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Hi-C e thehiloeng ho Chromatin Interaction
Hi-C ke mokhoa o etselitsoeng ho hapa tlhophiso ea genomic ka ho kopanya litšebelisano tse thehiloeng ho proximity le tatellano ea maemo a holimo. Mokhoa ona o thehiloe ho chromatin crosslinking le formaldehyde, e lateloa ke tšilo ea lijo le ho kopanya hape ka tsela eo likaroloana tse hokahaneng ka kopanelo li tla theha lihlahisoa tsa ligation. Ka tatellano ea lihlahisoa tsena tsa ligation, hoa khoneha ho ithuta mokhatlo oa 3D oa genome. Hi-C e thusa ho ithuta kabo ea likarolo tsa genome tse pakiloeng hanyenyane (A compartments, euchromatin) 'me ho ka etsahala hore e be transcriptionally active, le libaka tse pakiloeng ka thata (B compartments, Heterochromatin). Hi-C e ka boela ea sebelisoa ho supa Topologically Associated Domains (TADs), libaka tsa genome tse nang le meaho e menahaneng 'me ho ka etsahala hore li be le lipaterone tse tšoanang tsa polelo, le ho khetholla li-loops tsa chromatin, libaka tsa DNA tse hokahaneng hammoho ke liprotheine le tse ling. hangata e ruisoa ka likarolo tsa taolo. Ts'ebeletso ea tatellano ea tatellano ea Hi-C ea BMKGene e matlafatsa bafuputsi ho lekola boholo ba sebaka sa genomics, ho bula mekhoa e mecha ea ho utloisisa taolo ea genome le litlamorao tsa eona ho bophelo bo botle le mafu.
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Sequencing ea Chromatin Immunoprecipitation (ChIP-seq)
Chromatin Immunoprecipitation (CHIP) ke mokhoa o sebelisang li-antibodies ho ntlafatsa liprotheine tse tlamang DNA le sepheo sa tsona sa genomics. Ho kopanngoa ha eona le NGS ho nolofaletsa tlhaloso e pharalletseng ea genome ea lipheo tsa DNA tse amanang le phetoho ea histone, lintlha tsa transcription, le liprotheine tse ling tse tlamang DNA. Mokhoa ona o matla o thusa ho bapisa libaka tse tlamang ho pholletsa le mefuta e fapaneng ea lisele, lisele kapa maemo. Ts'ebeliso ea ChIP-Seq e qala ho ithuta melaoana ea mongolo le mekhoa ea nts'etsopele ho isa ho ho hlakisa mekhoa ea mafu, e e etsa sesebelisoa sa bohlokoa sa ho utloisisa maemo a taolo ea genomic le ho nts'etsapele lintlha tsa kalafo.
Sethala: Illumina NovaSeq
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Whole genome bisulfite sequencing(WGBS)
Whole Genome Bisulfite Sequencing (WGBS) e eme e le mokhoa o tloaelehileng oa khauta bakeng sa ho fuputsa ka botebo DNA methylation, haholo-holo boemo ba bohlano ho cytosine (5-mC), molaoli oa bohlokoa oa polelo ea lefutso le tšebetso ea liselefouno. Molao-motheo o thehiloeng ho WGBS o kenyelletsa phekolo ea bisulfite, e susumetsang phetoho ea li-cytosine tse se nang methylated ho uracil (C ho ea ho U), ha li ntse li siea li-cytosine tsa methylated li sa fetohe. Mokhoa ona o fana ka tharollo ea motheo o le mong, o lumellang bafuputsi ho etsa lipatlisiso ka botlalo ka methylome le ho sibolla mekhoa e sa tloaelehang ea methylation e amanang le maemo a fapaneng, haholo mofets'e. Ka ho sebelisa WGBS, bo-ramahlale ba ka fumana leseli le ke keng la bapisoa mabapi le genome-wide methylation landscapes, ho fana ka kutloisiso e fapaneng ea mekhoa ea epigenetic e bakang lits'ebetso le mafu a fapaneng a tlhaho.
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Assay for Transposase-Accessible Chromatin with High Throughput Sequencing (ATAC-seq)
ATAC-seq ke mokhoa o phahameng oa tatellano o sebelisoang bakeng sa tlhahlobo ea phihlello ea chromatin ea genome. Tšebeliso ea eona e fana ka kutloisiso e tebileng ea mekhoa e rarahaneng ea taolo ea lefats'e ea epigenetic holim'a liphatsa tsa lefutso. Mokhoa ona o sebelisa hyperactive Tn5 transposase ho arola ka nako e le 'ngoe le ho tšoaea libaka tse bulehileng tsa chromatin ka ho kenya li-adapter tsa tatellano. Kholiso e latelang ea PCR e hlahisa laeborari ea tatellano, e lumellang ho tsebahatsa libaka tse bulehileng tsa chromatin tlas'a maemo a itseng a sebaka. ATAC-seq e fana ka pono e akaretsang ea libaka tse fihlellehang tsa chromatin, ho fapana le mekhoa e shebaneng feela le libaka tse tlamang tsa transcription factor kapa libaka tse itseng tse fetotsoeng tsa histone. Ka tatellano ea libaka tsena tse bulehileng tsa chromatin, ATAC-seq e senola libaka tse nang le monyetla oa ho ba le tatellano e sebetsang ea taolo le libaka tse tlamang tse ka bang teng, tse fanang ka leseli la bohlokoa mabapi le phetoho e matla ea polelo ea lefutso ho genome.
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Representation Bisulfite Sequencing (RRBS)
Reduced Representation Bisulfite Sequencing (RRBS) e hlahile e le mokhoa o sa sebetseng hantle le o sebetsang hantle oa Whole Genome Bisulfite Sequencing (WGBS) lipatlisisong tsa DNA methylation. Le ha WGBS e fana ka lintlha tse felletseng ka ho hlahloba genome eohle ka qeto e le 'ngoe ea motheo, litšenyehelo tsa eona tse phahameng e ka ba ntho e fokotsang. RRBS ka maano e fokotsa phephetso ena ka ho khetha karolo e emelang ea genome. Mokhoa ona o ipapisitse le ntlafatso ea libaka tse ruileng tsa lihlekehleke tsa CpG ke MspI cleavage e lateloang ke khetho ea boholo ba likhechana tsa 200-500/600 bps. Ka lebaka leo, ke libaka tse haufi le lihlekehleke tsa CpG feela tse latellanang, athe tse nang le lihlekehleke tse hole tsa CpG li sa kengoa tlhahlobong. Ts'ebetso ena, e kopantsoeng le tatellano ea bisulfite, e lumella ho lemoha ho phahameng ka ho fetisisa ha DNA methylation, le mokhoa oa ho latellana, PE150, o lebisa tlhokomelo ka ho khetheha lipheletsong tsa ho kenya ho e-na le bohareng, ho eketsa katleho ea profiling ea methylation. RRBS ke sesebelisoa sa bohlokoahali se nolofalletsang lipatlisiso tsa DNA methylation tse theko e tlaase le ho ntlafatsa tsebo ea mekhoa ea epigenetic.
