity. Thus PRC2 recruitment in Arabidopsis relies in large part on binding of trans-acting factors to cis-localized DNA sequence motifs.

Notes:

Related External Link

Plant PRE paper by JUN XIAO published in NATURE GENETICS

https://www.eurekalert.org/pub_releases/2017-08/uop-pbs082117.php

Dr. Jun Xiao’s manuscript titled “Cis- and trans-determinants of epigenetic silencing by Polycomb Repressive Complex 2 in Arabidopsis” has been accepted for publication in an upcoming issue of Nature Genetics. Other contributing authors of the paper are Run Jin, Xiang Yu, Max Shen, John Wagner, Armaan Pai, Claire Song, Michael Zhuang, Samantha Klasfeld, Chongsheng He, Alexandre M. Santos, Chris Helliwell, Jose L Pruneda-Paz, Steve A Kay, Xiaowei Lin, Sujuan Cui, Meilin Fernandez Garcia, Oliver Clarenz, Justin Goodrich, Xiaoyu Zhang, Ryan S. Austin, Roberto Bonasio, and Doris Wagner.

Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction.

Citation:

Bossi, F., Fan, J., Xiao, J., Chandra, L., Shen, M., Dorone, Y., Wagner, D., & Rhee, S. Y. (2017). Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC genomics, 18(1), 480.

Abstract:

Background

The molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized.

Results

To identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription.

Conclusions

Our results demonstrate the feasibility of assigning molecular function to proteins of unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.

Notes:

NA

Related External Link

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants

Citation:

Xiao, J., Jin, R., & Wagner, D. (2017). Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome biology, 18(1), 88.

Abstract:

Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.

Notes:

NA

Related External Link