Where have all the regulations gone?

Posted by Hamed Shateri Najafabadi

Three weeks ago, Lila Koumandou and her colleagues from University of Cambridge reported a thorough analysis of  the transport-associated transcriptome of Trypanosoma brucei, a work conducted at Mark Field’s lab. Although previous works have also addressed developmental regulation of mRNA level in T. brucei using microarray analysis of transcriptome, this is the first report in which expression profiles of a wide range of genes are examined at different conditions, including geneticly manipulated cells and varying environmental conditions – To have an idea how such analysis can revolutionize the knowlede of regulatory mechanisms of an organism, take a look at this classic paper by Beer and Tavazoie. The results section of Lila and colleagues’ paper start with the expected corroboration of previous studies, indicating that many genes in T. brucei are developmentally regulated at mRNA level. However, the surprise is waiting where we find out that the transcriptome of T. brucei shows a very limited response to the altered environment and genetic background. Nevertheless, protein levels change in accordance to the alterations. These results suggest that within a life stage, regulation of mRNA level has little to say when the organism needs to adapt to a different milieu, and perhaps the answer should be sought at translation and post-translational levels.

The field of proteomics is yet, if not naive, not as mature as genomics. Even qualitative determination of the set of proteins being expressed by a cell cohort is a tremendous task. WIth advances in the resolution and throughput of mass spectrometry techniques and differential labeling of protein samples, it has become more feasible to quantitatively compare the proteomes of several samples. Yet, analysis of the proteome of T. brucei, with the same extent as what Lili and her colleagues have presented for its transcriptome, requires resources way beyond the affordability of most of the labs that work in this field. In fact, such analysis has not been done yet for any organism, and it is reasonable to assume that the first would be a model organism, rather than a trypanosomatid.

Transcriptional flexibility and inflexibility in differentiation and responsiveness. Upper panel: flexible system. Gene cohorts 1 and 3 are developmentally regulated, and either highly expressed or not expressed; examples of these types of gene products are the trypanosome surface antigens, VSG in the bloodstream form (red) and procyclin in the insect stage (green). The vast majority of genes fall into cohort 2, where, for example, either small or large changes to transcription could result from alterations to the environment (light and dark blue), or a more continually altering transcriptional profile is present that may seek to track changing conditions (purple). This behavior may propagate from one life stage to the next (light and dark blue) or be lost (purple) resulting in altered transcriptional flexibility for genes between life stages. Such a profile is found in higher eukaryotes, including humans and yeast, and probably also many protists, including E. gracilis. Lower panel: inflexible system. In this model gene cohorts 1 and 3 behave as before, but transcription of the genes in cohort 2 remains unchanged. The relative levels of mRNAs from the genes in this cohort may remain constant following differentiation (light blue) or be significantly altered (dark blue and purple). Such a profile is observed here for T. brucei and has been reported previously for P. falciparum, and is potentially a result of a parasitic life style where the host is responsible for provision of a homeostatic environment.

Koumandou et al. BMC Genomics 2008 9:298   doi:10.1186/1471-2164-9-298


Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species

Posted by Hamed Shateri Najafabadi

The title of this post is in fact the title of a recent paper published by Annie Rochette and her colleagues in BMC Genomics (2008, 9:255). This work, which has been done in Barbara Papadopoulou‘s lab at Laval University, reveals unexpected differences between developmental regulation of genes at mRNA level between the two closely related trypanosomatids Leishmania major and Leishmania infantum. I asked Annie to write a summary of her paper in her own point of view. I hope you agree with me that the author’s point of view should be well reflected in the abstract of the paper, so was the case for this article. Here is the abstract as Annie sent to me:

“Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major) to life-threatening visceral diseases (e.g., L. infantum). The high conservation in gene content and genome organization between Leishmania major and Leishmania infantum contrasts their distinct pathophysiologies, suggesting that highly regulated hierarchical and temporal changes in gene expression may be involved. We used a multispecies DNA oligonucleotide microarray to compare whole-genome expression patterns of promastigote (sandfly vector) and amastigote (mammalian macrophages) developmental stages between L. major and L. infantum. Seven percent of the total L. infantum genome and 9.3% of the L. major genome were differentially expressed at the RNA level throughout development. The main variations were found in genes involved in metabolism, cellular organization and biogenesis, transport and genes encoding unknown function. Remarkably, this comparative global interspecies analysis demonstrated that only 10-12% of the differentially expressed genes were common to L. major and L. infantum. Differentially expressed genes are randomly distributed across chromosomes further supporting a posttranscriptional control, which is likely to involve a variety of 3’UTR elements. This study highlighted substantial differences in gene expression patterns between L. major and L. infantum. These important species-specific differences in stage-regulated gene expression may contribute to the disease tropism that distinguishes L. major from L. infantum.”

Thanks to Annie and her colleagues for this beautiful paper.

I would also like to highlight another paper by Nagalakshmi and colleagues which was published in Science about a month ago. In this work, the transcriptome of yeast is analyzed, but not using microarrays. They used massive high-throughput Illumina sequencing to sequence the whole transcriptome of yeast. This approach, in addition to providing precise estimates for the extent at which each part of the genome is transcribed, gives a plethora of other information that is extremely difficult to gain by routine microarray analysis. First of all, it does not need any a priori assumption regarding the regions that are being transcribed, similar to tiling arrays with the difference that the resolution is several folds higher than any affordable tiling array. It also provides information regarding post-transcriptional modifications of RNAs, such as splicing, alternative splicing, poly-adenylation, etc (see Hani’s blog). Trypanosomatids have surprised us several times, by showing us that a mature RNA can look nothing like its precursor due to the high extent of editing and trans-splicing. They have shown us that it is possible to transcribe almost half of a complete chromosome in just one huge RNA, or that a chromosome can be extensively transcribed from both strands. I am sure these surprises will be nothing once we have the data from sequencing the whole transcriptome of a trypanosomatid species; two will be better!