Cold adaptive methanogenic Archaea(methanoarchaea)contribute significantly to methane emission from cold wetlands,however,the cold adaptation mechanism remains less understood.Posttranscriptional regulation is believed to play a role in the cold adaptation of life,as cold induced mRNA secondary structure would affect translation and turn-over of the mRNAs.It determined that cold induced rnRNA secondary structure of the E.coli cold shock protein CspA largely depended on its large 5untranslated region(UTR).Our recent work also demonstrated that the large 5UTRs of mta mRNAs contribute to the transcripts stability,especially at cold.Aims to reveal detailed genome-wide transcdpt architecture in a psychrophilic methanogen M.psychrophilus R15 in response to cold,and open an avenue for the regulation mechanisms of archaeal cold-adaptation,this work,through integrating Illumina-based differential RNA-sequencing(dRNA-seq)and the whole-transcript sequencing approaches,obtained the genome-wide transcription start site(TSS)maps for R15 growing at 18and 8℃ respectively.We detected 1680 primary TSSs(gTSS)for 1534 OREs,accounting for 48.4%of total 3167 ORFs,or for 91%predicated operons.We found that multiple TSSs were used by a single gene that was prevalent in gTSSs.Remarkably,different TSSs were preferentially used at different temperatures,suggesting that transcriptional regulation is involved in cold adaptation as well.Using 5RACE,multiple TSSs in an ORF were verified;and by Primer Extension assay,mRNA isoforms generated by temperature-responded TSS selections were confirmed.gTSS switch generated varied 5UTR mRNA isoforms of a hsp20 gene showed distinct translation efficiencies,indicating that transcriptional and posttranscriptional co-regulation can be involved in the cold adaptation of Archaea.To test the role of 5UTR in the transcript stability,operons for Mta(key complex in methanol-derived methanogenesis)and Pta-ackA(a protein complex for the initial step of acetate-derived methanogenesis)in a cold adaptive methanogen zm-15 were studied.The mta transcripts carry large 5UTRs(270 nt and 238 nt),while pta mRNA carries a 27nt-5UTR.The in vivo half-lives ofmtaA1 and mtaC1B1 mRNAs were similar in 30℃-and 15℃-cultures.However,the half-life of the pta-ackA mRNAs was significantly reduced in 15℃-culture than in 30℃-culture.Removal of the 5UTRs significantly reduced the in vitro half-lives of mtaA1 and mtaC1B1 mRNAs.Remarkably,fusion of the mtaA1 or mtaC1B1 5UTRs to pta-ackA mRNA increased its in vitro half-life at both 30 ℃ and 15 ℃,thus demonstrate that the large 5UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold adapted M.mazei zm-15.This study provides an unexpected dynamic transcription scenario of a psychrophilic archaeon in response to cold,and shed a light on understanding the transcriptional and posttranscriptional regulations in Archaea.