1 / 29

Functional Non-Coding DNA Part I Non-coding genes and non-coding elements of coding genes

Functional Non-Coding DNA Part I Non-coding genes and non-coding elements of coding genes. BNFO 602/691 Biological Sequence Analysis Mark Reimers, VIPBG. What D oes ‘Functional N on-Coding DNA’ Mean?. DNA whose sequence affects transcripts made from DNA in some way

vicky
Télécharger la présentation

Functional Non-Coding DNA Part I Non-coding genes and non-coding elements of coding genes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Functional Non-Coding DNAPart INon-coding genes and non-coding elements of coding genes BNFO 602/691 Biological Sequence Analysis Mark Reimers, VIPBG

  2. What Does ‘Functional Non-Coding DNA’ Mean? • DNA whose sequence affects transcripts made from DNA in some way • Could affect transcription levels, splicing or sequestering of RNA • Three main ways to identify functional non-coding elements • Sequence characteristics – favored bases • Genomic conservation • Epigenetic marks and open chromatin • especially outside of genes

  3. Types of Non-Coding Elements • Non-coding RNAs • miRNAs, lncRNAs, etc • Non-coding gene elements • UTRs, splice sites, poly-adenylation sites, splice sites and regulating element, RNA-binding sites • DNA elements outside genes – our main focus • Promoters • Enhancers/Silencers • Insulators

  4. Types of Non-Coding RNA • microRNAs • Silencing RNAs • Small nuclear/nucleolar RNAs • Piwi-Interacting RNAs • Long Non-Coding RNAs • Circular RNAs • Still other RNAs??? • Comprehensive data base at www.ncrna.org

  5. Micro-RNAs • Micro-RNAs are small non-coding RNA molecules, about 21–25 nucleotides in length • They are processed from much longer genes, or from introns within mRNA, by several molecular pathways • Micro-RNAs base-pair with complementary sequences within mRNA molecules, often in 3’ or 5’ UTR. • miRNA binding usually results in gene repression either via translational stalling or by triggering mRNA degradation Image by Charles Mallery, U of Miami

  6. Micro-RNAs • The human genome encodes over 1500 miRNAs, which are believed to affect more than half of human genes • miRNAs are abundant in many cell types • Thousands of copies per cell of some miRNAs • Those within gene introns share regulation • miRNAs are well-conserved across vertebrates • No orthologs between plant and animal miRNAs • miRBase is the comprehensive repository of micro-RNAs

  7. Other Short RNAs: siRNA • Small interfering RNAs are double-stranded with an overhang • They are processed by some of the same machinery as miRNAsand have some of the same effects

  8. Other Short RNAs: piRNA • Piwi-Interacting RNAs are longer 26-31 base single-stranded RNAs • PIWI (P-element Induces Wimpy Testis) protein • Over 50,000 sequences known in mouse • They are the largest class of nc-RNA • They seem to play an ancient role in defenseagainst retro-viruses and transposons

  9. Other Short RNAs: snRNAs & snoRNAs • Small nuclear RNAs (snRNAs) are typically ~ 150 bases long, and associate with protein • Many conserved copies of each snRNA gene • U1-U6 snRNAs key parts of splicing machinery • Small nucleolar RNAs (snoRNAs) • Guide chemical modifications of other RNAs • Prader-Willi syndrome results from deletion of region containing 29 copies of SNORD116 on chr 15q11 U6 snRNA

  10. Long Non-Coding RNAs • Many long (>200bp) stretches of genome are transcribed and have epigenetic marks like those of protein-coding genes • Most of these are spliced RNAs with two (or more) exons • GENCODE v15 has 13.5K lncRNA • See also • Derrien et al, Genome Research 2012 • Lee, Science 2012 From Derrien et al Genome Res 2012

  11. Many lncRNAs Induce Silencing • Coat nearby gene(s) and silence them • Xist binds to gene clusters first • Xist binds disparate parts of chromosome • Many lncRNA are antisense to genes • Some lncRNAs maintain pluripotency of stem cells From Jeannie Lee lab (Harvard) website

  12. Long Non-Coding RNAs - 2 • Most lncRNAs are expressed in only a few tissues • Most human lncRNAs are specific to the primate lineage From Derrien et al Genome Res 2012

  13. Circular RNAs • Several thousand non-coding RNAs apparently form circular structures • Many form complexes with AGO and seem to absorb attached miRNAs, blocking processing • CDR1 has 70 conserved binding sites for mir7

  14. Functional Pseudo-Genes • Pseudo-genes are copies of genes that are decaying and rarely (never) make proteins • Some pseudo-genes act to absorb negative regulators of the original gene – eg. SRGAP2B

  15. How to Identify Non-Coding RNAs? • Short (and long) RNA transcriptomes • Promoter chromatin marks for independent (non-embedded) miRNAs and lncRNAs

  16. DEMO: Display HOTAIR & XIST Tracks in UCSC Browser

  17. Non-Coding Elements of Genes • TSS • 5' UTRs • Introns • Splicing regulation sites • 3' UTRs • Termination/Poly-adenylation sites

  18. Transcription Start Sites • Transcription of most genes may initiate at several distinct clusters of locations with distinct promoters for each TSS • Two major types of metazoan TSS: CG-rich broad TSS, and narrow (often tissue-specific) TSS

  19. Transcription Start Sites Transcription often starts at CG within promoter

  20. 5’ Untranslated Regions • First exon often contains dozens to thousands of bases before Start codon (median 150) • Sometimes contains regulatory sequences, e.g. binding sites for RNA binding proteins, and translation initiators

  21. Splice Regulatory Sites • Splicing is achieved through binding of spliceosome to recognition sequences on nascent RNA molecule

  22. Splice Regulatory Sites • Tissue-specific splice regulatory sites are highly conserved From Merkin et al Science 2012

  23. Splicing Patterns Evolve in All Tissues Except Brain From Merkin et al Science 2012

  24. Non-Coding Elements in Coding Exons • Many regulatory sites occur within coding exons, esp. toward 5’ end • These constrain some codons as much as protein sequence • Many human SNPs break TFBS but have little effect on protein (AFAWK) From Stergachis et al Science 2013

  25. 3’ Untranslated Regions • Longest exon is usually 3’UTR (>1000 nt) • Typically 1/3 – 1/2 of a gene is in 5’ & 3’ UTRs • 3’UTR has binding sites for miRNAs and RNA binding proteins • AU-rich elements (AREs) stabilize mRNA • Proteins recognize complex secondary structure GRIK4 3’UTR secondary structure is conserved

  26. RNA Binding-Protein Sites • mRNAs are usually further processed (e.g. transported or sequestered) • RNA binding proteins recognize specific motifs within secondary structure of 3’ or 5’ UTR • These sites are often highly conserved From Ray et al Nature 2013

  27. Poly-adenylation/Termination Sites • Transcripts can be terminated and poly-adenylated at sites with specific sequences • Most genes have alternate poly-adenylation sites • Median lengths of 3’UTR are 250 & 1773 bp(mouse)

  28. Poly-adenylation/Termination Sites • Rapidly proliferating cells express gene isoforms with short 3’ UTRs • Neurons typically have longer 3’ UTRs Types of alternate poly-adenylation Elkon et al, NRG 2013

  29. DEMO: GAPDH and GABRA1 in UCSC Browser

More Related