Introduction to Molecular Cell Introduction to Molecular Cell BiologyBiology

Transcription Transcription RegulationRegulation

Dr. Fridoon Jawad AhmadDr. Fridoon Jawad Ahmad

HEC Foreign ProfessorHEC Foreign ProfessorKing Edward Medical UniversityKing Edward Medical University

Visiting Professor LUMS-SSEVisiting Professor LUMS-SSE

Gene Regulation

• Some of genes are expressed in all cells all the time. Housekeeping genes are responsible for the routine metabolic functions (e.g. respiration).

• Some are expressed as a cell enters a particular pathway of differentiation.

• Some are expressed all the time in only those cells that have differentiated in a particular way.

• Some are expressed only as conditions around and in the cell change. For example, the arrival of a hormone may turn on/off certain genes in that cell.

Gene Regulation

Transcription Transcription RegulationRegulationin E. Coliin E. Coli

Inducible & Constitutive EnzymesInducible & Constitutive Enzymes

Transcription RegulationTranscription Regulationin E. Coliin E. Coli

Transcription Transcription RegulationRegulation

E. ColiE. Coli

The Eukaryotic DilemmaThe Eukaryotic Dilemma

For a cell to develop and function properly it must For a cell to develop and function properly it must turn on the right genes and right time.turn on the right genes and right time.

Genes are located in the nucleus in a tangled Genes are located in the nucleus in a tangled chromatin material wrapped around histones.chromatin material wrapped around histones.

The structure of chromatin The structure of chromatin dictates whether a gene can dictates whether a gene can

be transcribed not.be transcribed not.

Eu & Hetero ChromatinEu & Hetero Chromatin

DNA OrganizationDNA Organization

Most of DNA is highly ordered and tightly coiled Most of DNA is highly ordered and tightly coiled around positively charged histone proteins and is around positively charged histone proteins and is

virtually inaccessible to RNA polymerase.virtually inaccessible to RNA polymerase.

ReorganizationReorganization

In response to specific In response to specific signal a cell may signal a cell may

produce or activate a produce or activate a transcription activator.transcription activator.

Transcription activator Transcription activator recognizes and binds a recognizes and binds a specific sequence of a specific sequence of a specific gene and work specific gene and work

in conjunction with other in conjunction with other proteins that can alter proteins that can alter chromatin structure. chromatin structure.

ReorganizationReorganization

The alteration may occur by addition of acetyl The alteration may occur by addition of acetyl groups to histones which reduce positive charge.groups to histones which reduce positive charge.

Chromatin Chromatin remodeling remodeling

complex can also complex can also alter the structure alter the structure

of chromatin to of chromatin to make it accessible make it accessible

to transcription to transcription factors that attract factors that attract

RNA Pol.RNA Pol.

ReorganizationReorganization

RNA Pol then with help of remodeling complex can RNA Pol then with help of remodeling complex can move along the gene and make an RNA.move along the gene and make an RNA.

Detailed ViewDetailed View

Transcribed region has coding information for Transcribed region has coding information for making proteins and is in copied into RNA.making proteins and is in copied into RNA.

Promoter is upstream of TR and is the core Promoter is upstream of TR and is the core regulatory region where RNA Pol binds.regulatory region where RNA Pol binds.

Upstream of promoter Upstream of promoter are PPE where specific are PPE where specific transcription regulatory transcription regulatory

factors activators or factors activators or repressors bind here.repressors bind here.

Detailed ViewDetailed View

Activators can recruit the CRC.Activators can recruit the CRC.

Many genes also have enhancer (1000 nucleotide Many genes also have enhancer (1000 nucleotide away) where specific activators only made by certain away) where specific activators only made by certain

cells can bind.cells can bind.

Detailed ViewDetailed View

Activators recruit TFIID to the promoter.Activators recruit TFIID to the promoter.

TBP a protein with in TFIID bind TATA sequence TBP a protein with in TFIID bind TATA sequence (called TATA box) of DNA.(called TATA box) of DNA.

Most eukaryote Most eukaryote promoters have promoters have

TATA box, TATA box, which is which is

located 25bp located 25bp upstream of upstream of

start site.start site.

Detailed ViewDetailed View

TFIID and other factors are required to bind DNA TFIID and other factors are required to bind DNA before RNA Pol can recruited.before RNA Pol can recruited.

The core transcription complex then initiates The core transcription complex then initiates transcription.transcription.

Transcribing Transcribing Multiple GenesMultiple Genes

The simultaneous The simultaneous regulation of widely regulation of widely separated genes is separated genes is possible through possible through

common sequences in common sequences in their promoters, to their promoters, to

which the same which the same regulatory proteins regulatory proteins

bind.bind.

RNA ProcessingRNA Processing

pre-mRNA (freshly transcribed) is processed to pre-mRNA (freshly transcribed) is processed to make it functional.make it functional.

1-Introns are removed during RNA maturation1-Introns are removed during RNA maturation

Mature mRNAMature mRNA

The EvidenceThe Evidence

The MechanismThe Mechanism

Intron-exon bounderies have Intron-exon bounderies have consensus sequences were consensus sequences were

snRNPs bindsnRNPs bind

RNA of U1 has complementary RNA of U1 has complementary bases that bind CS at 5’ exon-bases that bind CS at 5’ exon-

intron boundery.intron boundery.

RNA of U2 has complementary RNA of U2 has complementary bases that bind CS near 3’ intron-bases that bind CS near 3’ intron-

exon boundery.exon boundery.

RNA ProcessingRNA Processing

2) The transcribed pre-mRNA is altered by the 2) The transcribed pre-mRNA is altered by the addition of a G cap (modified GTP) at the 5′ end to addition of a G cap (modified GTP) at the 5′ end to

protect RNA and facilitate translation. protect RNA and facilitate translation.

3) After the last codon a poly A tail (100-300) is 3) After the last codon a poly A tail (100-300) is added at the 3′ end for export and protectionadded at the 3′ end for export and protection