CRISPR Direct Repeat Sequences Olivia Ho-Shing 22 November 2009.

Slides:

Advertisements

Similar presentations

Parallel BioInformatics Sathish Vadhiyar. Parallel Bioinformatics  Many large scale applications in bioinformatics – sequence search, alignment, construction.

Advertisements

Bioinformatics Phylogenetic analysis and sequence alignment The concept of evolutionary tree Types of phylogenetic trees Measurements of genetic distances.

Multiple Sequence Alignment

Bioinformatics Finding signals and motifs in DNA and proteins Expectation Maximization Algorithm MEME The Gibbs sampler Lecture 10.

A Very Basic Gibbs Sampler for Motif Detection Frances Tong July 28, 2004 Southern California Bioinformatics Summer Institute.

Tutorial 5 Motif discovery.

Introduction to Bioinformatics - Tutorial no. 5 MEME – Discovering motifs in sequences MAST – Searching for motifs in databanks TRANSFAC – The Transcription.

Protein Modules An Introduction to Bioinformatics.

Multiple sequence alignments and motif discovery Tutorial 5.

Pattern databases in protein analysis Arthur Gruber Instituto de Ciências Biomédicas Universidade de São Paulo AG-ICB-USP.

Prosite and UCSC Genome Browser Exercise 3. Protein motifs and Prosite.

Exploring Protein Sequences Tutorial 5. Exploring Protein Sequences Multiple alignment –ClustalW Motif discovery –MEME –Jaspar.

CIS786, Lecture 8 Usman Roshan Some of the slides are based upon material by Dennis Livesay and David.

Assessment of sequence alignment Lecture Introduction The Dot plot Matrix visualisation matching tool: – Basics of Dot plot – Examples of Dot plot.

Chapter 5 Multiple Sequence Alignment.

Assessment of sequence alignment Lecture Introduction The Dot plot Matrix visualisation matching tool: – Basics of Dot plot – Examples of Dot plot.

By: Kristen Wade. Short (~4 bps), non- contacted DNA sequences that do not directly interact with the binding protein Image adapted from:

CRISPRs: An Exploration into Spacers and Captured Viral Similarity By: Katie Richeson November 19, 2009 Genomics Laboratory Methods Davidson College, Davidson,

Multiple Sequence Alignments  Assemble DNA sequences into a ‘contig’  Identify conserved residues and domains.

Sequence analysis: Macromolecular motif recognition Sylvia Nagl.

O AK R IDGE N ATIONAL L ABORATORY U.S. D EPARTMENT OF E NERGY A Comparison of Methods for Aligning Genomic Sequences Ja’Nera Mitchom Fisk University Research.

CRISPR-associated Proteins

Motif discovery Tutorial 5. Motif discovery MEME Creates motif PSSM de-novo (unknown motif) MAST Searches for a PSSM in a DB TOMTOM Searches for a PSSM.

Archaeal extreme halophiles (halobacteria, haloarchaea) require high concentration of NaCl for growth found in Great Salt Lake, Dead Sea, evaporation ponds.

CS5263 Bioinformatics Lecture 20 Practical issues in motif finding Final project.

Protein Secondary Structure, Bioinformatics Tools, and Multiple Sequence Alignments Finding Similar Sequences Predicting Secondary Structures Predicting.

Bioinformatics Ayesha M. Khan 9 th April, What’s in a secondary database?  It should be noted that within multiple alignments can be found conserved.

Motif discovery and Protein Databases Tutorial 5.

Basic Local Alignment Search Tool BLAST Why Use BLAST?

Protein Domain Database

Genome annotation and search for homologs. Genome of the week Discuss the diversity and features of selected microbial genomes. Link to the paper describing.

RBP1 Splicing Regulation in Drosophila Melanogaster Fall 2005 Jacob Joseph, Ahmet Bakan, Amina Abdulla This presentation available at

CHAPTER 9 Proteins and Their Synthesis CHAPTER 9 Proteins and Their Synthesis Copyright 2008 © W H Freeman and Company.

Lecture-7 Genome editing CRISPR

Doug Raiford Lesson 5.  Dynamic programming methods  Needleman-Wunsch (global alignment)  Smith-Waterman (local alignment)  BLAST Fixed: best Linear:

Guidelines for sequence reports. Outline Summary Results & Discussion –Sequence identification –Function assignment –Fold assignment –Identification of.

Arabidopsis Thaliana A Study of Genes and Embryo Development By Garen Polatoglu.

Introduction to Bioinformatics - Tutorial no. 5 MEME – Discovering motifs in sequences MAST – Searching for motifs in databanks TRANSFAC – the Transcription.

While hiking, a student decided to collect and eat berries from the plants he came across on the AT trail. Unfortunately, he became very ill and had to.

Finding Motifs Vasileios Hatzivassiloglou University of Texas at Dallas.

Gene Expression Ilana Granovsky Jonathan Laserson.

3.3b1 Protein Structure Threading (Fold recognition) Boris Steipe University of Toronto (Slides evolved from original material.

CRISPR BTE 302 FINAL PRESENTATION.  Ehsan Sakib ( )  Prateem Das ( )  Olia (136032)

Bioinformatics Computing 1 CMP 807 – Day 4 Kevin Galens.

Regulatory RNAs. RNA DNA mRNA rRNA tRNA snRNA snoRNAmicroRNA siRNAribozymes Protein synthesis Splicing of mRNA Processing of rRNA Regulation of gene expression.

Introduction to Bioinformatics Resources for DNA Barcoding

Generating Multiple Sequence Alignments with ClustalW

CRISPR + CAS = Defensive or Immune System

Nucleic Acid Interactions Practicalities

There are four levels of structure in proteins

RNA – A New Role Amy Anderson.

In the power 52 , the base is In the power 52 , the base is

Sequence Searching and Alignment

Identify D. melanogaster ortholog

Basic Local Alignment Search Tool

Phosphopeptides identified harboring minimal binding motifs

GLUTAMINASE - Phylogenetic tree construction

Generating Multiple Sequence Alignments with Clustal Omega

Figure 1 Adaptive immune system of bacteria and archaea

Properties of H. volcanii tRNA Intron Endonuclease Reveal a Relationship between the Archaeal and Eucaryal tRNA Intron Processing Systems Karen Kleman-Leyer,

RNAi: Prokaryotes Get in on the Act

Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins and the domains of HB-EGF. Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins.

Identification of the DNA-binding preferences of Ste12 and Tec1 by HT-SELEX. Identification of the DNA-binding preferences of Ste12 and Tec1 by HT-SELEX.

The Bov-A2 element is conserved in the NOS2 gene of bovid species.

Fig. 4 p100/TSN enables E2F1 to interact with alternatively spliced transcripts. p100/TSN enables E2F1 to interact with alternatively spliced transcripts.

Phosphopeptides identified harboring minimal binding motifs

Volume 16, Issue 11, Pages (September 2016)

Gene regulatory regions of the insect/crustacean egr-B homologs.

Exponent practice.

Multiple alignment of type I and III IFNs from Xenopus, chicken, and human. Multiple alignment of type I and III IFNs from Xenopus, chicken, and human.

Presentation transcript:

CRISPR Direct Repeat Sequences Olivia Ho-Shing 22 November 2009

QUESTIONS: Do different halophile species share similar direct repeat sequences? Can direct repeats indicate phylogeny? Is there any structure to the direct repeats for some potential function? 21 – 37 bp in length Surround spacers that may contain viral sequences Not palindromic, some dyad symmetry ----GACTAC----CTG----GTAGTC---- degenerate DR

CRISPR Finder H. mukohataei CRISPR 1_12 H. californiae H. denitrificans H. mediterranei H. mucosum H. sinaiiensis H. sulfurifontis H. volcanii H. vallismortis*

H. mukohataei direct repeats match hits in: Haloarcula marismortui Halorhabdus utahensis Natronomonas pharaonis Do different halophile species share similar direct repeat sequences?

CLUSTAL multiple sequence alignment Sulfurifontis_17_ GCTTCAATCCCACAAGGGTTCGTCTGAAAC Denitrificans_10_x GCTTCAATCCCACAAGGGTTCGTCTGAAAC Mukohataei_2_ GCTTCAATCCCACAAGGGTCCGTCTGAAAC Sinaiiensis_116_ GCTTCAATCCCACATGGGTTCGTCTGAAAC Californiae_86_ GCTTCAACCCCACGAGGGTCCGTCTGTAAC Utahensis_1_ GCTTCAACCCCACGAGGGTCCGTCTGAAAC Marismortui_1_ GCTTCAACCCCACAAGGGTCCGTCTGAAAC Californiae_86_ GCTTCAACCGCCCAAGGGTCCGTCTGAAAC Mediterranei_5_x GCTTCAACCCAACTAGGGTTCGTCTGTAAC Mucosum_17_ GCTTCAACCCAACTAGGGTTCGTCTGTAACC Mediterranei_13_x GCTTCAACCCAACTAGGGTTCGTCTGTAAC Mucosum_10_x GCTTCAACCCAACTAGGGTTCGTCTGTAAC Mukohataei_1_ GTTTCAGACGGACCCTTGTGGGATTGAAGC Californiae_65_ GTTTCAGACGGACCCTTGGGCGGTTGAAGC Mucosum_4_x GTTACAGACGAACCCTAGTTGGGTTGAAGC Mucosum_11_ GTTACAGACGAACCCTAGTTGGGTTGAAGC Californiae_108_ GTTACAGACGGACCCTCGTGGGGTTGAAGC Denitrificans_5_x GTTTCAGACGAACCCTTGTGGGGTTGAAGC Npharaonis_1_ GTTTCAGACGAACCCTTGTGGGGTTGAAGC Volcanii_16_x GTTTCAGACGAACCCTTGTGGGGTTGAAGC Sulfurifontis_12_ AGTTTCAGACGAACCCTTGTGGGATTGAAGC Sinaiiensis_116_ GTTTCAGACGAACCCTTGTGGGATTGAAGC Volcanii_72_ GGTTTCAGACGAACCCTTGTGGGTTTGAAGC Sulfurifontis_21_ GTTTCAGACGAACCCTTGTTGGGTTGAAGT Sulfurifontis_26_ GTTTCAATC---CCGTTCTGGGTTTCTACCGCATCGCGAC 37 Sinaiiensis_46_ AACCAGAGCGAACAGGGACCACC Sulfurifontis_19_1 GTCGCGATGCGGTAGAAAC---CCAGAACGGGATTGAAAC Sulfurifontis_26_2 GTCGCAGGGCAATAGAAAC---CCAGAACGGGATTGAAAC Npharaonis_1_4 GTCGAGACGGACTGAAAAC---CCAGAACGGGATTGAAAC Sulfurifontis_13_ CCGACACCGACGGCGACGGTCTCGACGACGG Californiae_37_ CTTGTCCTTGACCTCGGTCGTCTTGTCTTT Do different halophile species share similar direct repeat sequences?

H. sinaiiensis H. sinaiiensis H. sinaiiensis 46-1 N. pharaonis 1-1 N. pharaonis 1-4 H. californiae H. californiae H. californiae H. californiae H. californiae 37-1 H. mukohataei 1-12 H. mukohataei 2-1 H. mediterranei 13(x2) H. mediterranei 5(x3) H. mucosum 10(x4) H. mucosum 17-1 H. mucosum 11-1 H. mucosum 4(x4) H. denitrificans 10(x2) H. denitrificans 5(x3) H. volcanii 16(x2) H. volcanii H. sulfurifontis 17-1 H. sulfurifontis 19-1 H. sulfurifontis 26-2 H. sulfurifontis 13-1 H. sulfurifontis 26-1 H. sulfurifontis 12-2 H. sulfurifontis 21-1 ClustalW alignment grouped by species Do different halophile species share similar direct repeat sequences?

H. californiae H. denitrificans H. marismortui H. mediterranei H. mucosum H. mukohataei H. sinaiiensis H. sulfurifontis H. utahensis H. volcanii N. pharaonis H. vallismortis

Can direct repeats indicate phylogeny? Phylogram based on direct repeat sequences H. californiae H. denitrificans H. marismortui H. mediterranei H. mucosum H. mukohataei H. sinaiiensis H. sulfurifontis H. utahensis H. volcanii N. pharaonis H. vallismortis

Can direct repeats indicate phylogeny? Phylogram based on 16S rRNA sequences H. californiae H. denitrificans H. marismortui H. mediterranei H. mucosum H. mukohataei H. sinaiiensis H. sulfurifontis H. utahensis H. volcanii N. pharaonis H. vallismortis

Is there any structure to the direct repeats for some potential function? Characterizing a halophile consensus direct repeat sequence G T T T C A A A C G A A C C [AC] [GT] G G T G G G T T T G A A [AG] C

Is there any structure to the direct repeats for some potential function? Comparing consensus halophile sequence to other species CLUSTAL multiple sequence alignment Consensus_Halophile -GTTTCAAACGAACCCGGGTGGGTTTGAAAC Hmarismortui_2 -GCTTCAACCCCACAAGGGTCCGTCTGAAAC NostocPCC_6 -GTTTCCATCCCCGTGAGGGGTA--AAGGAATTAAAAC- 35 NostocPCC_12 -GTTTCCATCCCCGTGAGGGGTA--AGAGATTAAAAAC- 35 NostocPCC_14 -GTTTCAATCCCTGATAGGGATTTTTGTTAGTTAAAAC- 37 NostocPCC_15 -GTTTCAATCCCTGATAGGGATTTTTGTTAGTTAAAAC- 37 Rxylan_2 -GTTTCAATCCCTTATAGGTAGGCTCAAAAC Ecoli_4 -CGGTTTATCCCCGCTGGCGCGGGGAACTC Ecoli_5 --GGTTTATCCCCGCTGGCGCGGGGAACAC Hmarismortui_C1_2 ---GGCGGTCCCTGTTCGCTCTGGTT NostocPCC_2 GTTACTTACCATCACTTCCCCGCAAGG-GGATGGAAAC- 37 NostocPCC_18 -CTTTCAACCCTCCCATTACTGGAAGGAGGGTTGCAACG 38 NostocPCC_7 -GTTTTAATTCCTTTACCCCT-CACGG-GGATGGAAAC- 35 NostocPCC_8 GTTTCTATTAACACA-AATCCCTATCAGGGATTGAAAC- 37 NostocPCC_17 -GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC- 37 Rxylan_3 --TACCAGGCGTGGATCTTGCCCTCGGACAC

Is there any structure to the direct repeats for some potential function?

Conclusions Halophile direct repeats are similar to each other (significant e-values) – swapping, functionality Interesting triplet motifs in dyad symmetry of direct repeats – Binding site for CRISPR-associated proteins? – Folding site for siRNA? Direct repeats may be more indicative of phylogeny in a larger more widespread group of species