Mapping Regulatory Determinants in Plants

Frontiers in Genetics
Mary GalliAndrea Gallavotti

Abstract

The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable ele...Continue Reading

References

May 15, 2004·Science·Shozo KobayashiHirohiko Hirochika
Apr 15, 2006·Science·Saeko KonishiMasahiro Yano
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Oct 18, 2007·Proceedings of the National Academy of Sciences of the United States of America·J Marcela HernandezErich Grotewold
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Oct 23, 2009·Nature·Antoine MartinAbdelhafid Bendahmane
Nov 6, 2009·Nature·Melissa J FullwoodYijun Ruan
Oct 15, 2010·Nature Biotechnology·Bas van Steensel, Job Dekker
Sep 22, 2011·Nature Immunology·Benjamin L KidderKeji Zhao
Jun 19, 2012·Nature Reviews. Genetics·Ross C Hardison, James Taylor
Jul 11, 2012·Proceedings of the National Academy of Sciences of the United States of America·Que KongLing Yuan
Jul 26, 2012·The Plant Cell·Jong-Jin HanRobert Martienssen
Aug 3, 2012·Genes & Development·Nathalie BolducSarah Hake
Aug 8, 2012·Nature Reviews. Genetics·François Spitz, Eileen E M Furlong
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Dec 29, 2012·PLoS Genetics·Steven R EichtenNathan M Springer
Jan 19, 2013·Science·Cosmas D ArnoldAlexander Stark
Jan 22, 2013·Cell·Arttu JolmaJussi Taipale
Aug 6, 2013·Frontiers in Plant Science·Kenneth M Olsen, Jonathan F Wendel
Oct 4, 2013·Proceedings of the National Academy of Sciences of the United States of America·Qin YangMingliang Xu
Nov 19, 2013·Nature Reviews. Genetics·Rachel S Meyer, Michael D Purugganan
Mar 13, 2014·G3 : Genes - Genomes - Genetics·Sara CastellettiSilvio Salvi
Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Apr 30, 2014·Trends in Genetics : TIG·Anne-Laure TodeschiniReiner A Veitia
Jun 25, 2014·Proceedings of the National Academy of Sciences of the United States of America·Alessia ParaGloria M Coruzzi
Jun 27, 2014·Nature Communications·Leandro QuadranaFernando Carrari
Aug 19, 2014·Trends in Biochemical Sciences·Matthew SlatteryRemo Rohs
Sep 16, 2014·Cell Reports·Alessandra M SullivanJohn A Stamatoyannopoulos
Nov 5, 2014·Genome Research·Congmao WangDetlef Weigel
Nov 3, 2015·Current Opinion in Biotechnology·Wusheng Liu, C Neal Stewart
Feb 16, 2016·Trends in Plant Science·Gwen SwinnenLaurens Pauwels
May 18, 2016·Proceedings of the National Academy of Sciences of the United States of America·Eli Rodgers-MelnickEdward S Buckler

❮ Previous
Next ❯

Citations

Aug 15, 2021·Current Opinion in Plant Biology·Alexandre P Marand, Robert J Schmitz
Sep 4, 2021·The New Phytologist·Bradley W TonnessenJan E Leach

❮ Previous
Next ❯

Methods Mentioned

BETA
ChIP-seq
transfection
transgenic
HT-SELEX
dissection
Hi-C
Hi-ChIP

Software Mentioned

Hi
STARR
CUT

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.