Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva

BMC Genomics
Kyle TretinaJoana Silva

Abstract

Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annotation now available for this parasite, offer an unprecedented opportunity to characterize the genomic features associated with gene regulation in this species. Our previous analyses revealed a T. parva genome even more gene-dense than previously thought, with many adjacent loci overlapping each other, not only at the level of untranslated sequences (UTRs) but even in coding sequences. Despite this compactness, Theileria intergenic regions show a pattern of size distribution indicative of monocistronic gene transcription. Three previously described motifs are conserved among Theileria species and highly prevalent in promoter regions near or at the transcription start sites. We found novel motifs at many transcription termination sites, as well as upstream of parasite genes thought to be critical for host transformation. Adjacent genes that could be regulated by antisense transcription from an overlapping transcriptional unit ...Continue Reading

References

Dec 10, 1998·Nucleic Acids Research·K HigoT Korenaga
Jul 19, 2000·Genome Research·E BeaudoingD Gautheret
Mar 19, 2002·Genome Biology·Flavio MignoneGraziano Pesole
Jan 10, 2003·Nucleic Acids Research·V MatysE Wingender
Jan 28, 2003·International Journal for Parasitology·J D BarryR McCulloch
Apr 26, 2003·Trends in Biochemical Sciences·Gavin S WilkieNicola K Gray
Sep 3, 2004·Genome Research·Thomas J TempletonL Aravind
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Feb 8, 2005·Journal of Molecular Evolution·Karol SzafranskiGernot Glöckner
Feb 16, 2005·Genome Research·Dvir DaharyRotem Sorek
Jul 5, 2005·Science·Malcolm J GardnerVishvanath Nene
Mar 9, 2006·BMC Bioinformatics·Kenzie D MacIsaacErnest Fraenkel
Mar 17, 2006·RNA·Jeremy R BabendureRoger Y Tsien
Jan 24, 2007·PLoS Computational Biology·Thomas A DownTim J P Hubbard
May 5, 2007·Nucleic Acids Research·Shaun Mahony, Panayiotis V Benos
May 9, 2007·Nature Reviews. Genetics·Albin SandelinDavid A Hume
Oct 17, 2007·BMC Genomics·Hideo ImamuraJeffrey H Chuang
Apr 2, 2008·Trends in Genetics : TIG·Rutger HermsenSarah Teichmann
Oct 10, 2008·Nucleic Acids Research·Lorenz BülowReinhard Hehl
Mar 28, 2009·PloS One·Jacqueline Schmuckli-MaurerDirk A E Dobbelaere
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Jun 3, 2009·Genes & Development·Patricia Richard, James L Manley
Aug 18, 2009·Developmental Biology·Tamar Juven-Gershon, James T Kadonaga
Nov 13, 2009·Nucleic Acids Research·Elodie Portales-CasamarAlbin Sandelin
Mar 5, 2010·BMC Genomics·Kobby Essien, Christian J Stoeckert
Nov 10, 2010·Nucleic Acids Research·Alper YilmazErich Grotewold
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Apr 8, 2011·Nucleic Acids Research·Ivica Letunic, Peer Bork
Apr 14, 2011·Nature Reviews. Molecular Cell Biology·Jason N KuehnerClaire Moore
Jul 21, 2011·BMC Biology·A Taylor Bright, Elizabeth A Winzeler
Oct 9, 2012·Molecular Cell·David J HobsonJesper Q Svejstrup
Nov 10, 2012·BMC Genomics·Lowell S KappmeyerKelly A Brayton
Jan 15, 2013·Current Opinion in Genetics & Development·Jie JiaPaul L Fox
Nov 13, 2013·Nature Reviews. Genetics·Vicent Pelechano, Lars M Steinmetz

❮ Previous
Next ❯

Methods Mentioned

BETA
genetic modification
RNAseq
the
RNA-seq

Software Mentioned

AthaMap
MEME
STAMP
FIMO
iTOL
DPInteract
MAST
BLASTP

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.