Functional requirement of terminal inverted repeats for efficient ProtoRAG activity reveals the early evolution of V(D)J recombination

Guardian of the Genome: An Alternative RAG/Transib Co-Evolution Hypothesis for the Origin of V(D)J Recombination

The appearance of adaptive immunity in jawed vertebrates is termed the immunological 'Big Bang' because of the short evolutionary time over which it developed. Underlying it is the recombination activating gene (RAG)-based V(D)J recombination system, which initiates the sequence diversification of the immunoglobulins and lymphocyte antigen receptors. It was convincingly argued that the RAG1 and RAG2 genes originated from a single transposon. The current dogma postulates that the V(D)J recombination system was established by the split of a primordial vertebrate immune receptor gene into V and J segments by a RAG1/2 transposon, in parallel with the domestication of the same transposable element in a separate genomic locus as the RAG recombinase. Here, based on a new interpretation of previously published data, we propose an alternative evolutionary hypothesis suggesting that two different elements, a RAG1/2 transposase and a Transib transposon invader with RSS-like terminal inverted repeats, co-evolved to work together, resulting in a functional recombination process. This hypothesis offers an alternative understanding of the acquisition of recombinase function by RAGs and the origin of the V(D)J system.

Substantial decrease in CO2 emissions from Chinese inland waters due to global change

Carbon dioxide (CO2) evasion from inland waters is an important component of the global carbon cycle. However, it remains unknown how global change affects CO2 emissions over longer time scales. Here, we present seasonal and annual fluxes of CO2 emissions from streams, rivers, lakes, and reservoirs throughout China and quantify their changes over the past three decades. We found that the CO2 emissions declined from 138 ± 31 Tg C yr-1 in the 1980s to 98 ± 19 Tg C yr-1 in the 2010s. Our results suggest that this unexpected decrease was driven by a combination of environmental alterations, including massive conversion of free-flowing rivers to reservoirs and widespread implementation of reforestation programs. Meanwhile, we found increasing CO2 emissions from the Tibetan Plateau inland waters, likely attributable to increased terrestrial deliveries of organic carbon and expanded surface area due to climate change. We suggest that the CO2 emissions from Chinese inland waters have greatly offset the terrestrial carbon sink and are therefore a key component of China's carbon budget.

IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences

BACKGROUND

An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets.

RESULTS

We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats.

CONCLUSION

Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.

Functional regulation of an ancestral RAG transposon ProtoRAG by a trans-acting factor YY1 in lancelet

The discovery of ancestral RAG transposons in early deuterostomia reveals the origin of vertebrate V(D)J recombination. Here, we analyze the functional regulation of a RAG transposon, ProtoRAG, in lancelet. We find that a specific interaction between the cis-acting element within the TIR sequences of ProtoRAG and a trans-acting factor, lancelet YY1-like (bbYY1), is important for the transcriptional regulation of lancelet RAG-like genes (bbRAG1L and bbRAG2L). Mechanistically, bbYY1 suppresses the transposition of ProtoRAG; meanwhile, bbYY1 promotes host DNA rejoins (HDJ) and TIR-TIR joints (TTJ) after TIR-dependent excision by facilitating the binding of bbRAG1L/2 L to TIR-containing DNA, and by interacting with the bbRAG1L/2 L complex. Our data thus suggest that bbYY1 has dual functions in fine-tuning the activity of ProtoRAG and maintaining the genome stability of the host.