Regulation of gene expression by long non-coding RNAs


Gene regulation is a really complicated thing. We have covalent marks to DNA, histones and transcription factors. Chromatin remodeling and long range enhancer interactions. Enhancer elements located in introns of genes hundreds of kilobases away from the gene they're controlling. Transcriptional control from microRNA networks and now there is an emerging model for the function of some of the thousands of long non-coding RNAs which are just now being uncovered with high resolution (directional) transcriptome analysis.

 Many of you which studied molecular biology at Uni would (should) remember the model for how X chromosome inactivation is achieved. The mechanism centers around XIST, one of the first non-coding RNA genes identified. Expression of XIST from the inactive X chromosome essentially wraps it up at the same time that repressive epigenetic marks are established through its interaction with the Polycomb Repressive Complex 2 (PRC2). Sounds simple enough, but the model also involves two other non-coding RNA genes JPX and FTX as well as two protein coding genes TSX and CNBP2.

 But there's one problem, how does XIST keep expression up when the rest of the chromosome is becoming repressed? Well the answer lies in the action of TSIX the antisense transcript of XIST. 
High levels of the TSIX transcript from the locus compete for the binding of PRC, so when TSIX expression is low, PRC2 is free to start binding with the XIST RNA RepA. This RepA/PRC2 complex then loads onto XIST chromatin with the help of YY1 and confers DNA methylation, at which point XIST RNA is transcribed, leading to methylation of the entire chromosome guided by PRC2.

 More generally, the emerging model of lncRNA action involves the transcription of the lncRNA followed by pausing of the POL2 transcription complex resulting in an RNA tail attached at the 3' end but freely swimming around at the 5' end. The ncRNA contains a tethering or binding motif which can be targeted by proteins such as PRC2. The PRC2 complex can then be pulled to the chromatin by factors which bind RNA and DNA simultaneously such as YY1. This mechanism enables large complexes such as PRC2 to be recruited to the chromatin to deposit epigenetic marks on nearby genes.


Traditionally transcriptional control is thought to be mediated by transcription factors binding to DNA motifs in promoters where epigenetic modifications are permissive, but this new model highlights that transcription factors and chromatin remodellers might actually be dependent on lncRNAs for additional locus specificity. Moreover, this model provides a mechanism for the understanding of the long-range (hundreds of kilobases even interchromosomal) chromatin interactions that are apparent in ChIA-PET, 5C and DNase hypersensitivity profiling datasets.

The lessons learned from Xist in the field of epigenetics over the past 20 or so years are becoming mainstream ideas in modern molecular biology. It also seems that an understanding of the importance of DNA methylation cannot be complete without understanding the RNA neighborhood.
Location: St Kilda VIC 3182, Australia

Popular posts from this blog

Two subtle problems with over-representation analysis

Image
Over-representation analysis is a helpful and really frequently used technique for understanding trends from omics data and gene lists more generally. Just to demonstrate this, I tabulated the number of citations of some of the most popular web tools and packages, which reaches a massive 191k citations! But if you have used some of these tools, you will notice that they yield subtly different results. We were curiuous about that and ran a whole bunch of investigations into the internal workings of these tools, in particular clusterProfiler. We identified two subtle problems with clusterProfiler, which we unpack in detail in our new publication , but here I will give you a quick overview. Problem #1: The background problem The first one we call the “background problem,” because it involves the software eliminating large numbers of genes from the background list if they are not annotated as belonging to any category. This results in removing a large number of unannotated genes from the b...
Read more

Data analysis step 8: Pathway analysis with GSEA

Image
In our RNA-seq series so far we've performed differential analysis and generated some pretty graphs, showing thousands of differentially expressed genes after azacitidine treatment. In order to understand the biology underlying the differential gene expression profile, we need to perform pathway analysis. We use Gene Set Enrichment Analysis ( GSEA ) because it can detect pathway changes more sensitively and robustly than some methods. A 2013 paper compared a bunch of gene set analyses software with microarrays and is worth a look. Generate a rank file The rank file is a list of detected genes and a rank metric score. At the top of the list are genes with the "strongest" up-regulation, at the bottom of the list are the genes with the "strongest" down-regulation and the genes not changing are in the middle. The metric score I like to use is the sign of the fold change multiplied by the inverse of the p-value, although there may be better methods out there...
Read more

Uploading data to GEO - which method is faster?

If you have had to upload omics data to GEO before, you'll know it's a bit of a hassle and takes a long time. There are a few methods suggested by the GEO team if you are using the Unix command line: Using 'ncftp' ncftp set passive on set so-bufsize 33554432 open  ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.gov cd uploads/your @mail.com_ yourfolder put -R Folder_with_submission_files Using 'lftp' lftp  ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.gov cd uploads/ your @mail.com _ yourfolder mirror -R Folder_with_submission_files Using 'sftp' (expect slower transfer speeds since this method encrypts on-the-fly) sftp  geoftp @s ftp-private.ncbi.nlm.nih.gov password: yourpasscode cd uploads/ your @mail.com _ yourfolder mkdir new_geo_submission cd new_geo_submission put file_name Using 'ncftpput' (transfers from the command-line without entering an interactive shell) Usage example: ncftpput -F -R -z -u  geoftp  -p "yourpasscode...
Read more