NcRNA Jeremy Logue. The Expanding Repertoire of RNA Adapted from Soares and Valcarcel (2006) EMBO.

Slides:

Advertisements

Similar presentations

Gene Expression Chapter Eleven. What is Gene Expression? When a gene is expressed – that gene’s protein product is made: 1.DNA is transcribed into RNA.

Advertisements

Outline Questions from last lecture? P. 40 questions on Pax6 gene Mechanism of Transcription Activation –Transcription Regulatory elements Comparison between.

Spatial partitioning of the regulatory landscape of the X-inactivation centre Elphège P. Nora, Bryan R. Lajoie, Edda G. Schulz, Luca Giorgetti, Ikuhiro.

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.

The Y Chromosome *PAR - Pseudoautosomal region

Imprinting Expression of only one allele of a locus Only ~100 genes in mammals are imprinted Most imprinted genes are involved in growth control or postnatal.

X-inactivation. Males are haploid for X-linked genes.

[Bejerano Fall10/11] 1.

Non-coding RNAs (ncRNAs)

Chris Chander, Luke Adea BioSci D145 Feb. 12, 2015

mRNA-Seq: methods and applications

Identification of obesity-associated intergenic long noncoding RNAs

X Chromosome Inactivation Nature Genetics 30, 77 – 80 (2002) Peters et al.

Epigenetics: Genomic imprinting. Genomic Imprinting Preferential expression (or repression) of one parental allele Epigenetic modification mechanism (CpG.

Regulatory RNAs. Cells produce several types of RNA.

Next Generation Sequencing and its data analysis challenges Background Alignment and Assembly Applications Genome Epigenome Transcriptome.

Alberts • Bray • Hopkin • Johnson • Lewis • Raff • Roberts • Walter

Silence of the Genes. Genetics The study of inheritance.

Stefan Aigner Christian Carson Rusty Gage Gene Yeo Crick-Jacobs Center Salk Institute Analysis of Small RNAs in Stem Cell Differentiation.

2003 Silver Fleece Awards 1. Clonaid- Claim to have cloned humans –Says that cloning will “enable mankind to reach eternal life” –Claims that memories.

The generalized transcription of the genome Víctor Gámez Visairas Genomics Course 2014/15.

[BejeranoWinter12/13] 1 MW 11:00-12:15 in Beckman B302 Prof: Gill Bejerano TAs: Jim Notwell & Harendra Guturu CS173 Lecture 6:

Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520

Imprinting Expression of only one allele of a locus

The Power of “Genetics” LOSS OF FUNCTION Easy in yeast Difficult in mammals Powerful tool to address roles in developmental or signaling networks Gene.

Lecture 20 – Epigenomics – Animals Lecture 20 – Epigenomics – Animals BIOL 5190/6190 Cellular & Molecular Singal Transduction Prepared by Bob Locy Last.

Today: Genomic Imprinting and Epigenetics. haploid diploid X 23 in humans X 23 in humans X 23 in humans Inheritance = The interaction between genes inherited.

Imprinting Expression of only one allele of a locus

From Genes to Genomes: Concepts and Applications of DNA Technology, Jeremy W. Dale, Malcolm von Schantz and Nick Plant. © 2012 John Wiley & Sons, Ltd.

Can genes help explain our evolution? - What type of changes (regulatory or structural mutations?) - How many genes are involved?

Epigenetic mechanisms of gene regulation Chromatin structure Chromatin structure Slows transcription Slows transcription Hypercondensation stops transcription.

Sex Chromosomes Chapter 5 1. Outline Sex chromosomes Sex determination 2.

X-chromosome inactivation: molecular mechanism and genetic consequences By: Ambaye, S. & Mujahed, H.

Alessandro Raganelli and Varun Rao.  Prokaryotes and eukaryotes alter gene expression in response to their changing environment  In multicellular eukaryotes,

Different microarray applications Rita Holdhus Introduction to microarrays September 2010 microarray.no Aim of lecture: To get some basic knowledge about.

Genetics of Calico cats

Human long non ‐ coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors by Shi.

Do we know it all?. John L. Rinn and Howard Y. Chang Annu. Rev. Biochem

Squeezing out the histone modifications data Wieslawa Mentzen with Matteo Floris and Paolo Uva Connections between epigenetics and microRNAs during embryonic.

X inactivation and Practice Questions

Halfway Feedback (yours)

Figure 2 The US Centers for Disease Control and

Volume 58, Issue 5, Pages (June 2015)

Mechanisms of lncRNA function.

GENETICS A Conceptual Approach

Molecular Biology Select

Nat. Rev. Clin. Oncol. doi: /nrclinonc

Figure 1 Evolution of genetic concepts underlying risk of cardiovascular disease Figure 1 | Evolution of genetic concepts underlying risk of cardiovascular.

Malat1 is a neuron‐enriched nuclear‐retained ncRNA that is localized to nuclear speckles. Malat1 is a neuron‐enriched nuclear‐retained ncRNA that is localized.

Noncoding RNA Landmarks of Pluripotency and Reprogramming

Figure 3 The Beckwith–Wiedemann syndrome locus at chromosome 11p15.5

Profs: Serafim Batzoglou, Gill Bejerano TAs: Cory McLean, Aaron Wenger

Nat. Rev. Gastroenterol. Hepatol. doi: /nrgastro

Genetic variation in DREs could be a causative factor in dysregulation of distal target gene expression. Genetic variation in DREs could be a causative.

Putting Two Heads Together to Build a Better Brain

Healing Genes in the Nervous System

Figure 3. Genes differentially expressed in batch cultures during adaptation to low temperature. Genes differentially expressed in batch cultures during.

Stop that Noise and Turn Up the Antisense Transcription

Mapping of small RNAs to LINE‐1 sequence (related to Figs 3 and 4)‏

GENETICS A Conceptual Approach

X Chromosome Inactivation Is Mediated by Xist RNA Stabilization

Non-coding RNA characterization

MexT-associated downregulation of oprD expression.

Transcriptome Encyclopedia of Early Human Development

Bernard Mulvey, Joseph D. Dougherty Cell

Brain Evolution and Uniqueness in the Human Genome

Figure 1 ASO functions ASO functions Target mRNA fates depending on ASO mechanism of action that is determined by where the ASO is targeted and by ASO.

JAK2V617F leads to 5-hmC gain in vivo that correlates with gene expression. JAK2V617F leads to 5-hmC gain in vivo that correlates with gene expression.

TUF Love for “Junk” DNA Cell

Presentation transcript:

ncRNA Jeremy Logue

The Expanding Repertoire of RNA Adapted from Soares and Valcarcel (2006) EMBO

Adapted from Huttenhofer, A et al. (2005) Trends in Genetics The Expanding World of Non-coding RNAs

HAR1-associated transcripts in genomic context Of the 49 HARS identified (Human Accelerated Regions), 96% are in non-coding regions.

Predicted RNA secondary structure for HAR1F

Expression of HAR1F and HAR1R in the developing neocortex Cajal-Retzius cells establish early neuronal circuitry in the developing brain

Expression of HAR1F in other parts of the developing brain

What does this all mean? Fill in the blank…

X - Inactivation

Dosage Compensation Adapted from Straub and Becker (2007) Nature Reviews Genetics

Imprinted Versus Random X-inactivation Adapted from Avnir and Heard (2001) Nature Reviews Genetics

The X-inactivation Center Adapted from Avnir and Heard (2001) Nature Reviews Genetics

Differentiation Xist Transcription in Embryonic Stem Cells Adapted from Avnir and Heard (2001) Nature Reviews Genetics 48 hrs.

Adapted from Avnir and Heard (2001) Nature Reviews Genetics Potential Roles for Xist Antisense Transcription

What does a silenced X look like? Adapted from Chow, JC et al. (2005) Annu. Rev. Genomic Hum. Genet.

Co-localization and 3D - Microscopy

How confident are we that these co-localize?

Figure 1G from Chaumeil, J. et al. (2007) Gen Dev Problems Associated with Co-localization Resolution = λ/(2NA) z-axis problem Calculating a cross-correlation can also aid in determining co-localization

3D - Microscopy