Variation and conservation of enhancer elements in animal evolution
Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. One example of such non-coding elements capable of binding transcription factors and enhancing the expression of target genes are so-called enhancers. They vary in size of the element and distance from the target gene, with some enhancers operating over megabases of DNA. In recent years, considerable effort has been made to identify enhancers and to attempt to understand how these function within the chromatin organization of the chromosome. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. This notion is supported by recent findings showing that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease. A recent review by Drs Adam Douglas and Robert Hill focusses on a proportion of these regulatory sequences, namely enhancer elements, discussing how our understanding of enhancer conservation and variability can shed light on animal evolution.
Reference
Douglas A T and Hill R D. Transcription 2014; 5:3: e28848; http://dx.doi.org/10.4161/trns.28848
CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia
There is an unmet need for new diagnostic biomarkers that can improve the detection of adenomas and colorectal cancer (CRC) in a cost-effective manner for population screening programs. Genes whose epression changes markedly in association with colorectal neoplasia could be used as potential biomarkers, especially if the change can be detected in a non-invasive patient sample such as blood or stool. A potential candiate is the CAHM gene (Colorectal Adenocarcinoma HyperMethylated) encoding a long non-coding RNA, which has found to be frequently hypermethylated in cancer. The intronless CAHM gene is located on chromosome six, adjacent to the gene QKI, which encodes an RNA binding protein. A new study by Dr Peter Molloy and colleagues used a quantitative methylation-specific PCR to characterize and compare additional tissue samples. The CAHM assay was positive in 2/26 normal colorectal tissues (8%), 17/21 adenomas (81%), and 56/79 CRC samples (71%). CAHM RNA levels correlated negatively with the level of CAHM methylation, and therefore CAHM gene expression is typically decreased in CRC. The methylation-specific PCR was also applied to DNA isolated from plasma specimens from 220 colonoscopy-examined patients. The researchers found methylated CAHM sequences in the plasma DNA of 40/73 (55%) of CRC patients compared with 3/73 (4%) from subjects with adenomas and 5/74 (7%) from subjects without neoplasia. Both the frequency of detection and the amount of methylated CAHM DNA released into plasma increased with increasing cancer stage. These findings suggest that methylated CAHM DNA has potential as a plasma biomarker for use in screening for CRC.
Reference
Pedersen S K, Mitchell S M, Graham L D, McEvoy A, Thomas M L, Baker R T, Ross J P, Xu ZZ, Ho T, LaPointe L T, et al. Epigenetics 2014; 9:8: 1071-1082; http://dx.doi.org/10.4161/epi.29046
Mutually exclusive alternative splicing in C. elegans
Alternative processing of precursor mRNAs is a major source of protein diversity and plays crucial roles in development, differentiation, and diseases in higher eukaryotes. Mutually exclusive (ME) selection of one exon in a cluster of exons is a rare form of alternative pre-mRNA splicing. The ME exons occur only as pairs in vertebrates, but the number of ME exons in a cluster in invertebrates can be more than two in some genes. The process obviously requires strict regulation, however, the repertoires of regulation mechanisms for the ME splicing in vivo are still unknown. A new study by Dr Hidehito Kuroyanagi and colleagues experimentally explores putative ME exons in C. elegans to demonstrate that 29 ME exon clusters in 27 genes were actually selected in a mutually exclusive manner. Twenty-two of the clusters consisted of two to four homologous ME exons. Five clusters had too short intervening introns to be excised between the ME exons. The researchers found that fidelity of ME splicing relies at least in part on nonsense-mediated mRNA decay for 14 clusters. Nevertheless, many of the ME exon clusters appeared to be strictly regulated. The study results thus characterize all the repertoires of ME splicing in C. elegans, and further molecular and functional analyses of such clusters will help elucidate novel mechanisms for mutually exclusive selection of the ME exons in vivo.
Reference
Kuroyanagi H, Takei S, and Suzuki Y. Worm 2014; 3:1; e28459; http://dx.doi.org/10.4161/worm.28459
Cockayne syndrome: At least in part a consequence of ribosomopathy
Cockayne syndrome (CS) is a childhood disorder of premature aging and early death. Mutations in the Cockayne syndrome A (CSA) protein account for 20% of CS cases. Hitherto, CSA has exclusively been described as DNA repair factor of the transcription-coupled branch of nucleotide excision repair. Now, a new study identified a novel function of CSA as transcription factor of RNA polymerase I in the nucleolus. Dr Sebastian Iben and colleagues showed that knockdown of CSA reduces pre-ribosomal RNA (pre-rRNA) synthesis by RNA polymerase I. CSA was found to associate with RNA polymerase I and the active fraction of the ribosomal DNA (rDNA) and stimulated re-initiation of rDNA transcription by recruiting the Cockayne syndrome proteins TFIIH and CSB. Moreover, compared with CSA deficient parental CS cells, CSA transfected CS cells revealed significantly more rRNA with induced growth and enhanced global translation. In summary, the study suggests that a previously unknown global dysregulation of ribosomal biogenesis most likely contributes to the reduced growth and premature aging of CS patients.
Reference
Koch S, Gonzalez O G, Assfalg R, Schelling A, Schäfer P, Scharffetter-Kochanek K, and Iben S. Cell Cycle 2014; 13:13; 2029-2037; http://dx.doi.org/10.4161/cc.29018